diff --git a/thesis/1_GeneIntro/GeneIntro.tex b/thesis/1_GeneIntro/GeneIntro.tex index f455809..2788ca0 100644 --- a/thesis/1_GeneIntro/GeneIntro.tex +++ b/thesis/1_GeneIntro/GeneIntro.tex @@ -15,7 +15,7 @@ %\section{Molecular Clusters} -The term \textit{cluster} was coined by Cotton in the early 1960s to refer to compounds containing metal-metal bonds such as [Re$_2$Cl$_8$]$^{2-}$ +The term \textit{cluster} was coined by F. A. Cotton in the early 1960s to refer to compounds containing metal-metal bonds such as [Re$_2$Cl$_8$]$^{2-}$ and [Re$_2$Br$_8$]$^{2-}$.\cite{Cotton1964} He defined metal atom cluster compounds as "\textit{those containing a finite group of metal atoms which are held together entirely, mainly, or at least to a significant extent, by bonds directly between the metal atoms even though some non-metal atoms may be associated intimately with the cluster}". Subsequently, the study of clusters, also referred to as aggregates, has greatly diversified @@ -92,8 +92,8 @@ potential energy surface (PES), or energy landscape, can be extremely complex an exist. The properties of a given cluster can significantly differ from the properties of the corresponding bulk material. For instance, the magnetic moment of small iron particles at room temperature is smaller than that of the bulk.\cite{Kimura1991} However, a gradual transition occurs between the properties of the clusters and those of the corresponding bulk as cluster size increases.\cite{Jortner1992} This transition can be rough or continuous depending -on the considered species and properties. For instance, Landman \textit{et al.} reported that anionic gold clusters favor planar structures -up to $\sim$13 atoms.\cite{Hakkinen2002} L'Hermite \textit{et al.} also reported that the transition temperature extracted from he +on the considered species and properties. For instance, U. Landman \textit{et al.} reported that anionic gold clusters favor planar structures +up to $\sim$13 atoms.\cite{Hakkinen2002} J.-M. L'Hermite \textit{et al.} also reported that the transition temperature extracted from he heat capacity curve of protonated water clusters (H$_{2}$O)$_{n}$H$^{+}$ has a strong size dependence as seen in Figure~\ref{T_trans}.\cite{Boulon2014} Consequently, the study of clusters allow to bridge the gap between single molecule or atom properties and bulk materials, which can be of help to reveal microscopic aspects which are hardly observable in the bulk only. @@ -140,7 +140,7 @@ in order to determine the lowest energy isomer of a given cluster. For instance, conducted to determine the low energy structures of (H$_2$O)$_n$ and (H$_2$O)$_n$H$^+$ aggregates. Among them, we can mention the studies performed by D. Wales and co-workers using the basin-hopping algorithm.\cite{Wales1997,Wales1998,Wales1999,James2005} In more difficult cases, the probe properties result from the contribution of several isomers which have to be taken into account. When -considering finite-temperature properties, an ergodic exploration of the PES also need to be performed. For instance, Boulon \textit{et al.} +considering finite-temperature properties, an ergodic exploration of the PES also need to be performed. For instance, J. Boulon \textit{et al.} reported heat capacity curves as a function of temperature of mass selected protonated water clusters and highlighted a stronger steepness of the curve of (H$_2$O)$_{21}$H$^+$ as compared to adjacent sizes.\cite{Boulon2014} Theoretical simulations latter provided explanations for this peculiar behavior.\cite{Korchagina2017} When considering dissociation of clusters, which can be a non-equilibrium process, theoretical @@ -190,8 +190,8 @@ It is therefore often necessary to make a choice between computational efficienc and accuracy. This balance determines the nature of the questions that can be addressed. Furthermore, the aforementioned \textbf{enhanced sampling methods} generally require to repeat a large amount of calculations. Therefore, they need to be combined with computationally -efficient approaches to compute the PES. As presented in Chapter~\ref{chap:comput_method}, the method -I use within this thesis is the \textbf{self-consistent-charge density functional based tight-binding} (SCC-DFTB) method. +efficient approaches to compute the PES. As presented in chapter~\ref{chap:comput_method}, the method +I use within this thesis is the \textbf{self-consistent-charge density-functional based tight-binding} (SCC-DFTB) method. \end{itemize} %Hydrogen bonding is arguably the most extensively studied among all the noncovalent interactions. Hydrogen bonding governs many chemical @@ -228,7 +228,7 @@ the existence of charged molecular aggregates in the stratosphere,\cite{Arnold19 and ammonium/ammonia containing aggregates.\cite{Payzant1973, Berden1996} In the latter case, \textbf{ammonia has been highlighted as an important component of atmospheric nucleation} together with water and sulphuric acid.\cite{Kulmala1995, Kirkby2011, Dunne2016} This important role of ammonia and ammonium water clusters, and the lake of theoretical studies devoted to these species, motivated a thorough benchmark of -the SCC-DFTB approach to model these systems which is presented in Chapter~\ref{chap:structure}. In parallel, understanding the \textbf{properties of +the SCC-DFTB approach to model these systems which is presented in chapter~\ref{chap:structure}. In parallel, understanding the \textbf{properties of the proton} and how it can impact the solvation properties of molecules of biological interest is of paramount importance for understanding fundamental processes in biology and chemistry. In particular, uracil, one of the nucleobases, plays a key role in the encoding and expression of genetic information in living organisms. The study of \textbf{water clusters containing uracil} is therefore a good playground to probe how uracil properties @@ -313,12 +313,11 @@ simulation time of several hundred picoseconds. This approach has thus been use collision-induced dissociation experiments. To summarize, the goal of this thesis is to go a step further into the theoretical description of the properties of molecular clusters -in the view to complement complex experimental measurements. It has focused on two different types of molecular clusters. First, -we have focused on water clusters containing an impurity, \textit{i.e.} an additional ion or molecule. We have first focused our +in the view to complement complex experimental measurements. It has focused on two different types of molecular clusters. First, I focused on water clusters containing an impurity, \textit{i.e.} an additional ion or molecule. I have first focused my studies on \textbf{ammonium and ammonia water clusters} in order to thoroughly explore their PES to characterize in details -low-energy isomers for various cluster sizes. We then tackle the study of \textbf{protonated uracil water clusters} through two +low-energy isomers for various cluster sizes. Then I tackle the study of \textbf{protonated uracil water clusters} through two aspects: characterize low-energy isomers and model collision-induced dissociation experiments to probe dissociation mechanism -in relation with recent experimental measurements. Finally, we address the study of the \textbf{pyrene dimer cation} to explore collision +in relation with recent experimental measurements. Finally, I address the study of the \textbf{pyrene dimer cation} to explore collision trajectories, dissociation mechanism, energy partition, mass spectra, and cross-section. To introduce, develop, and conclude on these different subjects, this manuscript is organised as follow: diff --git a/thesis/2_Introduction/.DS_Store b/thesis/2_Introduction/.DS_Store index 92ef9a5..2c7c431 100644 Binary files a/thesis/2_Introduction/.DS_Store and b/thesis/2_Introduction/.DS_Store differ diff --git a/thesis/2_Introduction/introduction.aux b/thesis/2_Introduction/introduction.aux index 700d8ad..85763b0 100644 --- a/thesis/2_Introduction/introduction.aux +++ b/thesis/2_Introduction/introduction.aux @@ -22,11 +22,11 @@ \@writefile{toc}{\contentsline {section}{\numberline {2.2}Born-Oppenheimer Approximation}{16}{section.2.2}\protected@file@percent } \newlabel{BO_approx}{{2.2}{16}{Born-Oppenheimer Approximation}{section.2.2}{}} \citation{Born1927} +\citation{Born1927} \@writefile{brf}{\backcite{Born1927}{{17}{2.2}{section.2.2}}} \newlabel{BO}{{2.6}{17}{Born-Oppenheimer Approximation}{equation.2.2.6}{}} \newlabel{H_e}{{2.7}{17}{Born-Oppenheimer 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The eigenstates obtained from equation \ref{TISE} are the stationary states of the system and form a complete basis of +where $c_k$ is a coefficient. %at t=0. +The eigenstates obtained from equation \ref{TISE} are the stationary states of the system and form a complete basis of orthonormal vectors. The lowest energy eigenstate is called the ground state usually denoted as $\Psi_0$ and $E_0$ is the corresponding energy. In a system made up of $M$ nuclei and $N$ electrons, the Hamiltonian operator (in a non-relativistic framework) is written as following: @@ -115,8 +117,10 @@ In a system made up of $M$ nuclei and $N$ electrons, the Hamiltonian operator (i \label{operatorH} \end{align} %\end{eqnarray} -in which the atomic unit system is used. The energy is thus expressed in Hartree. The mass is in unit of the mass of electron and the length is in Bohr. The vectorial variables are in bold in this present manuscript. $M_\alpha$ refers to the mass of nucleus $\alpha$ (in atomic unit) and $Z_\alpha$ is the atomic number of $a$. $\hat{T}_n$ and $\hat{T}_e$ are the kinetic energy operators of nuclei and electrons, respectively. $\hat{V}_{nn}$, $\hat{V}_{ee}$ and $\hat{V}_{ne}$ denote the potential energy operators of the repulsion between the nuclei, repulsion between the electrons and electrostatic attraction between nuclei and electrons, respectively. -\textbf{$\nabla^2$} is the Laplace operator. For nucleus $\alpha$ in Cartesian coordinates in three dimensions, its position vector is \textbf{R}$_\alpha$=(X$_\alpha$, Y$_\alpha$, Z$_\alpha$) and \textbf{$\nabla^2$} is expressed as following: +in which the atomic unit system is used. The energy is thus expressed in Hartree. The mass is in unit of the mass of electron and the length is in Bohr. $M_\alpha$ refers to the mass of nucleus $\alpha$ (in atomic unit) and $Z_\alpha$ is the atomic number. +%of atom $\alpha$. +$\hat{T}_n$ and $\hat{T}_e$ are the kinetic energy operators of nuclei and electrons, respectively. $\hat{V}_{nn}$, $\hat{V}_{ee}$ and $\hat{V}_{ne}$ denote the potential energy operators of the repulsion between the nuclei, repulsion between the electrons and electrostatic attraction between nuclei and electrons, respectively. +\textbf{$\nabla^2$} is the Laplace operator. For nucleus $\alpha$ in three dimensions using Cartesian coordinates, its position vector is \textbf{R}$_\alpha$=(X$_\alpha$, Y$_\alpha$, Z$_\alpha$) and \textbf{$\nabla^2$} is expressed as following: \begin{eqnarray} \label{laplace} \mathbf{\nabla}^2 = \frac{\partial^2}{\partial{X}_\alpha^2} + @@ -127,7 +131,9 @@ in which the atomic unit system is used. The energy is thus expressed in Hartree Electrons are very light particles which can not be described correctly even qualitatively through classical mechanics. If we want to describe the electron distribution in details, quantum mechanics must be applied, \textit{i.e.} solving the Schr{\"o}dinger equation. Usually in atomic and molecular systems, -it is very hard, if not impossible, to obtain the ex­act so­lu­tions of Schr{\"o}dinger equation, as this requires to separate variables. It is only possible in the +it is very hard, if not impossible, to obtain the ex­act so­lu­tions of Schr{\"o}dinger equation. +%as this requires to separate variables. +It is only possible in the system containing one nucleus and one electron, \textit{i.e.}, the hydrogen atom or hydrogenic ions. For molecular species, the mathematical complexity to solve the Schr{\"o}dinger equation will increase with the number of degrees of freedom of the system. Thus, it is necessary to resort to approximations in almost all cases. @@ -150,7 +156,7 @@ BO approximation consists of expressing the total wavefunction of a molecule as an electronic wavefunction, which enables a separation of the Hamiltonian operator into the fast electronic term and the usually much slower nuclear term, where the coupling between electrons and nuclei is neglected so that the two smaller and non-coupled systems can be solved more efficiently. In mathematical terms, the total wavefunction $\Psi_\mathrm{tot}$ of a molecule can be expressed as an expansion in the complete set of electronic -wavefunctions $\psi_k^e$ with the expansion coefficients being functions of the nuclei coordinates $\psi^n$: +wavefunctions $\psi_k^e$ with the expansion coefficients being parametric functions of the nuclei coordinates \textbf{R}$_\alpha$: \begin{eqnarray} \label{BO} \Psi_\mathrm{tot}(\mathbf{R}_\alpha, \mathbf{r}_j) = \sum_{k=1}^{\infty} @@ -180,26 +186,26 @@ where the eigenvalue $E_k^e$, electronic energy, depends on the chosen positions In the second step, the nuclear kinetic energy ${T}_n$ is reintroduced, and the Schr{\"o}dinger equation for the nuclear motion is: \begin{eqnarray} \label{nucSeq} -(\hat{T}_n + E_{k}^e(\mathbf{R}_\alpha) + \langle \Psi_k \vert \mathbf{\nabla}_n^2 \vert \Psi_k \rangle )\psi_k^n(\mathbf{R}_\alpha) = E_\mathrm{tot}\psi_k^n(\mathbf{R}_\alpha) +(\hat{T}_n + E_{k}^e(\mathbf{R}_\alpha) + \langle \Psi_k \vert \mathbf{\nabla}_n^2 \vert \Psi_k \rangle )\psi_k^n(\mathbf{R}_\alpha) = E_k^\mathrm{tot}\psi_k^n(\mathbf{R}_\alpha) \end{eqnarray} -The eigenvalue $E_\mathrm{tot}$ is the total energy of the molecule, which includes the overall rotation translation of the molecule, contributions from electrons, +The eigenvalue $E_k^\mathrm{tot}$ is the total energy of the molecule, which includes the overall rotation translation of the molecule, contributions from electrons, and nuclear vibrations. This second step involves a separation of vibrational, translational, and rotational motions. -Born and Oppenheimer assumed that the integral $\langle \Psi_k \vert \mathbf{\nabla}_n^2 \vert \Psi_k \rangle$ (diagonal correction) weakly depends on the nuclear coordinates, +M. Born and R. Oppenheimer assumed that the integral $\langle \Psi_k \vert \mathbf{\nabla}_n^2 \vert \Psi_k \rangle$ (diagonal correction) weakly depends on the nuclear coordinates, so that it can be ignored. \cite{Born1927} Therefore, the Born-Oppenheimer approximation allows to describe the movement of nuclei in the corresponding potential to an adiabatic electronic state by the following equation: \begin{eqnarray} \label{ESeq} -(\hat{T}_n + E_{k}^e(\mathbf{R}_\alpha))\psi_k^n(\mathbf{R}_\alpha) = E_\mathrm{tot}\psi_k^n(\mathbf{R}_\alpha) +(\hat{T}_n + E_{k}^e(\mathbf{R}_\alpha))\psi_k^n(\mathbf{R}_\alpha) = E_0^\mathrm{tot}\psi_k^n(\mathbf{R}_\alpha) \end{eqnarray} -In this thesis, we will assume electrons adapt fast to reach their electronic ground state. +In this thesis, I will assume electrons adapt fast to reach their electronic ground state. %I only focus on the electronic ground state. The potential energy $E_0^e$ thus equals the ground state electronic energy $E_{0}$ and the total energy is then $E_0^\mathrm{tot}=T_\mathrm{n} + E_{0}$. The Schr{\"o}dinger equation for $\psi_0^n(\mathbf{R}_\alpha)$ can therefore be written as: \begin{eqnarray} \label{classical} -(\hat{T}_n + E_{0})\psi_0^n(\mathbf{R}_\alpha) = E_\mathrm{tot}\psi_0^n(\mathbf{R}_\alpha) +(\hat{T}_n + E_{0})\psi_0^n(\mathbf{R}_\alpha) = E_0^\mathrm{tot}\psi_0^n(\mathbf{R}_\alpha) \end{eqnarray} The next step is usually to consider the nuclei can be described classically. One can then consider that they evolve classically \textit{i.e.} following new Newton's equation, on a PES defined by the ground state electronic energy. The calculation of the ground state electronic energy is discussed in section~\ref{electronicEnergy} %<<<<<<< HEAD @@ -247,7 +253,7 @@ Experimental spectroscopic investigations help in understanding the electronic s emission and scattering. These measurements can often provide a detailed picture of molecular systems but sometimes they are difficult to interpret. In the last few decades, molecular electronic-structure theory has developed to a stage where it can provide invaluable assistance in the interpretation of experimental measurements of a wide range of important properties of molecules in rotational and vibrational spectroscopies, -magnetic-resonance spectroscopies, ultraviolet/visible spectroscopies, and otherss.\cite{Puzzarini2010, Helgaker1999, Pedone2010, Fleming1986, Laane1999, Helgaker2012} +magnetic-resonance spectroscopies, ultraviolet/visible spectroscopies, and others.\cite{Puzzarini2010, Helgaker1999, Pedone2010, Fleming1986, Laane1999, Helgaker2012} Electronic wavefunction of systems including three or more interacting particles can not be obtained analytically, so approximations must be applied. Many approximations have been proposed to obtain approximate solutions of the exact electronic wavefunction. Each one of them is usually the basis @@ -260,14 +266,14 @@ Post-HF theory usually generates more accurate results by considering the electr DFT methods in the Kohn-Sham formulation can be regarded as an improvement over the HF theory as it considers approximated electronic correlation. Density-functional based tight-binding (DFTB) formalism is an approximated DFT method that involves additional approximations.\cite{dftb1, dftb2, Elstner1998, Elstner2014} -PES can be explored with \textit{ab initio} methods.\cite{Cremer1993} +%PES can be explored with \textit{ab initio} methods.\cite{Cremer1993} Compared with quantum chemical (QM) methods that require considerable computer resources, molecular mechanics (MM) calculations are much cheaper but -present severe limitations in the treatment of chemical reactivity.. The possibility to model chemical reactions using \textit{ab initio} MD calculation is also -severely hindered by the short simulation time accessible with such methods. QM/MM techniques that combine QM for the reactive region and MM for the +present severe limitations in the treatment of chemical reactivity. +%The possibility to model chemical reactions using \textit{ab initio} MD calculation is also severely hindered by the short simulation time accessible with such methods. +QM/MM techniques that combine QM for the reactive region and MM for the remainder are very promising, especially for large systems.\cite{Singh1986, Gao1996, Mordasini1998} -The following section focuses on the description of wavefunction based methods, density functional theory method, and the density-functional based -tight-binding methods used to solve Schr{\"o}dinger equation and the electronic structure problem. +The following section focuses on the description of wavefunction based methods, DFT method, and the DFTB methods used to solve Schr{\"o}dinger equation and the electronic structure problem. \subsection{Wavefunction based Methods} @@ -283,31 +289,30 @@ Hartree proposed that the electronic wavefunction could be approximated by assum \end{eqnarray} The HF theory assumes that every electron moves in an average field of all the other electrons and the nuclei in the molecule, which is an example of a mean-field approximation. -The HF equations for an individual electron $j$ moving in the mean field \textit{V}$_i^{HF}$, can be expressed: - +The HF equations for an individual electron $j$ moving in the mean field \textit{V}$_i^{HF}$, can be expressed as: \begin{equation} \left(-\frac{1}{2}\mathbf{\nabla}_j^2 + V_\sigma(\mathbf{r}_j) + V_\mathrm{H}(\mathbf{r}_j)\right)\psi^\mathrm{HF}_\sigma (\mathbf{r}_j)- \sum_{k=1}^{N_\sigma} \int d^3 {r'} \frac{\psi_{k\sigma}^{\mathrm{HF*}}(\mathbf {r'})\psi_{k\sigma}^\mathrm{HF}(\mathbf r_j)}{\mid \mathbf r_j-\mathbf{r'}\mid}\psi^\mathrm{HF}_{\sigma} (\mathbf{r'})= E_\sigma^\mathrm{HF} \psi_\sigma^\mathrm{HF}(\mathbf{r}_j) \label{HF-individual} \end{equation} - +where $\nabla_j^2$ depends on the $j$th electron coordinates. $V_\sigma(\textbf{r}_j)$ refers to the external potential. $\sigma$ is the spin. The last term on the left-hand side is the HF exchange potential. +Using the electronic density, we can obtain: \begin{equation} V_\mathrm{H}(\mathbf{r}_j) = \int d^3 {r}_j \frac{\rho (\mathbf{r'})}{\mid \mathbf{r}_j - \mathbf{r'} \mid} \label{Hartreepotential} \end{equation} - +$V_{H}(\mathbf{r}_j)$ is the Hartree potential: \begin{equation} \rho(\mathbf{r}_j) =\sum_\sigma\sum_j^{N_\sigma}\rho_\sigma(\mathbf{r}_j)=\sum_\sigma\sum_j^{N_\sigma} \mid \psi_{\sigma}^\mathrm{H}(\mathbf {r}_j)\mid^2 \label{HF-idensity} \end{equation} +\textbf{r'} refers to the positions of all other electrons except electron $j$. %density means the probability of findind an electron -where $\nabla_j^2$ depends on the $j$th electron coordinates. -$V_\sigma(\textbf{r}_j)$ refers to the external potential. $\sigma$ is the spin. $V_{H}(\mathbf{r}_j)$ is the Hartree potential + % Hartree potential is a local potential. %j\sigma refers to a state. -The last term on the left-hand side of eq \ref{HF-individual} is the HF exchange potential. %which can be viewed as an operator acting on the ortital $\psi^{\mathbf{HF}_{j\sigma}(\mathbf r_j)$ in such a way that the result of its action at position $(\mathbf{r}_j}$ involves an integration of $\psi^{\mathbf{HF}_{j\sigma} over all \mathbf{r'}. -\textbf{r'} refers to the positions of all other electrons except electron $j$. + %The solutions of the individual Hartree equations depend on the solutions of all the other individual Hartree equations via \textit{V}$_i^{\mathrm{HF}}$. Thus, they have to be solved iteratively. %<<<<<<< HEAD %%First, an initial guess for the individual one-electron wavefunctions is needed. After this, iterate continues until all \psi$_{i}$ stay the same, which means a self-consistent field (SCF) has been achieved. @@ -372,28 +377,24 @@ more CSFs. Standard multiconfigurational approaches are the CI, CC, and perturba For a long time, approximations based on the wavefunction were systematically applied to solve the Schr{\"o}dinger equation. However, it is usually impractical to perform a wavefunction based calculation with chemical accuracy for complex or large systems. Density functional theory is based on the electron density rather than the electronic wavefunction.\cite{Kohn1965, kohn1999nobel} -Because DFT displays a more favourable scaling of computational resources with respect to system size, DFT is nowadays the most -widely used method available in computational chemistry, computational physics, and condensed-matter physics for ground state +Because DFT displays a more favourable scaling of computational resources with respect to system size, DFT is nowadays the most widely used method available in computational chemistry, computational physics, and condensed-matter physics for ground state calculation of large and complex systems. +Although DFT has a history almost as old as the Schr{\"o}dinger equation, the modern form dates back to the paper published by P. Hohenberg and W. Kohn \cite{Hohenberg1964} +that introduced the two Hohenberg–Kohn (HK) theorems in 1964 and the extension by M. Levy in 1979.\cite{Levy1979} The theory is usually applied in the form latter suggested by W. Kohn and L. J. Sham in 1965.\cite{Kohn1965} DFT makes it possible to transform the problem of electrons interacting and evolving in a nuclear potential to a problem of independent electrons evolving in an effective potential. The electron density $\rho$(\textbf{r}) corresponds to the number of electrons per unit volume in a given state. -The central idea of DFT is to promote $\rho$($\mathbf{r}$) (function which only depends on three spatial coordinates) as the -key variable in the determination of the electronic energy of a system. From the electronic wavefunction of the system, $\rho$($\mathbf{r}$) -is written as: - -%>>>>>>> 92023a10c3aa8b7dc4ace43987c1d571fb99a738 \begin{eqnarray} \label{density} \rho(\mathbf{r})=N\int \Psi^*(\mathbf{r}, \mathbf{r}_2, \mathbf{r}_3, ..., \mathbf{r}_N) \Psi(\mathbf{r}, \mathbf{r}_2, \mathbf{r}_3,..., \mathbf{r}_N) d\mathbf{r}_2 d\mathbf{r}_3...d\mathbf{r}_N \end{eqnarray} +The central idea of DFT is to promote $\rho$($\mathbf{r}$) (function which only depends on three spatial coordinates) as the +key variable in the determination of the electronic energy of a system. +%From the electronic wavefunction of the system, $\rho$($\mathbf{r}$) is written as: -This idea originates from the the model of the uniform electron gas in the phase space around an atom developed in 1927 by Thomas \cite{Thomas1927} and Fermi \cite{Fermi1928}, which is the predecessor to density functional theory. Nevertheless, the Thomas-Fermi model is unable to correctly describe molecular bonds because it does not take into account the exchange and correlation energies. - -Although DFT has a history almost as old as the Schr{\"o}dinger equation, the modern form dates back to the paper published by P. Hohenberg and W. Kohn \cite{Hohenberg1964} -that introduced the two Hohenberg–Kohn (HK) theorems in 1964 and the extension by Levy in 1979.\cite{Levy1979} The theory is usually applied in the form latter suggested -by Kohn and Sham in 1965.\cite{Kohn1965} +%>>>>>>> 92023a10c3aa8b7dc4ace43987c1d571fb99a738 +This idea originates from the the model of the uniform electron gas in the phase space around an atom developed in 1927 by L. H. Thomas \cite{Thomas1927} and E. Fermi \cite{Fermi1928}, which is the predecessor to density functional theory. Nevertheless, the Thomas-Fermi model is unable to correctly describe molecular bonds because it does not take into account the exchange and correlation energies. The first HK theorem shows that, for a many-electron system in its ground state, the energy is uniquely determined by the electron density $\rho$(\textbf{r}). In other words, the first HK theorem shows that it is not necessary to know the wavefunction of the system to obtain its energy and that the knowledge of the electron @@ -410,12 +411,12 @@ and $N$ can be obtained via the normalization of $\rho$(\textbf{r}): \label{N} \int \rho(\mathbf{r}) d\mathbf{r}=N \end{eqnarray} -and $N$ and $V_\mathrm{ext}$(\textbf{r}) determine the electronic Hamiltonian. $\rho$(\textbf{r}) determines the energy and all other ground state electronic properties of a system. This is clearly shown in Figure \ref{variables}. +$N$ and $V_\mathrm{ext}$(\textbf{r}) determine the electronic Hamiltonian. $\rho$(\textbf{r}) determines the energy and all other ground state electronic properties of a system. This is clearly shown in Figure \ref{variables}. \figuremacro{variables}{Interdependence of basic variables in the Hohenberg-Kohn theorem.} \\ -The second HK theorem is a variational electron density theorem which defines an energy functional for a system. -For a given external potential $V_\mathrm{ext}$(\textbf{r}), the ground state energy $E_0$ of the system is the minimum -value of the energy functional obtained for the exact ground state electron density $\rho$(\textbf{r}) of the system. +The second HK theorem is a variational electron density theorem which defines an energy functional of the electronic density for a system. +For a given external potential $V_\mathrm{ext}$(\textbf{r}), the ground state energy $E_0$ of the system is obtained by minimizing this energy function with respect to the electronic density, the corresponding density is exactly the ground state electronic density $\rho$(\textbf{r}). +%the minimum value of the energy functional obtained for the exact ground state electron density $\rho$(\textbf{r}) of the system. %% From the HK theorems, we can write the functional of the total energy of the system as a sum of the kinetic energy of th electrons $T_\mathrm{e}$[$\rho$(\textbf{r})], and the electronic interaction energy $E_\mathrm{ee}$[$\rho$(\textbf{r})]: @@ -445,8 +446,7 @@ $T_\mathrm{no}$[$\rho$(\textbf{r})] is the kinetic energy of a system of non-int T_\mathrm{no}[\rho(\mathbf{r})]=\sum_{i}^{N} \left \langle \Psi_i \left|-\frac{1}{2}\nabla^2 \right | \Psi_i \right \rangle \end{eqnarray} -$E_H$[$\rho$(\textbf{r})] represents the Hartree energy which corresponds to the interaction energy of a classical charge distribution -of density $\rho$(\textbf{r}): +$E_H$[$\rho$(\textbf{r})] represents the Hartree energy which corresponds to the interaction energy of a classical charge distribution of density $\rho$(\textbf{r}): \begin{eqnarray} \label{Ehartree} @@ -456,34 +456,33 @@ E_\mathrm{H}[\rho(\textbf{r})]=\frac{1}{2} \int \int \frac{\rho(\mathbf{r})\rho( $V_\mathrm{ext}$(\textbf{r}) is the external potential. The remaining energy components are assembled in the exchange-correlation energy $E_\mathrm{xc}$[$\rho$(\textbf{r})] functional containing the difference between the kinetic energy of the real system $T$[$\rho$(\textbf{r})] and that of the non-interacting system $T_n$[$\rho$(\textbf{r})] -and the non-classical part of $E_\mathrm{ee}$[$\rho$]. +and the non-classical part of $E_\mathrm{ee}$[$\rho$], adding the difference between $V_\mathrm{ee} [\rho(\mathbf{r})$ and $E_\mathrm H[\rho(\textbf{r})]$. The $E_\mathrm{xc}$[$\rho$(\textbf{r})] functional can thus be expressed as: \begin{eqnarray} \label{Exc} E_\mathrm{xc}[\rho(\mathbf{r})]=(T[\rho(\mathbf{r})]-T_\mathrm{no}[\rho(\mathbf{r})])+(V_\mathrm{ee}[\rho(\mathbf{r})]-E_\mathrm H[\rho(\textbf{r})]) \end{eqnarray} -To minimize the energy $E$[$\rho$(\textbf{r})] with respect to $\rho$(\textbf{r}) applying by the variational principle +In practice, to minimize the energy $E$[$\rho$(\textbf{r})] with respect to $\rho$(\textbf{r}) applying by the variational principle while considering the constraints of orbital orthogonality, one performs an optimization under the constraints using Lagrange multipliers. -For the optimal $\rho$(\textbf{r}), the energy $E$[$\rho$(\textbf{r})] does not change upon the variation of $\rho$($\mathbf{r}$), providing that -$\rho$(\textbf{r}) obey to equation~\ref{N}: -\begin{eqnarray} -\label{Delta} -\delta(E[\rho(\mathbf{r})]-\mathcal{L}\rho(\mathbf{r}))=0 -\end{eqnarray} -where $\mathcal{L}$ is a corresponding Lagrange multiplier. -Combining eqs \ref{E_KS}, \ref{Tn}, \ref{Ehartree}, and \ref{Delta}, the Euler equation can be written as: - -\begin{eqnarray} -\label{Lagrange} -\mathcal{L}=V_\mathrm{eff}[\rho(\mathbf{r})]+ \frac{\delta T_n[\rho(\mathbf{r})]}{\delta \rho(\mathbf{r})} -\end{eqnarray} -where the effective potential $V_\mathrm{eff}$[$\rho$($\mathbf{r}$)] is introduced: +%%For the optimal $\rho$(\textbf{r}), the energy $E$[$\rho$(\textbf{r})] does not change upon the variation of $\rho$($\mathbf{r}$), providing that $\rho$(\textbf{r}) obey to equation~\ref{N}: +%\begin{eqnarray} +%\label{Delta} +%\delta(E[\rho(\mathbf{r})]-\mathcal{L}\rho(\mathbf{r}))=0 +%\end{eqnarray} +%where $\mathcal{L}$ is a corresponding Lagrange multiplier. +%Combining eqs \ref{E_KS}, \ref{Tn}, \ref{Ehartree}, and \ref{Delta}, the Euler equation can be written as: +%\begin{eqnarray} +%\label{Lagrange} +%\mathcal{L}=V_\mathrm{eff}[\rho(\mathbf{r})]+ \frac{\delta T_n[\rho(\mathbf{r})]}{\delta \rho(\mathbf{r})} +%\end{eqnarray} +Combining eqs \ref{E_KS}, \ref{Tn}, and \ref{Ehartree}, the effective potential $V_\mathrm{eff}$[$\rho$($\mathbf{r}$)] can be introduced as: \begin{align} -V_\mathrm{eff}[\rho(\mathbf{r})] &=V_\mathrm{ext}[\rho(\mathbf{r})]+V_\mathrm{H}[\rho(\mathbf{r})]+V_\mathrm{xc}[\rho(\mathbf{r})] \nonumber \\ -&=V_\mathrm{ext}[\rho(\mathbf{r})]+\int\frac{\rho(\mathbf{r'})}{|\mathbf{r}-\mathbf {r'}|}d\mathbf{r'} +\frac{\delta E_\mathrm{xc}[\rho(\mathbf{r})]}{\delta \rho(\mathbf{r})} +V_\mathrm{eff}[\rho(\mathbf{r})]&=V_\mathrm{ext}[\rho(\mathbf{r})]+V_\mathrm{H}[\rho(\mathbf{r})]+V_\mathrm{xc}[\rho(\mathbf{r})] \nonumber \\ +&=V_\mathrm{ext}[\rho(\mathbf{r})]+\int\frac{\rho(\mathbf{r'})}{|\mathbf{r}-\mathbf {r'}|}d\mathbf{r'} +\frac{\delta E_\mathrm{xc}[\rho(\mathbf{r})]}{\delta \rho(\mathbf{r})} \\ +&=\frac{\delta E_\mathrm{eff}[\rho(\mathbf{r})]}{\delta\rho(\mathbf{r})} \label{Veff} \end{align} where $V_{H}$[$\rho$(\textbf{r})] refers to the Hartree potential and $V_{xc}$[$\rho$(\textbf{r})] is the exchange-correlation potential. @@ -527,11 +526,10 @@ The computational cost for the incorporation of electron correlation is the one DFT is in principle correct if one knows the “exact” exchange-correlation functional. However, despite a lot of work aimed at determining this exact functional, its form is still unknown and a systematic strategy for improvement is not available. Therefore, it is always necessar - to use an approximate functional that is characterized by more or less important artefacts in effective calculations. Over the last decades, - many exchange-correlation functionals have been proposed. Although they are different, it is possible to classify them into families according + to use an approximate functional that is characterized by more or less important artefacts in effective calculations. Over the last decades, many exchange-correlation functionals have been proposed. Although they are different, it is possible to classify them into families according to some common characters. \textbf{Local Density Approximation} (LDA), \textbf{Generalized Gradient Approximation} (GGA), \textbf{meta-GGA}, and \textbf{hydrid functionals} (containing to some extent a contribution of HF exact-exchange) are some of the most widely used approximations. -\textbf{LDA} is the first approximation of $E_{xc}$[$\rho$(\textbf{r})] proposed by Kohn and Sham,\cite{Kohn1965} which is based on the description +\textbf{LDA} is the first approximation of $E_{xc}$[$\rho$(\textbf{r})] proposed by W. Kohn and L. J. Sham,\cite{Kohn1965} which is based on the description of the homogeneous electron gas. For atomic or molecular systems, when densities vary rapidly in space, the assumption of a uniform electron density is not correct and the LDA approximation is not applicable any more. For example, binding energies in molecules are usually overestimated by the LDA approximation. To solve this problem, a new family of functionals, \textbf{GGA functional}, which includes a contribution of the electron @@ -565,7 +563,7 @@ provides a computational tool with a remarkable quality and computationally less DFT is computationally too expensive for systems with more than hundreds of atoms especially when one needs to perform global optimization or to perform molecular dynamics (MD) simulations with sufficient statistical sampling of the initial conditions or to perform fairly long trajectories. -It is therefore necessary to further simplify the method in order to reduce the computational cost. To do so, Foulkes and Haydock showed that +It is therefore necessary to further simplify the method in order to reduce the computational cost. To do so, W. Foulkes and R. Haydock showed that tight-binding models can be derived from the DFT.\cite{Foulkes1989} Later, DFTB was proposed by D. Porezag $et ~ al.$.\cite{Porezag1995} Non-self-consistent DFTB scheme is suitable to study systems in which polyatomic electronic density is well described by a sum of atom-like densities. @@ -841,7 +839,7 @@ located on the same atom. This differs from DFT that explicitly considers atomic As presented above, DFTB was initially developed with Mulliken charges; However, other definitions of atomic charges are possible such as Natural Bond Order (NBO)\cite{Bader1985, Bader1990, Glendening1998, Glendening2012} and Electrostatic Potential Fitting (EPF) charges.\cite{Singh1984, Besler1990} EPF has a fairly good representation of the electrostatic term of a molecule dominated by the Van der Waals interactions. CM3 (Class IV / Charge Model 3) -charges were proposed by Li $et al.$ in 1998 and they have been considered in DFTB. They give good results for the description of the electric dipole +charges were proposed by J. Li $et al.$ in 1998 and they have been considered in DFTB. They give good results for the description of the electric dipole and the electrostatic potential, partial atomic charges in molecules, and Coulombic intermolecular potential of polycyclic aromatic hydrocarbon clusters.\cite{Li1998, Kalinowski2004, Kelly2005, Rapacioli2009corr} The CM3 charges are defined as: \begin{align} @@ -909,7 +907,7 @@ V(R_{\alpha\beta}) = D_{eq}\left(1-e^{-a(R_{\alpha\beta}-R_{eq})} \right)^2 where $D_{eq}$ is the depth of the Morse potential well. Parameter $a$ determines the width of the potential, the smaller $a$ the larger the well. The force constant of the bond can be found via the Taylor expansion of $V(R_{\alpha\beta})$ around $R_{\alpha\beta}=R_{eq}$ to the second derivative of the potential energy function, from which it can obtain $a=(k_{eq}/{2D_{eq}})^{\frac{1}{2}}$ in which $k_{eq}$ is the force constant of the minimum well. -Lennard-Jones potential as known as LJ potential or 12-6 potential is a pair potential, which is proposed by John Lennard-Jones in 1924.\cite{Jones1924, Lennard1924} It models soft repulsive and attractive interactions, therefore, the LJ potential describes electronically neutral atoms or molecules. +Lennard-Jones potential as known as LJ potential or 12-6 potential is a pair potential, which is proposed by J. Lennard-Jones in 1924.\cite{Jones1924, Lennard1924} It models soft repulsive and attractive interactions, therefore, the LJ potential describes electronically neutral atoms or molecules. Because of its simple mathematical form, it is one of the most widely used intermolecular potentials especially to describe the interaction within noble gas molecules. The total energy can be written as the sum of the interaction energy of all atomic pairs, which is defined as follows:\cite{Lennard1931} \begin{align} V_\mathrm{LJ}(R_{\alpha\beta}) = 4\varepsilon_0 \left[ \left(\frac{\sigma}{R_{\alpha\beta}}\right)^{12}- \left(\frac{\sigma}{R_{\alpha\beta}}\right)^6 @@ -1014,8 +1012,7 @@ for a more efficient sampling of the PES. The Monte Carlo, classical MD and PTMD The term Monte Carlo denotes a class of algorithmic methods that aims at a probabilistic description, relying on the use of random numbers. The name Monte Carlo alludes to the games of chance taking place at the Monte Carlo casino. The -Monte Carlo method was introduced in 1947 by Metropolis,\cite{Metropolis1987} and was first published in 1949 by -Metropolis in collaboration with Ulam.\cite{Metropolis1949} Monte Carlo methods have been widely applied in computational +Monte Carlo method was introduced in 1947 by N. Metropolis,\cite{Metropolis1987} and was first published in 1949 by N. Metropolis in collaboration with S. Ulam.\cite{Metropolis1949} Monte Carlo methods have been widely applied in computational physics, computational statistics, biomedicine, machine learning, industrial engineering, economics and finance, and other fields.\cite{Kroese2014} \textbf{Monte Carlo methods can} generally be roughly \textbf{divided into two categories}. The first category is applied to problems that have inherent randomness, and the computing power of the computer can directly simulate this random process. For example, @@ -1070,7 +1067,7 @@ point in $\Omega$: \label{thermalAverage} \end{align} in which $Z$ is the partition function, and $k_B$ is the Boltzmann constant. $T$ refers to the temperature, and $H(\textbf X)$ denotes the Hamiltonian of the system. -To illustrate the general application of Monte Carlo techniques, we take here the standard example of the one-dimensional integral $I$ over integration space $\Omega$: +To illustrate the general application of Monte Carlo techniques, here the standard example of the one-dimensional integral $I$ over integration space $\Omega$ is taken: \begin{align} I=\int_\Omega f(\mathbf x)d\mathbf x \label{SingleIntegral} @@ -1153,14 +1150,14 @@ In the case of symmetrical movements, $\eta (\mathbf x_i \rightarrow \mathbf x_j %======= MD is a powerful tool for analyzing the physical movements of atoms and molecules of many-body systems. MD was originally developed following the earlier successes of Monte Carlo simulations. The first work about -MD was published in 1957 by Alder \textit{et al.} which focused on the integration of classical equations of +MD was published in 1957 by B. Alder \textit{et al.} which focused on the integration of classical equations of motion for a system of hard spheres.\cite{Alder1957} Before long, radiation damage at low and moderate energies were studied using MD in 1960 and MD was also applied to simulate liquid argon in 1964.\cite{Gibson1960, Rahman1964} MD experienced an extremely rapid development in the years that followed. MD simulations have been applied in chemistry, biochemistry, physics, biophysics, materials science, and branches of engineering, which is often coupled with experimental measurements to facilitate interpretation. MD has a strong predictive potential thus making it possible to motivate the implementation of new experiments. The diversity, broadness, - and sophistication level of MD techniques have been continuously reported.\cite{Allen2017, Cicccotti1987, Van1990, Berne1998, Tuckerman2000, Frenkel2001, Karplus2002, Rapaport2004, Tavan2005, Van2006} The range of applications of MD simulations is extremely wide, for instance, + and sophistication level of MD techniques have been continuously reported.\cite{Allen2017, Cicccotti1987, Van1990, Berne1998, Tuckerman2000, Frenkel2001, Karplus2002, Rapaport2004, Tavan2005, Van2006} The range of applications of MD simulations is extremely wide, for instance, the study of structure,\cite{Parrinello1980, Ballone1988, Gutierrez1996, Karplus2002} thermodynamic,\cite{Briant1975, Postma1982,Honeycutt1987, Dang1997, Coveney2016} diffusion,\cite{Charati1998, Yeh2004, Braga2014, Pranami2015} @@ -1188,7 +1185,7 @@ The reduction from a full quantum description of all particles, electrons and nu main approximations. The first one is the BO approximation as described in section~\ref{BO_approx} which allows to treat separately electrons and nuclei. The second one treats the nuclei (much heavier than electrons) as point charge particles that follow classical Newtonian dynamics. -In this thesis, \textbf{classical molecular dynamics was used} to perform simulations and we use the term MD to denote +In this thesis, \textbf{classical molecular dynamics was used} to perform simulations and use the term MD to denote classical molecular dynamics only. \textbf{Principles.} @@ -1339,16 +1336,15 @@ bottoms of the wells can not be explored comprehensively. Therefore, it is not p and thoroughly explore the bottom of the wells using a unique MD simulation at a given temperature. Many methods have been proposed to solve this question and are referred to as \textbf{enhanced sampling methods} They are classified into two groups: \textbf{biased methods} and \textbf{non-biased methods}. -In \textbf{biased methods}, the dynamics of the system is influenced by a external factor, usually a non-physical -orce, which makes it possible to push the system outside of the wells even at low $T$.\cite{Torrie1977, Hansmann1993, Marchi1999, Bartels2000, Darve2001} +In \textbf{biased methods}, the dynamics of the system is influenced by a external factor, usually a non-physical force, which makes it possible to push the system outside of the wells even at low $T$.\cite{Torrie1977, Hansmann1993, Marchi1999, Bartels2000, Darve2001} For instance, Metadynamics is a biased method.\cite{Laio2002, Iannuzzi2003, Barducci2011} In \textbf{non-biased methods}, the dynamics of the system is not modified directly. Examples are simulated annealing,\cite{Kirkpatrick1983, Van1987} and multi-replica approaches such as the \textbf{parallel-tempering molecular dynamics} approach, which has been used in this thesis. %For simulated annealing method, a MD or Monte Carlo simulation is performed in the canonical ensemble by slowly decreasing the temperature of the thermostat in order to find a stable structure. The system is then heated again to be out from the basin that was just explored and then it is cooled again to find a new isomer. This mechanism should be done a lot of times in order to get the most stable structure. -The replica exchange approach also termed parallel-tempering was originally devised by Swendsen $et~ al.$ in 1986 \cite{Swendsen1986} +The replica exchange approach also termed parallel-tempering was originally devised by R. H. Swendsen $et~ al.$ in 1986 \cite{Swendsen1986} then extended by Geyer and coauthor in 1991 \cite{Geyer1991} and was further developed by Hukushima and Nemoto,\cite{Hukushima1996} -Falcioni and Deem,\cite{Falcioni1999} Earl and coworker.\cite{Earl2005} Sugita and Okamoto formulated a MD version of parallel tempering +M. Falcioni and M. W. Deem,\cite{Falcioni1999} D. J. Earl and coworker.\cite{Earl2005} Y. Sugita and Y. Okamoto formulated a MD version of parallel tempering to enhance conformational sampling.\cite{Sugita1999} PTMD is a method which aims at enhancing the ergodicity of MD simulations. 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Important hydrogen-bond distances are indicated in bold and are given in \AA }{figure.caption.36}{}} +\@writefile{lof}{\contentsline {figure}{\numberline {3.26}{\ignorespaces Lowest-energy structures of (H$_2$O)$_{11}$UH$^+$ obtained at the MP2/Def2TZVP level of theory. Relative ($E_\textrm {rel}$) and binding energies ($E_\textrm {bind}$) are given in kcal.mol$^{-1}$. Important hydrogen-bond distances are indicated in bold and are given in \r A.}}{94}{figure.caption.37}\protected@file@percent } +\newlabel{11a-f}{{3.26}{94}{Lowest-energy structures of (H$_2$O)$_{11}$UH$^+$ obtained at the MP2/Def2TZVP level of theory. Relative ($E_\textrm {rel}$) and binding energies ($E_\textrm {bind}$) are given in kcal.mol$^{-1}$. Important hydrogen-bond distances are indicated in bold and are given in \AA }{figure.caption.37}{}} +\@writefile{lof}{\contentsline {figure}{\numberline {3.27}{\ignorespaces Lowest-energy structures of (H$_2$O)$_{12}$UH$^+$ obtained at the MP2/Def2TZVP level of theory. Relative ($E_\textrm {rel}$) and binding energies ($E_\textrm {bind}$) are given in kcal.mol$^{-1}$. Important hydrogen-bond distances are indicated in bold and are given in \r A.}}{95}{figure.caption.38}\protected@file@percent } +\newlabel{12a-f}{{3.27}{95}{Lowest-energy structures of (H$_2$O)$_{12}$UH$^+$ obtained at the MP2/Def2TZVP level of theory. Relative ($E_\textrm {rel}$) and binding energies ($E_\textrm {bind}$) are given in kcal.mol$^{-1}$. Important hydrogen-bond distances are indicated in bold and are given in \AA }{figure.caption.38}{}} \@setckpt{3/structure_stability}{ -\setcounter{page}{98} +\setcounter{page}{96} \setcounter{equation}{3} \setcounter{enumi}{5} \setcounter{enumii}{0} diff --git a/thesis/3/structure_stability.tex b/thesis/3/structure_stability.tex index bf722f3..135000f 100644 --- a/thesis/3/structure_stability.tex +++ b/thesis/3/structure_stability.tex @@ -1,4 +1,4 @@ -Conclusions% this file is c\emph{•}alled up by thesis.tex +%Conclusions% this file is c\emph{•}alled up by thesis.tex % content in this file will be fed into the main document %%\chapter{Aims of the project} % top level followed by section, subsection @@ -20,9 +20,9 @@ combination of the \textbf{self-consistent-charge density functional based tight energy surfaces (PES) and the \textbf{parallel-tempering molecular dynamics} (PTMD) approach for their exploration. All low-energy isomers reported in this chapter are discussed in terms of structure, relative energy and binding energy which are compared to the literature when available. Calculations at higher level of theory are also performed to refine the results obtained at the SCC-DFTB level or to -validate the results it provides. In particular, in this chapter, we propose an improve set of parameters to describe sp$^3$ nitrogen +validate the results it provides. In particular, in this chapter, an improve set of parameters is proposed to describe sp$^3$ nitrogen containing compounds at the SCC-DFTB level. Our results are also used to complement collision-induced dissociation experiments -performed by S. Zamith and J.-M. l'Hermite at the \textit{Laboratoire Collisions Agr\'egats R\'eactivit\'e} (LCAR). +performed by S. Zamith and J.-M. L'Hermite at the \textit{Laboratoire Collisions Agr\'egats R\'eactivit\'e} (LCAR). %The background of the systems studied in this thesis and theoretical methods related to the projects of this thesis have been introduced in chapter \ref{chap:general_intro} and chapter \ref{chap:comput_method}. Then the two kinds of projects investigated in my Phd will be shown in the following chapter \ref{chap:structure} and chpater \ref{chap:collision}. @@ -37,20 +37,16 @@ of the method are presented in section~\ref{sec:DFTB} of chapter~\ref{chap:compu %DFTB is an approximated DFT scheme whose computational efficiency depends on the use of parameterized integrals.\cite{Elstner2014, Elstner1998, dftb1, dftb2} The mio-set for the Slater-Koster tables of integrals was used.\cite{Elstner1998} However, it has been shown that these integrals do not properly described sp$^3$ hybridized nitrogen, in particular, proton affinity.\cite{Gaus2013para} Consequently, in order to avoid spurious deprotonation of the sp$^3$ hybridized -nitrogen in NH$_4^+$ and to correctly reproduce binding energies calculated at the MP2/Def2TZVP level, we propose to modify the original mio-set for -Slater-Koster tables of N-H integrals by applying them a multiplying factor. Several of them were tested and we present here the results -we obtained for two of them: 1.16 and 1.28. For the sp$^2$ nitrogen of uracil, the original integrals of the mio-set were used. To improve +nitrogen in NH$_4^+$ and to correctly reproduce binding energies calculated at the MP2/Def2TZVP level, I propose to modify the original mio-set for +Slater-Koster tables of N-H integrals by applying them a multiplying factor. Several of them were tested and I present here the results obtained for two of them: 1.16 and 1.28. For the sp$^2$ nitrogen of uracil, the original integrals of the mio-set were used. To improve description of the intermolecular interactions, the original Mulliken charges were replaced by the CM3 charges,\cite{Li1998, Thompson2003, Rapacioli2009corr} (see equation~\ref{CM3} in section~\ref{sec:DFTB}) and an empirical correction term (see equation~\ref{dispersionE} in section~\ref{sec:DFTB}) was used -to describe dispersion interactions.\cite{Rapacioli2009corr, Elstner2001, Zhechkov2005} Simon \textit{et al.} developed a SCC-DFTB potential that leads -to geometries, frequencies, and relative energies close to the corresponding experimental and CCSD(T)/aug-cc-pVTZ results.\cite{Simon2012, Odutola1980} -The corresponding $D_{OH}$ parameter, \textit{i.e.} 0.129, is retained in the studies presented in thus chapter. $D_{NH}$ is tested in the study of -ammonium/ammonia water clusters and two values were retained and thoroughly tested: 0.12 and 0.14. D$_{NO}$ is set to zero. +to describe dispersion interactions.\cite{Rapacioli2009corr, Elstner2001, Zhechkov2005} A. Simon \textit{et al.} developed a SCC-DFTB potential that leads to geometries, frequencies, and relative energies close to the corresponding experimental and CCSD(T)/aug-cc-pVTZ results.\cite{Simon2012, Odutola1980} The corresponding $D_{OH}$ parameter, \textit{i.e.} 0.129, is retained in the studies presented in thus chapter. $D_{NH}$ is tested in the study of ammonium/ammonia water clusters and two values were retained and thoroughly tested: 0.12 and 0.14. D$_{NO}$ is set to zero. \subsection{SCC-DFTB Exploration of PES} To determine the lowest-energy isomers of (H$_2$O)$_{1-10,20}${NH$_4$}$^+$, (H$_2$O)$_{1-10}$NH$_3$ -and (H$_2$O)$_{1-7,11,12}$UH$^+$ clusters, we thoroughly explore their PES using PTMD \cite{Sugita1999, Sugita2000, Earl2005} +and \newline (H$_2$O)$_{1-7,11,12}$UH$^+$ clusters, their PES were thoroughly explored using PTMD \cite{Sugita1999, Sugita2000, Earl2005} simulations combined with a SCC-DFTB \cite{Elstner1998} description of the energies and gradients. I describe below the \textbf{detailed parameters used for all the simulations conducted within this chapter}. @@ -59,12 +55,12 @@ For (H$_2$O)$_{1-3}${NH$_4$}$^+$ and (H$_2$O)$_{1-3}${NH$_3$} clusters, 16 repl with a linear distribution of temperatures with a 15~K step ranging from 10 to 250 K. 40 replicas with a 6~K step ranging from 10 to 250~K were considered for (H$_2$O)$_{4-10,20}${NH$_4$}$^+$ and (H$_2$O)$_{4-10}${NH$_3$} species. All trajectories were 5~ns long and a time step of 0.5 fs was used to integrate the equations of motion. A Nos{\'e}-Hoover chain of 5 thermostats was employed for all the simulations to achieve -simulatons in the canonical ensemble.\cite{Nose1984M, Hoover1985} Thermostat frequencies were fixed at 400 cm$^{-1}$. +simulations in the canonical ensemble.\cite{Nose1984M, Hoover1985} Thermostat frequencies were fixed at 400 cm$^{-1}$. To identify low-energy isomers of (H$_2$O)$_{1-3}${NH$_4$}$^+$ and (H$_2$O)$_{1-3}${NH$_3$} clusters, 303 geometries were periodically selected from each replicas and further optimized at the SCC-DFTB level, which produced 4848 optimized geometries per cluster. For (H$_2$O)$_{4-10,20}${NH$_4$}$^+$ and (H$_2$O)$_{4-10}${NH$_3$} clusters, 500 geometries were periodically selected from each replicas leading to 20000 optimized geometries per cluster. For (H$_2$O)$_{20}${NH$_4$}$^+$, the initial structure used for the global -optimization process was the lowest-energy structure reported by Douady \textit{et al.}.\cite{Douady2009} The five lowest-energy +optimization process was the lowest-energy structure reported by J. Douady \textit{et al.}.\cite{Douady2009} The five lowest-energy isomers among the 4848 or 20000 optimized geometries were further optimized using the MP2/Def2TZVP method. See below for the details on MP2/Def2TZVP calculations. @@ -73,7 +69,7 @@ details on MP2/Def2TZVP calculations. A reasonable time interval for the PT exchanges was 2.5 ps. A Nos{\'e}-Hoover chain of five thermostats with frequencies of 800 cm$^{-1}$ was applied to achieve an exploration in the canonical ensemble.\cite{Nose1984M, Hoover1985} To avoid any spurious influence of the initial geometry on the PES exploration, three distinct PTMD simulations were carried out with distinct initial proton location: on the uracil in two cases -and on a water molecule in the other one. In the former cases, we used two isomers u178 and u138 of UH$^+$ shown in Figure~\ref{uracil_s} as +and on a water molecule in the other one. In the former cases, I used two isomers u178 and u138 of UH$^+$ shown in Figure~\ref{uracil_s} as the initial geometries.\cite{Wolken2000, Pedersen2014} 600 geometries per temperature were linearly selected along each PTMD simulation for subsequent geometry optimization leading to 72000 structures optimized at SCC-DFTB level. These structures were sorted in ascending energy order and checked for redundancy. 9, 23, 46, 31, 38, 45, 63, 20, and 29 structures were then selected for (H$_2$O)UH$^+$, @@ -91,8 +87,7 @@ level. See below for the details on MP2/Def2TZVP calculations. \subsection{MP2 Geometry Optimizations, Relative and Binding Energies} -Some low-energy isomers obtained at the SCC-DFTB level were further optimized at the MP2 level of theory in combination -with an all electron Def2TZVP basis-set.\cite{Weigend2005, Weigend2006} All calculations used a a tight criteria for geometry +Some low-energy isomers obtained at the SCC-DFTB level were further optimized at the MP2 level of theory in combinationwith an all electron Def2TZVP basis-set.\cite{Weigend2005, Weigend2006} All calculations used a a tight criteria for geometry convergence and an ultrafine grid for the numerical integration. All MP2 calculations were performed with the Gaussian 09 package.\cite{GaussianCode} @@ -102,7 +97,7 @@ Following SCC-DFTB optimizations, the five lowest-energy isomers of (H$_2$O)$_{1 In section~\ref{sec:ammoniumwater}, relatives energies with respect to the lowest-energy isomer of each cluster are reported. Impact of zero-point vibrational energy (ZPVE) corrections on relative energies were evaluated at MP2/Def2TZVP level. To evaluate the strength of water-ammonium and water-ammonia -interactions and to assess the accuracy of the SCC-DFTB method, we also report binding energies. +interactions and to assess the accuracy of the SCC-DFTB method, binding energies are also reported. Two distinct approaches were used to calculate binding energies. The first one considers only the binding energy between the water cluster as a whole and the impurity, {NH$_4$}$^+$ or NH$_3$, while the second one considers the binding energy between all the molecules of the cluster. In both cases, the geometry of the molecules @@ -149,23 +144,19 @@ basicity makes it a potential proton sink that can form a ionic center for nucle also found that even a small amount of atmospherically relevant ammonia can increase the nucleation rate of sulphuric acid particles by several orders of magnitude.\cite{Kirkby2011} The significance of ammonium and ammonia water clusters have thus motivated a large amount of experimental and theoretical studies during the past decades.\cite{Perkins1984, Herbine1985, Stockman1992, Hulthe1997, Wang1998, Chang1998, Jiang1999, Hvelplund2010, Douady2009, Douady2008, Morrell2010, Bacelo2002, Galashev2013} -As a few examples, in 1984, (H$_2$O)$_{2}${NH$_4$}$^+$ was identified using mass spectrometry by Perkin \textit{et al.}\cite{Perkins1984} In 1997, Stenhagen +As a few examples, in 1984, (H$_2$O)$_{2}${NH$_4$}$^+$ was identified using mass spectrometry by M. D. Perkin \textit{et al.}\cite{Perkins1984} In 1997, Stenhagen and co-workers studied the {(H$_2$O)$_{20}$H$_3$O}$^+$ and (H$_2$O)$_{20}${NH$_4$}$^+$ clusters and found that both species display a similar -structure.\cite{Hulthe1997} Hvelplund \textit{et al.} later reported a combined experimental and theoretical study devoted to protonated mixed ammonia/water +structure.\cite{Hulthe1997} P. Hvelplund \textit{et al.} later reported a combined experimental and theoretical study devoted to protonated mixed ammonia/water which highlighted the idea that small protonated mixed clusters of water and ammonia contain a central {NH$_4$}$^+$ core.\cite{Hvelplund2010} %The (H$_2$O)NH$_3$ complex has been experimentally investigated via radio frequency and microwave spectra by Herbine \textit{et al.}, and via microwave and tunable far-infrared spectroscopy by Stockman and co-workers.\cite{Herbine1985, Stockman1992} Theoretical calculations devoted to ammonium and ammonia water clusters have also been extensively conducted.\cite{Lee1996, Chang1998, -Skurski1998, Jiang1999, Donaldson1999, Sadlej1999, Hvelplund2010, Bacelo2002, Galashev2013} Among them, Novoa \textit{et al.} studied the (H$_2$O)$_4$NH$_3$ -aggregate and found the existence of a minimum in its potential energy surface corresponding to a (H$_2$O)$_{3}$···{NH$_4$}$^+$···OH$^-$ structure, resulting from -one proton transfer from a water molecule to the ammonia molecule.\cite{Lee1996} Bacelo later reported a number of low-energy minima for (H$_2$O)$_{3-4}$NH$_3$ -clusters obtained from \textit{ab initio} calculation and a Monte Carlo exploration of the potential energy surface (PES).\cite{Bacelo2002} More recently, Douady \textit{et al.} -performed a global optimization of (H$_2$O)$_{n}${NH$_4$}$^+$ (n = 1-24) clusters again using a Monte Carlo procedure in combination with a Kozack and Jordan -empirical force field.\cite{Douady2008, Kozack1992polar} +Skurski1998, Jiang1999, Donaldson1999, Sadlej1999, Hvelplund2010, Bacelo2002, Galashev2013} Among them, J. Novoa \textit{et al.} studied the (H$_2$O)$_4$NH$_3$ +aggregate and found the existence of a minimum in its potential energy surface corresponding to a (H$_2$O)$_{3}$···{NH$_4$}$^+$···OH$^-$ structure, resulting from one proton transfer from a water molecule to the ammonia molecule.\cite{Lee1996} D. Bacelo later reported a number of low-energy minima for (H$_2$O)$_{3-4}$NH$_3$ clusters obtained from \textit{ab initio} calculation and a Monte Carlo exploration of the PES.\cite{Bacelo2002} More recently, J. Douady \textit{et al.} performed a global optimization of (H$_2$O)$_{n}${NH$_4$}$^+$ ($n$ = 1-24) clusters again using a Monte Carlo procedure in combination with a Kozack and Jordan empirical force field.\cite{Douady2008, Kozack1992polar} In this study, the finite temperature properties as well as vibrational signature of several clusters thus highlighting the key contribution of simulations in understanding such species. Morrell and Shields also studied the -(H$_2$O)$_{n}${NH$_4$}$^+$ (n = 1-10) aggregates \textit{via} a mixed molecular dynamics and quantum mechanics methodology to calculate energies and free energies +(H$_2$O)$_{n}${NH$_4$}$^+$ ($n$ = 1-10) aggregates \textit{via} a mixed molecular dynamics and quantum mechanics methodology to calculate energies and free energies of formations which were in good agreement with previous experimental and theoretical results.\cite{Morrell2010} -More recently, Pei \textit{et al.} determined that (H$_2$O)$_{n}$NH$_4^+$ clusters start to adopt a closed-cage geometry at $n$=8.\cite{Pei2015} -Finally, Walters and collaborators determined the geometry of (H$_2$O)$_{16}$NH$_3$ and (H$_2$O)$_{16}$NH$_4^+$ at the HF/6-31G(d) level, +More recently, S. Pei \textit{et al.} determined that (H$_2$O)$_{n}$NH$_4^+$ clusters start to adopt a closed-cage geometry at $n$=8.\cite{Pei2015} +Finally, W. Walters and collaborators determined the geometry of (H$_2$O)$_{16}$NH$_3$ and (H$_2$O)$_{16}$NH$_4^+$ at the HF/6-31G(d) level, and observed strong hydrogen bonding between water and the lone pair of NH$_3$ and bewteen NH$_4^+$ and the four adjacent water molecules.\cite{Walters2018} As for the study of other molecular clusters, the range of applicability of theoretical simulations to describe ammonium and ammonia water clusters is dictated @@ -173,16 +164,16 @@ by the balance between accuracy, transferability and computational efficiency. W application to large species is more difficult, in particular when an exhaustive exploration of the PES is required. In contrast, force-field potentials are computationally extremely efficient and can be coupled to global optimization methods but their transferability is limited. The SCC-DFTB approach can be seen as an intermediate approach which combines the strengths of both \textit{ab-initio} and force-field methods. -Indeed, it can be as accurate as DFT while computationally more efficient and is more transferable than force fields (see Chapter~2) - In the recent years, SCC-DFTB has been successfully applied to the study of various molecular clusters: pure, protonated, and de-protonated water -clusters,\cite{Choi2010, Choi2013, Korchagina2017, Simon2019} water clusters on polycyclic aromatic hydrocarbons,\cite{Simon2012, Simon2013water} +Indeed, it can be as accurate as DFT while computationally more efficient and is more transferable than force fields (see chapter \ref{chap:comput_method}) + In recent years, SCC-DFTB has been successfully applied to the study of various molecular clusters: pure, protonated, and de-protonated water +clusters,\cite{Choi2010, Choi2013, Korchagina2017, Simon2019} water clusters on PAHs,\cite{Simon2012, Simon2013water} sulfate-containing water clusters,\cite{Korchagina2016} water clusters in an argon matrix,\cite{Simon2017formation} whether it is for global optimization or for the study of finite-temperature properties. However, in its original formulation, SCC-DFTB does not provide good results for the description of ammonia -and ammonium as nitrogen hybridization seems to be a problem for minimal basis-set methods like SCC-DFTB.\cite{Winget2003} Elstner and coworkers found +and ammonium as nitrogen hybridization seems to be a problem for minimal basis-set methods like SCC-DFTB.\cite{Winget2003} M. Elstner and coworkers found consistent errors (about 14.0 kcal.mol$^{-1}$) for deprotonation energies of sp$^3$ hybridized nitrogen containing systems, whereas sp$^1$ and sp$^2$ systems display much smaller errors.\cite{Gaus2013para} -In the present section, we first propose an improvement of the SCC-DFTB scheme to describe ammonium and ammonia water clusters by modifying +In this section, I first propose an improvement of the SCC-DFTB scheme to describe ammonium and ammonia water clusters by modifying both Hamiltonian and overlap N-H integrals and introducing optimized atomic charges.\cite{Thompson2003, Rapacioli2009} By combining this improved SCC-DFTB scheme with PTMD simulations, global optimization of the (H$_2$O)$_{1-10}${NH$_4$}$^+$ and (H$_2$O)$_{1-10}${NH$_3$} clusters is then performed which allows to report a number of low-energy isomers for these species. Among them, a selected number of structures @@ -196,7 +187,7 @@ A full paper devoted to this work is in preparation. \subsubsection{Dissociation Curves and SCC-DFTB Potential} -In order to define the best SCC-DFTB parameter to model ammonia and ammonium water clusters, we have tested various sets of corrections. +In order to define the best SCC-DFTB parameter to model ammonia and ammonium water clusters, I have tested various sets of corrections. Each correction involves two modifications of the potential, the first one is the CM3 charge parameter D$_{NH}$ and the second one is the multiplying factor, noted $xNH$, applied to the NH integrals in the Slater-Koster tables. So a given set is noted D$_{NH}$/$xNH$. Two sets of corrections have provided satisfactory results, 0.12/1.16 and 0.14/1.28. Figure~\ref{fig:E_nh4} and ~\ref{fig:E_nh3} present dissociation @@ -279,10 +270,10 @@ From en energetic point of view, it is interesting to first look at the relative (H$_2$O)$_{3}${NH$_4$}$^+$. Isomer 3-b is 2.12~kcal·mol\textsuperscript{-1} higher than 3-a at the SCC-DFTB level. At the MP2/Def2TZVP level, 3-b is 0.30~kcal·mol\textsuperscript{-1} lower than 3-a when ZPVE is not considered while it is 1.21 kcal·mol\textsuperscript{-1} higher when it is considered. In comparison, in the experimental results by -Chang and co-workers, 3-a is more stable than 3-b.\cite{Wang1998, Jiang1999} The aauhors also complemented their +H. Chang and co-workers, 3-a is more stable than 3-b.\cite{Wang1998, Jiang1999} The authors also complemented their measurements by theoretical calculations that show that at the B3LYP/6-31+G(d) level, 3-a is higher than 3-b but. In contrast, at the MP2/6-31+G(d) level corrected with ZPVE, the energy of 3-a is lower than that of 3-b while it is inverted -if ZPVE is taken into account.\cite{Wang1998, Jiang1999} Additionally, Spiegelman and co-workers, conducted a +if ZPVE is taken into account.\cite{Wang1998, Jiang1999} Additionally, F. Spiegelman and co-workers, conducted a global Monte Carlo optimizations with an intermolecular polarizable potential that lead to 3-a as lowest-energy isomer.\cite{Douady2008} All these results show that for the specific question of lowest-energy isomer of (H$_2$O)$_{3}${NH$_4$}$^+$, SCC-DFTB has an accuracy close to other \textit{ab initio} methods which confirms its applicability. @@ -352,10 +343,10 @@ isomers of clusters (H$_2$O)$_{4-10}${NH$_4$}$^+$ and (H$_2$O)$_{4-10}$NH$_3$ ar The five lowest-energy isomers of (H$_2$O)$_{4}${NH$_4$}$^+$ are depicted in Figure~\ref{fig:nh4-4-6w}. 4-a is the lowest-energy isomer obtained from the global SCC-DFTB optimization and also the lowest-energy configuration after optimization at MP2/Def2TZVP level with ZPVE corrections. This result is consistent with previous computational studies\cite{Wang1998, Jiang1999, Douady2008, Lee2004, Pickard2005} and -the experimental studies by Chang and co-workers.\cite{Chang1998, Wang1998} Isomer 4-a diplays four hydrogen bonds around the ionic +the experimental studies by H. Chang and co-workers.\cite{Chang1998, Wang1998} Isomer 4-a displays four hydrogen bonds around the ionic center which lead to no dangling N-H bonds. Other isomers of comparable stability are displayed in Figure~\ref{fig:nh4-4-6w} The energy ordering of 4-a to 4-e at SCC-DFTB level is consistent with that at MP2/Def2TZVP level with ZPVE correction, although they -are slightly higher by$\sim$2.0 kcal.mol$^{-1}$. Isomer 4-c was not reported in Chang’s study,\cite{Jiang1999} and the corresponding +are slightly higher by$\sim$2.0 kcal.mol$^{-1}$. Isomer 4-c was not reported in H. Chang’s study,\cite{Jiang1999} and the corresponding energy ordering of the five lowest-energy isomers was the same as ours which certainly results from the use of a different basis set. \begin{figure}[h!] @@ -418,92 +409,92 @@ energy ordering of the five lowest-energy isomers was the same as ours which cer The relative binding energy of SCC-DFTB method to MP2/Def2TZVP method with BSSE correction for isomers 4-a to 4-e are listed in Table \ref{reBindE}. When the four water molecules are considered as a whole part to calculate the binding energy, the relative binding energy of isomers 4-a to 4-e are -1.67, 0.00, 0.77, 0.77 and -4.04 kcal·mol\textsuperscript{-1}. As shown in Table \ref{reBindE}, for isomers 4-a to 4-e, when the four water molecules are separately considered using the geometry in the cluster to calculate the binding energy, the biggest absolute value of the relative binding energy is 0.87 kcal·mol\textsuperscript{-1}. This shows the results of SCC-DFTB are in good agreement with those of MP2/Def2TZVP with BSSE correction for (H$_2$O)$_{4}${NH$_4$}$^+$. From the relative binding energy of (H$_2$O)$_{4}${NH$_4$}$^+$, it indicates that all the water molecules considered as a whole part or separately has an effect on the relative binding energy for the cluster (H$_2$O)$_{4}${NH$_4$}$^+$ and the overall $\Delta E_{bind.}^{whole}$ are bigger than $\Delta E_{bind.}^{sep.}$. -For cluster (H$_2$O)$_{5}${NH$_4$}$^+$, the first five low-energy isomers are illustrated in Figure \ref{fig:nh4-4-6w}. The isomer 5-a is the most stable one, which is consistent with Spiegelman’s result using the global MC optimization and Shields’s results obtained with a mixed molecular dynamics/quantum mechanics moldel.\cite{Douady2008, Morrell2010} The energy order of 5-a to 5-e at SCC-DFTB level is consistent with that at MP2/Def2TZVP level with ZPVE correction. 5-a, 5-d and 5-e have a complete solvation shell while one dangling N-H bond is exposed in 5-b and 5-c. For the first five low-energy isomers, the energy order of our results are not exactly the same with Chang’s calculation results at MP2/6-31+G(d)level with ZPVE correction.\cite{Jiang1999} In Chang’s results, 5-d is the first low-energy isomer and 5-a is the second low-energy isomer. They didn’t find isomers 5-b and 5-c. From the comparison, it implies the combination of SCC-DFTB and PTMD is good enough to find the low-energy isomer and the basis set can affect the energy order when using the MP2 approach. +For cluster (H$_2$O)$_{5}${NH$_4$}$^+$, the five low-energy isomers are illustrated in Figure \ref{fig:nh4-4-6w}. The isomer 5-a is the most stable one, which is consistent with F. Spiegelman’s result using the global Monte Carlo optimization and G. Shields’s results obtained with a mixed molecular dynamics/quantum mechanics moldel.\cite{Douady2008, Morrell2010} The energy order of 5-a to 5-e at SCC-DFTB level is consistent with that at MP2/Def2TZVP level with ZPVE correction. 5-a, 5-d and 5-e have a complete solvation shell while one dangling N-H bond is exposed in 5-b and 5-c. For the five low-energy isomers, the energy order of our results are not exactly the same with H. Chang’s calculation results at MP2/6-31+G(d)level with ZPVE correction.\cite{Jiang1999} In H. Chang’s results, 5-d is the low-energy isomer and 5-a is the second low-energy isomer. They didn’t find isomers 5-b and 5-c. From the comparison, it implies the combination of SCC-DFTB and PTMD is good enough to find the low-energy isomer and the basis set can affect the energy order when using the MP2 approach. -When all the water molecules are considered as a whole part, the obtained binding energy has a deviation due to the interaction of water molecules. As listed in Table \ref{reBindE}, for isomers 5-a to 5-e, the relative binding energy $\Delta E_{bind.}^{whole}$ are -1.62, 0.72, 0.69, -1.08 and -2.08 kcal·mol\textsuperscript{-1} and $\Delta E_{bind.}^{sep.}$ are -0.56, 0.48, 0.55, -0.78 and 0.88 kcal·mol\textsuperscript{-1}, respectively. The $\Delta E_{bind.}^{whole}$ is bigger than corresponding $\Delta E_{bind.}^{sep.}$, which indicates it is better to calculate the binding energy with considering the water molecules separately. The $\Delta E_{bind.}^{sep.}$ is less than 1.00 kcal·mol\textsuperscript{-1} for the first five low-energy isomers of cluster (H$_2$O)$_{5}${NH$_4$}$^+$, so the SCC-DFTB method is good enough compared to MP2/Def2TZVP with BSSE correction for cluster (H$_2$O)$_{5}${NH$_4$}$^+$. +When all the water molecules are considered as a whole part, the obtained binding energy has a deviation due to the interaction of water molecules. As listed in Table \ref{reBindE}, for isomers 5-a to 5-e, the relative binding energy $\Delta E_{bind.}^{whole}$ are -1.62, 0.72, 0.69, -1.08 and -2.08 kcal·mol\textsuperscript{-1} and $\Delta E_{bind.}^{sep.}$ are -0.56, 0.48, 0.55, -0.78 and 0.88 kcal·mol\textsuperscript{-1}, respectively. The $\Delta E_{bind.}^{whole}$ is bigger than corresponding $\Delta E_{bind.}^{sep.}$, which indicates it is better to calculate the binding energy with considering the water molecules separately. The $\Delta E_{bind.}^{sep.}$ is less than 1.00 kcal·mol\textsuperscript{-1} for the five low-energy isomers of cluster (H$_2$O)$_{5}${NH$_4$}$^+$, so the SCC-DFTB method is good enough compared to MP2/Def2TZVP with BSSE correction for cluster (H$_2$O)$_{5}${NH$_4$}$^+$. -For cluster (H$_2$O)$_{6}${NH$_4$}$^+$, no N-H bond is exposed in the first five low-energy isomers displayed in Figure \ref{fig:nh4-4-6w}. 6-a is the first low-energy isomer at SCC-DFTB level, which is a symmetric double-ring species connected together by eight hydrogen bonds making it a robust structure. 6-a is also the first low-energy isomer obtained using the MC optimizations with the intermolecular polarizable potential.\cite{Douady2008} 6-d is the first low-energy isomer at MP2/Def2TZVP level with ZPVE correction but it is only 0.22 kcal·mol\textsuperscript{-1} lower than 6-a. In Shields’s results, 6-d is also the first low-energy isomer at MP2/aug-cc-pVDZ level.\cite{Morrell2010} In Chang’s study, 6-b with a three-coordinated H2O molecule is the first low-energy isomer for cluster (H$_2$O)$_{6}${NH$_4$}$^+$ at B3LYP/6-31+G(d) level.\cite{Wang1998} 6-b is also the first low-energy isomer at B3LYP/6-31++G(d,p) level including the harmonic ZPE contribution.\cite{Douady2008} The energy of 6-b is only 0.14 kcal·mol\textsuperscript{-1} higher than that of 6-a at MP2/Def2TZVP level with ZPVE correction. The energies of 6-a, 6-b and 6-d are very close at both SCC-DFTB and MP2/Def2TZVP with ZPVE correction levels, which implies it is easy to have a transformation among 6-a, 6-b and 6-d. It shows SCC-DFTB is good to find the low-energy isomers of cluster (H$_2$O)$_{6}${NH$_4$}$^+$ compared to MP2 and B3LYP methods. +For cluster (H$_2$O)$_{6}${NH$_4$}$^+$, no N-H bond is exposed in the five low-energy isomers displayed in Figure \ref{fig:nh4-4-6w}. 6-a is the first low-energy isomer at SCC-DFTB level, which is a symmetric double-ring species connected together by eight hydrogen bonds making it a robust structure. 6-a is also the first low-energy isomer obtained using the Monte Carlo optimizations with the intermolecular polarizable potential.\cite{Douady2008} 6-d is the first low-energy isomer at MP2/Def2TZVP level with ZPVE correction but it is only 0.22 kcal·mol\textsuperscript{-1} lower than 6-a. In Shields’s results, 6-d is also the first low-energy isomer at MP2/aug-cc-pVDZ level.\cite{Morrell2010} In H. Chang’s study, 6-b with a three-coordinated H2O molecule is the first low-energy isomer for cluster (H$_2$O)$_{6}${NH$_4$}$^+$ at B3LYP/6-31+G(d) level.\cite{Wang1998} 6-b is also the first low-energy isomer at B3LYP/6-31++G(d,p) level including the harmonic ZPE contribution.\cite{Douady2008} The energy of 6-b is only 0.14 kcal·mol\textsuperscript{-1} higher than that of 6-a at MP2/Def2TZVP level with ZPVE correction. The energies of 6-a, 6-b and 6-d are very close at both SCC-DFTB and MP2/Def2TZVP with ZPVE correction levels, which implies it is easy to have a transformation among 6-a, 6-b and 6-d. It shows SCC-DFTB is good to find the low-energy isomers of cluster (H$_2$O)$_{6}${NH$_4$}$^+$ compared to MP2 and B3LYP methods. As shown in Table \ref{reBindE}, for isomers 6-a to 6-e, the relative binding energy $\Delta E_{bind.}^{whole}$ are -1.71, -1.14, -2.06, -2.90 and -1.18 kcal·mol\textsuperscript{-1} and the $\Delta E_{bind.}^{sep.}$ are -0.38, -0.76, 0.27, -1.06 and -0.60 kcal·mol\textsuperscript{-1}, respectively. It indicates the binding energy are very close at SCC-DFTB and MP2/Def2TZVP with BSSE correction levels when water molecules are calculated separately. The $\Delta E_{bind.}^{whole}$ is bigger than corresponding $\Delta E_{bind.}^{sep.}$ because of the interaction of water molecules when all the water molecules are considered as a whole part. -For cluster (H$_2$O)$_{7}${NH$_4$}$^+$, the first five low-energy isomers are shown in Figure \ref{fig:nh4-7-10w}. The ion core {NH$_4$}$^+$ has a complete solvation shell in isomers 7-a to 7-e. 7-a and 7-b with three three-coordinated H$_2$O molecules are the first low-energy isomers at SCC-DFTB level. In Spiegelman’s study, 7-a is also the first low-energy isomer using the MC optimizations with the intermolecular polarizable potential.\cite{Douady2008} 7-c is the first low-energy isomer at MP2/Def2TZVP with ZPVE correction level including three three-coordinated water molecules. 7-c is also the first low-energy isomer at B3LYP/6-31++G(d,p) level including the harmonic ZPE contribution.\cite{Douady2008} 7-e is the first low-energy isomer with three three-coordinated H2O molecules at MP2/aug-cc-pVDZ level in Shields’s study.\cite{Morrell2010} As illustrated in Figure \ref{fig:nh4-7-10w}, the energy difference between 7-a, 7-c and 7-e at SCC-DFTB and MP2/Def2TZVP with ZPVE correction levels are less than 0.61 kcal·mol\textsuperscript{-1} so it is possible that the first low-energy iosmer is different when different method are applied. The energy of 7-a and 7-b are the same at both SCC-DFTB and MP2/Def2TZVP with ZPVE correction levels and their structures are similar, which indicates it is easy for them to transform to each other. The results for cluster (H$_2$O)$_{7}${NH$_4$}$^+$ verify the accuracy of SCC-DFTB approach. +For cluster (H$_2$O)$_{7}${NH$_4$}$^+$, the five low-energy isomers are shown in Figure \ref{fig:nh4-7-10w}. The ion core {NH$_4$}$^+$ has a complete solvation shell in isomers 7-a to 7-e. 7-a and 7-b with three three-coordinated H$_2$O molecules are the first low-energy isomers at SCC-DFTB level. In F. Spiegelman’s study, 7-a is also the first low-energy isomer using the Monte Carlo optimizations with the intermolecular polarizable potential.\cite{Douady2008} 7-c is the first low-energy isomer at MP2/Def2TZVP with ZPVE correction level including three three-coordinated water molecules. 7-c is also the first low-energy isomer at B3LYP/6-31++G(d,p) level including the harmonic ZPE contribution.\cite{Douady2008} 7-e is the first low-energy isomer with three three-coordinated H$_2$O molecules at MP2/aug-cc-pVDZ level in G. Shields’s study.\cite{Morrell2010} As illustrated in Figure \ref{fig:nh4-7-10w}, the energy difference between 7-a, 7-c and 7-e at SCC-DFTB and MP2/Def2TZVP with ZPVE correction levels are less than 0.61 kcal·mol\textsuperscript{-1} so it is possible that the first low-energy iosmer is different when different method are applied. The energy of 7-a and 7-b are the same at both SCC-DFTB and MP2/Def2TZVP with ZPVE correction levels and their structures are similar, which indicates it is easy for them to transform to each other. The results for cluster (H$_2$O)$_{7}${NH$_4$}$^+$ verify the accuracy of SCC-DFTB approach. \begin{figure}[h!] \includegraphics[width=1.0\linewidth]{nh4-7-10w.png} \centering - \caption{The first five low-energy isomers of clusters (H$_2$O)$_{7-10}${NH$_4$}$^+$ and the associated relative energies (in kcal·mol\textsuperscript{-1}) at MP2/Def2TZVP level with (bold) and without ZPVE correction and SCC-DFTB level (italic).} + \caption{The five low-energy isomers of clusters (H$_2$O)$_{7-10}${NH$_4$}$^+$ and the associated relative energies (in kcal·mol\textsuperscript{-1}) at MP2/Def2TZVP level with (bold) and without ZPVE correction and SCC-DFTB level (italic).} \label{fig:nh4-7-10w} \end{figure} As shown in Table \ref{reBindE}, for isomers 7-a to 7-e, the relative binding energy $\Delta E_{bind.}^{whole}$ are -2.95, -2.92, -2.17, -1.28 and -3.22 kcal·mol\textsuperscript{-1} and the $\Delta E_{bind.}^{sep.}$are only -0.39, -0.38, 0.09, -1.35 and -2.27 kcal·mol\textsuperscript{-1}, respectively. It indicates the binding energies of 7-a to 7-e at SCC-DFTB agree well especially for 7-a to 7-d with those at MP2/Def2TZVP with BSSE correction level when water molecules are calculated separately. When all the water molecules are regarded as a whole part, the results of SCC-DFTB are not as good as those of the MP2 with BSSE method. -For cluster (H$_2$O)$_{8}${NH$_4$}$^+$, 8-a to 8-e are the first five low-energy isomers displayed in Figure \ref{fig:nh4-7-10w}. In 8-a to 8-d, the ion core {NH$_4$}$^+$ has a complete solvation shell. 8-a is the first low-energy isomer in our calculation at SCC-DFTB level. In Spiegelman’s study, 8-b is the first low-energy isomer at B3LYP/6-31++G(d,p) level including the harmonic ZPE contribution.\cite{Douady2008} The structures of 8-a and 8-b are very similar and the energy differences are only 0.09 and 0.18 kcal·mol\textsuperscript{-1} at SCC-DFTB and MP2/Def2TZVP with ZPVE correction levels, respectively. 8-d with seven three-coordinated H$_2$O molecules in the cube frame is the first low-energy isomer in our calculation at MP2/Def2TZVP with ZPVE correction level, which is consistent with Spiegelman’s results obtained using MC optimizations.\cite{Douady2008} In 8-e, {NH$_4$}$^+$ has an exposed N-H bond and it also has seven three-coordinated H$_2$O molecules in its cage frame. The energies of isomers 8-a to 8-e are very close calculated using SCC-DFTB and MP2 methods, so it’s possible that the energy order will change when different methods or basis sets are applied. The results certificate the SCC-DFTB is good enough to find the low-energy isomers for cluster (H$_2$O)$_{8}${NH$_4$}$^+$. +For cluster (H$_2$O)$_{8}${NH$_4$}$^+$, 8-a to 8-e are the five low-energy isomers displayed in Figure \ref{fig:nh4-7-10w}. In 8-a to 8-d, the ion core {NH$_4$}$^+$ has a complete solvation shell. 8-a is the first low-energy isomer in our calculation at SCC-DFTB level. In F. Spiegelman’s study, 8-b is the first low-energy isomer at B3LYP/6-31++G(d,p) level including the harmonic ZPE contribution.\cite{Douady2008} The structures of 8-a and 8-b are very similar and the energy differences are only 0.09 and 0.18 kcal·mol\textsuperscript{-1} at SCC-DFTB and MP2/Def2TZVP with ZPVE correction levels, respectively. 8-d with seven three-coordinated H$_2$O molecules in the cube frame is the first low-energy isomer in our calculation at MP2/Def2TZVP with ZPVE correction level, which is consistent with F. Spiegelman’s results obtained using Monte Carlo optimizations.\cite{Douady2008} In 8-e, {NH$_4$}$^+$ has an exposed N-H bond and it also has seven three-coordinated H$_2$O molecules in its cage frame. The energies of isomers 8-a to 8-e are very close calculated using SCC-DFTB and MP2 methods, so it’s possible that the energy order will change when different methods or basis sets are applied. The results certificate the SCC-DFTB is good enough to find the low-energy isomers for cluster (H$_2$O)$_{8}${NH$_4$}$^+$. As shown in Table \ref{reBindE}, for isomers 8-a to 8-e, the relative binding energy $\Delta E_{bind.}^{whole}$are -2.20, -1.61, -3.71, -2.43 and -0.55 kcal·mol\textsuperscript{-1}, respectively and the biggest $\Delta E_{bind.}^{sep.}$ is -2.01 kcal·mol\textsuperscript{-1}. It shows the binding energies at SCC-DFTB level agree well with those at MP2/Def2TZVP with BSSE correction level when water molecules are calculated separately. From these results, when all the water molecules are considered as a whole part, the results of SCC-DFTB didn’t agree well with those of the MP2 with BSSE correction method. -For cluster (H$_2$O)$_{9}${NH$_4$}$^+$, the first five low-energy structures of (H$_2$O)$_{9}${NH$_4$}$^+$ are illustrated in Figure \ref{fig:nh4-7-10w}. 9-a with seven three-coordinated H$_2$O molecules in the cage frame is the first low-energy isomer at SCC-DFTB level. 9-a is also the first low-energy structure at B3LYP/6-31++G(d,p) level including the harmonic ZPE contribution in Spiegelman’s study.\cite{Douady2008} 9-b with one N-H bond exposed in {NH$_4$}$^+$ is the second low-energy isomer whose energy is only 0.22 kcal·mol\textsuperscript{-1} higher than that of 9-a in the results of SCC-DFTB calculation. 9-b is the first low-energy isomer at MP2/Def2TZVP with ZPVE correction level in our calculation and it is also the first low-energy isomer at B3LYP/6-31++G(d,p) level in Spiegelman’s study.\cite{Douady2008} 9-c, 9-d and 9-e have a complete solvation shell. All the water molecules are connected together in the structure of 9-c. The structures of 9-a and 9-e are very similar and their energy difference is only 0.11 kcal·mol\textsuperscript{-1} at MP2/Def2TZVP with ZPVE correction level. The energy difference of isomers 9-a to 9-e is less than 0.51 kcal·mol\textsuperscript{-1} at SCC-DFTB and less than 0.86 kcal·mol\textsuperscript{-1} at MP2/Def2TZVP with ZPVE correction, so it’s easy for them to transform to each other making it possible for the variation of the energy order. The results certificate the SCC-DFTB is good enough to find the low-energy isomers for cluster (H$_2$O)$_{9}${NH$_4$}$^+$. +For cluster (H$_2$O)$_{9}${NH$_4$}$^+$, the five low-energy structures of (H$_2$O)$_{9}${NH$_4$}$^+$ are illustrated in Figure \ref{fig:nh4-7-10w}. 9-a with seven three-coordinated H$_2$O molecules in the cage frame is the first low-energy isomer at SCC-DFTB level. 9-a is also the first low-energy structure at B3LYP/6-31++G(d,p) level including the harmonic ZPE contribution in F. Spiegelman’s study.\cite{Douady2008} 9-b with one N-H bond exposed in {NH$_4$}$^+$ is the second low-energy isomer whose energy is only 0.22 kcal·mol\textsuperscript{-1} higher than that of 9-a in the results of SCC-DFTB calculation. 9-b is the first low-energy isomer at MP2/Def2TZVP with ZPVE correction level in our calculation and it is also the first low-energy isomer at B3LYP/6-31++G(d,p) level in F. Spiegelman’s study.\cite{Douady2008} 9-c, 9-d and 9-e have a complete solvation shell. All the water molecules are connected together in the structure of 9-c. The structures of 9-a and 9-e are very similar and their energy difference is only 0.11 kcal·mol\textsuperscript{-1} at MP2/Def2TZVP with ZPVE correction level. The energy difference of isomers 9-a to 9-e is less than 0.51 kcal·mol\textsuperscript{-1} at SCC-DFTB and less than 0.86 kcal·mol\textsuperscript{-1} at MP2/Def2TZVP with ZPVE correction, so it’s easy for them to transform to each other making it possible for the variation of the energy order. The results certificate the SCC-DFTB is good enough to find the low-energy isomers for cluster (H$_2$O)$_{9}${NH$_4$}$^+$. As shown in Table \ref{reBindE}, for isomers 9-a to 9-e, the relative binding energy $\Delta E_{bind.}^{whole}$ are -2.20, -1.61, -3.71, -2.43 and -0.55 kcal·mol\textsuperscript{-1} and the relative binding energy $\Delta E_{bind.}^{sep.}$ are -1.39, -0.84, -0.85, -1.78, and -0.91 kcal·mol\textsuperscript{-1}, respectively. It is obvious that the absolute values of $\Delta E_{bind.}^{whole}$ are bigger than the corresponding $\Delta E_{bind.}^{sep.}$. It shows the binding energies at SCC-DFTB level agree well with those at MP2/Def2TZVP with BSSE correction level when water molecules are calculated separately. According to the results, When all the water molecules are considered as a whole part, the results of SCC-DFTB didn’t agree well with those of the MP2 with BSSE correction method. -For cluster (H$_2$O)$_{10}${NH$_4$}$^+$, 10-a to 10-e are the first five low-energy isomers in which the ion core {NH$_4$}$^+$ has a complete solvation shell shown in Figure \ref{fig:nh4-7-10w}. 10-a with eight three-coordinated H2O molecules in its big cage structure is the first low-energy isomer calculated using the SCC-DFTB approach. 10-a is also the first low-energy structure at B3LYP/6-31++G(d,p) level including the harmonic ZPE contribution in Spiegelman’s study.\cite{Douady2008} In 10-b and 10-e, there is a four-coordinated H$_2$O molecule in their cage structures. 10-d is the first low-energy structure in our calculation results using MP2/Def2TZVP with ZPVE correction, which is also the first low-energy isomer at B3LYP/6-31++G(d,p) level in Spiegelman’s study.\cite{Douady2008} The energy of 10-b is only 0.17 kcal·mol\textsuperscript{-1} higher than that of 10-a at SCC-DFTB level, and it is only 0.31 kcal·mol\textsuperscript{-1} lower than that of 10-a at MP2/Def2TZVP with ZPVE correction level. The energy of isomers 10-a to 10-e are very close at both SCC-DFTB and MP2/Def2TZVP levels, which indicates the results with SCC-DFTB agree well with those using MP2/Def2TZVP method for cluster (H$_2$O)$_{10}${NH$_4$}$^+$. +For cluster (H$_2$O)$_{10}${NH$_4$}$^+$, 10-a to 10-e are the five low-energy isomers in which the ion core {NH$_4$}$^+$ has a complete solvation shell shown in Figure \ref{fig:nh4-7-10w}. 10-a with eight three-coordinated H2O molecules in its big cage structure is the first low-energy isomer calculated using the SCC-DFTB approach. 10-a is also the first low-energy structure at B3LYP/6-31++G(d,p) level including the harmonic ZPE contribution in F. Spiegelman’s study.\cite{Douady2008} In 10-b and 10-e, there is a four-coordinated H$_2$O molecule in their cage structures. 10-d is the first low-energy structure in our calculation results using MP2/Def2TZVP with ZPVE correction, which is also the first low-energy isomer at B3LYP/6-31++G(d,p) level in F. Spiegelman’s study.\cite{Douady2008} The energy of 10-b is only 0.17 kcal·mol\textsuperscript{-1} higher than that of 10-a at SCC-DFTB level, and it is only 0.31 kcal·mol\textsuperscript{-1} lower than that of 10-a at MP2/Def2TZVP with ZPVE correction level. The energy of isomers 10-a to 10-e are very close at both SCC-DFTB and MP2/Def2TZVP levels, which indicates the results with SCC-DFTB agree well with those using MP2/Def2TZVP method for cluster (H$_2$O)$_{10}${NH$_4$}$^+$. As shown in Table \ref{reBindE}, for isomers 10-a to 10-e, the relative binding energies $\Delta E_{bind.}^{whole}$ and $\Delta E_{bind.}^{sep.}$ are not as small as the corresponding ones of clusters (H$_2$O)$_{1-9}${NH$_4$}$^+$, which implies the error of the relative binding energy increases with the number of water molecules in the cluster. The whole results of $\Delta E_{bind.}^{whole}$ are still bigger than those of $\Delta E_{bind.}^{sep.}$ for isomers 10-a to 10-e. \subsubsection{Properties of (H$_2$O)$_{4-10}${NH$_3$} Clusters} -For cluster (H$_2$O)$_{4}${NH$_3$}, the first five low-energy structures 4$^\prime$-a to 4$^\prime$-e are displayed in Figure \ref{fig:nh3-4-7w}. 4$^\prime$-a with three N-H bonds exposed is the first low-energy isomer at SCC-DFTB level. 4$^\prime$-b with two N-H bonds exposed is the second low-energy isomer at SCC-DFTB level but it is the first low-energy isomer at MP2/Def2TZVP with ZPVE correction level. The energy differences between 4$^\prime$-a to 4$^\prime$-b are only 0.20 and 0.07 kcal·mol\textsuperscript{-1} at SCC-DFTB and MP2/Def2TZVP with ZPVE correction level, respectively. The energy difference of isomers 4$^\prime$-a to 4$^\prime$-e is less than 0.75 kcal·mol\textsuperscript{-1} at MP2/Def2TZVP with ZPVE correction, so it’s possible for the variation of the energy order when different methods or basis sets are used. 4$^\prime$-d with a nearly planar pentagonal structure with nitrogen atom and the four oxygen atoms at the apexes is the first low-energy isomer at MP2/6-31+G(d,p) studied by Novoa et al\cite{Lee1996} 4$^\prime$-d is also the first low-energy isomer in Bacelo’s study using QCISD(T) for a single-point energy calculation based on the MP2/6-311++G(d,p) results.\cite{Bacelo2002} In addition, 4$^\prime$-a to 4$^\prime$-e are also the first five low-energy isomers in Bacelo’s study even the energy order is different.\cite{Bacelo2002} The results show the SCC- DFTB is good enough to find the low-energy isomers isomers for cluster (H$_2$O)$_{4}${NH$_3$}. +For cluster (H$_2$O)$_{4}${NH$_3$}, the five low-energy structures 4$^\prime$-a to 4$^\prime$-e are displayed in Figure \ref{fig:nh3-4-7w}. 4$^\prime$-a with three N-H bonds exposed is the first low-energy isomer at SCC-DFTB level. 4$^\prime$-b with two N-H bonds exposed is the second low-energy isomer at SCC-DFTB level but it is the first low-energy isomer at MP2/Def2TZVP with ZPVE correction level. The energy differences between 4$^\prime$-a to 4$^\prime$-b are only 0.20 and 0.07 kcal·mol\textsuperscript{-1} at SCC-DFTB and MP2/Def2TZVP with ZPVE correction level, respectively. The energy difference of isomers 4$^\prime$-a to 4$^\prime$-e is less than 0.75 kcal·mol\textsuperscript{-1} at MP2/Def2TZVP with ZPVE correction, so it’s possible for the variation of the energy order when different methods or basis sets are used. 4$^\prime$-d with a nearly planar pentagonal structure with nitrogen atom and the four oxygen atoms at the apexes is the first low-energy isomer at MP2/6-31+G(d,p) studied by J. Novoa et al\cite{Lee1996} 4$^\prime$-d is also the first low-energy isomer in D. Bacelo’s study using QCISD(T) for a single-point energy calculation based on the MP2/6-311++G(d,p) results.\cite{Bacelo2002} In addition, 4$^\prime$-a to 4$^\prime$-e are also the five low-energy isomers in D. Bacelo’s study even the energy order is different.\cite{Bacelo2002} The results show the SCC- DFTB is good enough to find the low-energy isomers isomers for cluster (H$_2$O)$_{4}${NH$_3$}. \begin{figure}[h!] \includegraphics[width=1.0\linewidth]{nh3-4-7w.png} \centering - \caption{The first five low-energy isomers of cluster (H$_2$O)$_{4-7}${NH$_3$} and the associated relative energies (in kcal·mol\textsuperscript{-1}) at MP2/Def2TZVP level with (bold) and without ZPVE correction and SCC-DFTB level (italic).} + \caption{The five low-energy isomers of cluster (H$_2$O)$_{4-7}${NH$_3$} and the associated relative energies (in kcal·mol\textsuperscript{-1}) at MP2/Def2TZVP level with (bold) and without ZPVE correction and SCC-DFTB level (italic).} \label{fig:nh3-4-7w} \end{figure} The relative binding energies of isomers 4$^\prime$-a to 4$^\prime$-e are shown in Table \ref{reBindE}. Except 4$^\prime$-d, the values of $\Delta E_{bind.}^{whole}$ for 4$^\prime$-a to 4$^\prime$-e are smaller than the corresponding values of $\Delta E_{bind.}^{sep.}$. The $\Delta E_{bind.}^{sep.}$ of 4$^\prime$-d is smaller than those of other isomers. 4$^\prime$-d has a nearly planar pentagonal structure that only contains three O-H···O hydrogen bonds among the four water molecules while other isomers contain four O-H···O hydrogen bonds among the four water molecules. So the intermolecular interaction of the four water molecules in 4$^\prime$-d is not as strong as it in other isomers, this may explain the $\Delta E_{bind.}^{sep.}$ of 4$^\prime$-d is smaller than those of other isomers. In general, both relative binding energies $\Delta E_{bind.}^{sep.}$ and $\Delta E_{bind.}^{sep.}$ are not big that indicates SCC-DFTB performs well compared to the MP2 method with BSSE correction for calculating the binding energy of cluster (H$_2$O)$_{4}${NH$_3$}. -For cluster (H$_2$O)$_{5}${NH$_3$}, 5$^\prime$-a to 5$^\prime$-e are the first five low-energy isomers shown in Figure \ref{fig:nh3-4-7w}. 5$^\prime$-a with four three-coordinated water molecules is the first low-energy structure at both SCC-DFTB and MP2/Def2TZVP with ZPVE correction levels. 5$^\prime$-b and 5$^\prime$-c are the second and third isomers at SCC-DFTB level and they are the third and second isomers at MP2/Def2TZVP level with ZPVE. The energy difference between 5$^\prime$-b and 5$^\prime$-c is only 0.05 and 0.44 kcal·mol\textsuperscript{-1} at SCC-DFTB level and MP2/Def2TZVP with ZPVE correction level, respectively. In addition, the structures of 5$^\prime$-b and 5$^\prime$-c are very similar so it is possible for them to transform to each other. 5$^\prime$-d with two three-coordinated water molecules is the fourth low-energy structure at both SCC-DFTB and MP2/Def2TZVP with ZPVE correction levels. 5$^\prime$-e with four three-coordinated water molecules is the fifth low-energy structure at both SCC-DFTB and MP2/Def2TZVP with ZPVE correction levels. The frames of 5$^\prime$-a and 5$^\prime$-e are almost the same but the water molecule who offers the hydrogen or oxygen to form the O-H···O hydrogen bonds has a small difference. The energy of 5$^\prime$-e is 1.51 kcal·mol\textsuperscript{-1} higher than that of 5$^\prime$-a at MP2/Def2TZVP with ZPVE correction level, which implies the intermolecular connection mode has an influence on the stability of the isomers. The results show the SCC-DFTB approach performs well to find the low-energy isomers for cluster (H$_2$O)$_{5}${NH$_3$} compared with MP2/Def2TZVP with ZPVE correction method. +For cluster (H$_2$O)$_{5}${NH$_3$}, 5$^\prime$-a to 5$^\prime$-e are the five low-energy isomers shown in Figure \ref{fig:nh3-4-7w}. 5$^\prime$-a with four three-coordinated water molecules is the first low-energy structure at both SCC-DFTB and MP2/Def2TZVP with ZPVE correction levels. 5$^\prime$-b and 5$^\prime$-c are the second and third isomers at SCC-DFTB level and they are the third and second isomers at MP2/Def2TZVP level with ZPVE. The energy difference between 5$^\prime$-b and 5$^\prime$-c is only 0.05 and 0.44 kcal·mol\textsuperscript{-1} at SCC-DFTB level and MP2/Def2TZVP with ZPVE correction level, respectively. In addition, the structures of 5$^\prime$-b and 5$^\prime$-c are very similar so it is possible for them to transform to each other. 5$^\prime$-d with two three-coordinated water molecules is the fourth low-energy structure at both SCC-DFTB and MP2/Def2TZVP with ZPVE correction levels. 5$^\prime$-e with four three-coordinated water molecules is the fifth low-energy structure at both SCC-DFTB and MP2/Def2TZVP with ZPVE correction levels. The frames of 5$^\prime$-a and 5$^\prime$-e are almost the same but the water molecule who offers the hydrogen or oxygen to form the O-H···O hydrogen bonds has a small difference. The energy of 5$^\prime$-e is 1.51 kcal·mol\textsuperscript{-1} higher than that of 5$^\prime$-a at MP2/Def2TZVP with ZPVE correction level, which implies the intermolecular connection mode has an influence on the stability of the isomers. The results show the SCC-DFTB approach performs well to find the low-energy isomers for cluster (H$_2$O)$_{5}${NH$_3$} compared with MP2/Def2TZVP with ZPVE correction method. The relative binding energies of isomers 5$^\prime$-a to 5$^\prime$-e are shown in Table \ref{reBindE}. The values of $\Delta E_{bind.}^{whole}$ are less than 0.82 kcal·mol\textsuperscript{-1} for 5$^\prime$-a to 5$^\prime$-e. The values of $\Delta E_{bind.}^{sep.}$ are bigger than the corresponding values of $\Delta E_{bind.}^{whole}$. It indicates SCC-DFTB agrees better with MP2/Def2TZVP $\Delta E_{bind.}^{whole}$ when all the water molecules are regarded as a whole part than considering separately for calculating the binding energy of cluster (H$_2$O)$_{5}${NH$_3$}. -For cluster (H$_2$O)$_{6}${NH$_3$}, the first five low-energy structures 6$^\prime$-a to 6$^\prime$-e are displayed in Figure \ref{fig:nh3-4-7w}. 6$^\prime$-a is the first low-energy structure at SCC-DFTB level. All water molecules in 6$^\prime$-a are three-coordinated. 6$^\prime$-b is the second low-energy isomer at SCC-DFTB level and it’s only 0.05 and 0.42 kcal·mol\textsuperscript{-1} higher than the ones of 6$^\prime$-a at SCC-DFTB level and MP2/Def2TZVP with ZPVE correction level, respectively. 6$^\prime$-c to 6$^\prime$-d are the third and fourth low-energy isomers in which the six water molecules form a triangular prism structure and there are one and two four-coordinated water molecules in 6$^\prime$-c to 6$^\prime$-d, respectively. 6$^\prime$-e is the fifth low-energy structure at SCC-DFTB level but it’s the first low-energy isomer at MP2/Def2TZVP with ZPVE correction level. The energy of 6$^\prime$-a to 6$^\prime$-e are very close at both SCC-DFTB and MP2/Def2TZVP with ZPVE correction levels that it is difficult to keep the energy order when different methods or basis sets are applied. This also shown the SCC-DFTB method we used is efficient to find the low-energy isomers of cluster (H$_2$O)$_{6}${NH$_3$}. +For cluster (H$_2$O)$_{6}${NH$_3$}, the five low-energy structures 6$^\prime$-a to 6$^\prime$-e are displayed in Figure \ref{fig:nh3-4-7w}. 6$^\prime$-a is the first low-energy structure at SCC-DFTB level. All water molecules in 6$^\prime$-a are three-coordinated. 6$^\prime$-b is the second low-energy isomer at SCC-DFTB level and it’s only 0.05 and 0.42 kcal·mol\textsuperscript{-1} higher than the ones of 6$^\prime$-a at SCC-DFTB level and MP2/Def2TZVP with ZPVE correction level, respectively. 6$^\prime$-c to 6$^\prime$-d are the third and fourth low-energy isomers in which the six water molecules form a triangular prism structure and there are one and two four-coordinated water molecules in 6$^\prime$-c to 6$^\prime$-d, respectively. 6$^\prime$-e is the fifth low-energy structure at SCC-DFTB level but it’s the first low-energy isomer at MP2/Def2TZVP with ZPVE correction level. The energy of 6$^\prime$-a to 6$^\prime$-e are very close at both SCC-DFTB and MP2/Def2TZVP with ZPVE correction levels that it is difficult to keep the energy order when different methods or basis sets are applied. This also shown the SCC-DFTB method used is efficient to find the low-energy isomers of cluster (H$_2$O)$_{6}${NH$_3$}. The relative binding energies of isomers 6$^\prime$-a to 6$^\prime$-e are listed in Table \ref{reBindE}. The smallest and the biggest values of $\Delta E_{bind.}^{whole}$ are -0.05 and -1.11 kcal·mol\textsuperscript{-1}, respectively. The smallest absolute value of $\Delta E_{bind.}^{sep.}$ is 1.96 kcal·mol\textsuperscript{-1}. The binding energies calculated with SCC-DFTB agree well with those calculated at MP2/Def2TZVP level for cluster (H$_2$O)$_{6}${NH$_3$} when all the water molecules are considered as a whole part. -For cluster (H$_2$O)$_{7}${NH$_3$}, the first five low-energy isomers 7$^\prime$-a to 7$^\prime$-e are illustrated in Figure \ref{fig:nh3-4-7w}. 7$^\prime$-a with a cubic structure is the first low-lying energy structure at both SCC-DFTB and MP2/Def2TZVP with ZPVE correction levels. 7$^\prime$-b is the second low-energy structure at both SCC-DFTB and MP2/Def2TZVP with ZPVE correction levels. 7$^\prime$-b has a similar structure with 7$^\prime$-a but the NH$_3$ in it has two exposed N-H bonds. 7$^\prime$-c and 7$^\prime$-d have similar structures and they are the third and fourth low-lying energy isomers at SCC-DFTB level and their energy difference is only 0.74 kcal·mol\textsuperscript{-1}. 7$^\prime$-e with three exposed N-H bonds is the fifth low-energy isomer at both SCC-DFTB and MP2/Def2TZVP with ZPVE correction levels. The results of SCC-DFTB method agree well with those of MP2/Def2TZVP with ZPVE correction for the first five low-energy isomers of cluster (H$_2$O)$_{7}${NH$_3$}. +For cluster (H$_2$O)$_{7}${NH$_3$}, the five low-energy isomers 7$^\prime$-a to 7$^\prime$-e are illustrated in Figure \ref{fig:nh3-4-7w}. 7$^\prime$-a with a cubic structure is the first low-lying energy structure at both SCC-DFTB and MP2/Def2TZVP with ZPVE correction levels. 7$^\prime$-b is the second low-energy structure at both SCC-DFTB and MP2/Def2TZVP with ZPVE correction levels. 7$^\prime$-b has a similar structure with 7$^\prime$-a but the NH$_3$ in it has two exposed N-H bonds. 7$^\prime$-c and 7$^\prime$-d have similar structures and they are the third and fourth low-lying energy isomers at SCC-DFTB level and their energy difference is only 0.74 kcal·mol\textsuperscript{-1}. 7$^\prime$-e with three exposed N-H bonds is the fifth low-energy isomer at both SCC-DFTB and MP2/Def2TZVP with ZPVE correction levels. The results of SCC-DFTB method agree well with those of MP2/Def2TZVP with ZPVE correction for the five low-energy isomers of cluster (H$_2$O)$_{7}${NH$_3$}. The smallest and the biggest values of $\Delta E_{bind.}^{whole}$ of isomers 7$^\prime$-a to 7$^\prime$-e are -0.02 and -1.11 kcal·mol\textsuperscript{-1}, respectively and the smallest absolute value of $\Delta E_{bind.}^{sep.}$ is 2.02 kcal·mol\textsuperscript{-1} shown in Table \ref{reBindE}. The binding energies calculated with SCC-DFTB agree well with those obtained using MP2/Def2TZVP for cluster (H$_2$O)$_{7}${NH$_3$} when all the water molecules are considered as a whole part. -For cluster (H$_2$O)$_{8}${NH$_3$}, 8$^\prime$-a to 8$^\prime$-e are the first five low-energy structures shown in Figure \ref{fig:nh3-8-10w}. 8$^\prime$-a in which eight water molecules constitute a cube is the first low-lying energy structure in SCC-DFTB calculation results. 8$^\prime$-b also with a water-cube structure is the second low-energy structure at SCC-DFTB level and it is the first low-energy isomer at MP2/Def2TZVP with ZPVE correction level. The energy differences between 8$^\prime$-a and 8$^\prime$-b are only 0.93 an 0.30 kcal·mol\textsuperscript{-1} at SCC-DFTB and MP2/Def2TZVP with ZPVE correction levels. From Figure \ref{fig:nh3-8-10w}, the fifth low-energy isomer 8$^\prime$-e includes less number of hydrogen bonds than other isomers and its energy has a clearly increase compared to other isomers. The results show the SCC-DFTB method performs well to obtain the low-energy isomers of cluster (H$_2$O)$_{8}${NH$_3$}. +For cluster (H$_2$O)$_{8}${NH$_3$}, 8$^\prime$-a to 8$^\prime$-e are the five low-energy structures shown in Figure \ref{fig:nh3-8-10w}. 8$^\prime$-a in which eight water molecules constitute a cube is the first low-lying energy structure in SCC-DFTB calculation results. 8$^\prime$-b also with a water-cube structure is the second low-energy structure at SCC-DFTB level and it is the first low-energy isomer at MP2/Def2TZVP with ZPVE correction level. The energy differences between 8$^\prime$-a and 8$^\prime$-b are only 0.93 an 0.30 kcal·mol\textsuperscript{-1} at SCC-DFTB and MP2/Def2TZVP with ZPVE correction levels. From Figure \ref{fig:nh3-8-10w}, the fifth low-energy isomer 8$^\prime$-e includes less number of hydrogen bonds than other isomers and its energy has a clearly increase compared to other isomers. The results show the SCC-DFTB method performs well to obtain the low-energy isomers of cluster (H$_2$O)$_{8}${NH$_3$}. \begin{figure}[h!] \includegraphics[width=1.0\linewidth]{nh3-8-10w.png} \centering - \caption{The first five low-energy isomers of clusters (H$_2$O)$_{8-10}${NH$_3$} and the associated relative energies (in kcal·mol\textsuperscript{-1}) at MP2/Def2TZVP level with (bold) and without ZPVE correction and SCC-DFTB level (italic).} + \caption{The five low-energy isomers of clusters (H$_2$O)$_{8-10}${NH$_3$} and the associated relative energies (in kcal·mol\textsuperscript{-1}) at MP2/Def2TZVP level with (bold) and without ZPVE correction and SCC-DFTB level (italic).} \label{fig:nh3-8-10w} \end{figure} The smallest and the biggest values of $\Delta E_{bind.}^{whole}$ of isomers 8$^\prime$-a to 8$^\prime$-e are -0.1 and -1.28 kcal·mol\textsuperscript{-1}, respectively while the smallest absolute value of $\Delta E_{bind.}^{sep.}$ is 3.04 kcal·mol\textsuperscript{-1} shown in Table \ref{reBindE}. The binding energies calculated with SCC-DFTB agree better with those obtained at MP2/Def2TZVP level when all the water molecules are considered as a whole part in cluster (H$_2$O)$_{8}${NH$_3$} than the ones when water molecules calculated separately. -For cluster (H$_2$O)$_{9}${NH$_3$}, 9$^\prime$-a to 9$^\prime$-e are the first five low-lying energy structures displayed in Figure \ref{fig:nh3-8-10w}. 9$^\prime$-a with a “chair” structure is the first low-energy structure at SCC-DFTB level. 9$^\prime$-b, 9$^\prime$-c and 9$^\prime$-d in which the nine water molecules have the similar configuration are the second, third and fourth isomers. In 9$^\prime$-b and 9$^\prime$-c, the NH$_3$ has three exposed N-H bonds and the energies of 9$^\prime$-b and 9-c are very close at both SCC-DFTB and MP2/Def2TZVP with ZPVE correction levels. The NH$_3$ has two exposed N-H bonds in 9$^\prime$-d. 9$^\prime$-e is the fifth low-energy isomer in the SCC-DFTB calculation results but it is the first low-energy isomer in the calculation results of MP2/Def2TZVP with ZPVE correction. 9$^\prime$-e has a pentagonal prism structure and all the water molecules in it are three-coordinated. The relative energy for each isomer between SCC-DFTB level and MP2/Def2TZVP with ZPVE correction level is less than 1.23 kcal·mol\textsuperscript{-1}. This shows our SCC-DFTB calculation results are consistent with the calculation results of MP2/Def2TZVP with ZPVE correction for low-energy isomers optimization of cluster (H$_2$O)$_{9}${NH$_3$}. +For cluster (H$_2$O)$_{9}${NH$_3$}, 9$^\prime$-a to 9$^\prime$-e are the five low-lying energy structures displayed in Figure \ref{fig:nh3-8-10w}. 9$^\prime$-a with a “chair” structure is the first low-energy structure at SCC-DFTB level. 9$^\prime$-b, 9$^\prime$-c and 9$^\prime$-d in which the nine water molecules have the similar configuration are the second, third and fourth isomers. In 9$^\prime$-b and 9$^\prime$-c, the NH$_3$ has three exposed N-H bonds and the energies of 9$^\prime$-b and 9-c are very close at both SCC-DFTB and MP2/Def2TZVP with ZPVE correction levels. The NH$_3$ has two exposed N-H bonds in 9$^\prime$-d. 9$^\prime$-e is the fifth low-energy isomer in the SCC-DFTB calculation results but it is the first low-energy isomer in the calculation results of MP2/Def2TZVP with ZPVE correction. 9$^\prime$-e has a pentagonal prism structure and all the water molecules in it are three-coordinated. The relative energy for each isomer between SCC-DFTB level and MP2/Def2TZVP with ZPVE correction level is less than 1.23 kcal·mol\textsuperscript{-1}. This shows our SCC-DFTB calculation results are consistent with the calculation results of MP2/Def2TZVP with ZPVE correction for low-energy isomers optimization of cluster (H$_2$O)$_{9}${NH$_3$}. The relative binding energies of isomers 9$^\prime$-a to 9$^\prime$-e are shown in Table \ref{reBindE}. The absolute values of $\Delta E_{bind.}^{whole}$ are less than 1.09 kcal·mol\textsuperscript{-1} while the smallest absolute value of $\Delta E_{bind.}^{sep.}$ is 2.57 kcal·mol\textsuperscript{-1}. The binding energies calculated with SCC-DFTB agree well with those acquired at MP2/Def2TZVP level when all the water molecules are considered as a whole part for cluster (H$_2$O)$_{9}${NH$_3$}. -For cluster (H$_2$O)$_{10}${NH$_3$}, 10$^\prime$-a to 10$^\prime$-e are the first five low-energy structures illustrated in Figure \ref{fig:nh3-8-10w}. The energy order for the first five low-energy structures is the same at SCC-DFTB and MP2/Def2TZVP with ZPVE correction levels. 10$^\prime$-a and 10$^\prime$-b are the first and second low-energy isomer in which the ten water molecules constitute the pentagonal prism. The energy differences of 10$^\prime$-a and 10$^\prime$-b are only 0.27 and 0.58 kcal·mol\textsuperscript{-1} at SCC-DFTB and MP2/Def2TZVP with ZPVE correction levels. 10$^\prime$-c and 10$^\prime$-d are the third and fourth low-energy isomers in which eight water molecules constitute a cube and the energy differences between 10$^\prime$-c and 10$^\prime$-d are very small calculated with SCC-DFTB or MP2/Def2TZVP with ZPVE correction. 10$^\prime$-e is the fifth low-energy structure in which eight water molecules also constitute a cube but its energy is obviously higher than those of 10$^\prime$-c and 10$^\prime$-d. The calculation results of SCC-DFTB are consistent with those of MP2/Def2TZ for the optimization of the low-energy isomers of cluster (H$_2$O)$_{10}${NH$_3$}. According to the structures of the first five low-energy isomers of clusters (H$_2$O)$_{1-10}${NH$_3$}, in most cases, the NH$_3$ usually contains two or three exposed N-H bonds. +For cluster (H$_2$O)$_{10}${NH$_3$}, 10$^\prime$-a to 10$^\prime$-e are the five low-energy structures illustrated in Figure \ref{fig:nh3-8-10w}. The energy order for the five low-energy structures is the same at SCC-DFTB and MP2/Def2TZVP with ZPVE correction levels. 10$^\prime$-a and 10$^\prime$-b are the first and second low-energy isomer in which the ten water molecules constitute the pentagonal prism. The energy differences of 10$^\prime$-a and 10$^\prime$-b are only 0.27 and 0.58 kcal·mol\textsuperscript{-1} at SCC-DFTB and MP2/Def2TZVP with ZPVE correction levels. 10$^\prime$-c and 10$^\prime$-d are the third and fourth low-energy isomers in which eight water molecules constitute a cube and the energy differences between 10$^\prime$-c and 10$^\prime$-d are very small calculated with SCC-DFTB or MP2/Def2TZVP with ZPVE correction. 10$^\prime$-e is the fifth low-energy structure in which eight water molecules also constitute a cube but its energy is obviously higher than those of 10$^\prime$-c and 10$^\prime$-d. The calculation results of SCC-DFTB are consistent with those of MP2/Def2TZ for the optimization of the low-energy isomers of cluster (H$_2$O)$_{10}${NH$_3$}. According to the structures of the five low-energy isomers of clusters (H$_2$O)$_{1-10}${NH$_3$}, in most cases, the NH$_3$ usually contains two or three exposed N-H bonds. The smallest and biggest values of $\Delta E_{bind.}^{whole}$ of isomers 10$^\prime$-a to 10$^\prime$-e are -0.03 and -1.10 kcal·mol\textsuperscript{-1} while the smallest absolute value of $\Delta E_{bind.}^{sep.}$ is 4.80 kcal·mol\textsuperscript{-1} shown in Table \ref{reBindE}. The values of $\Delta E_{bind.}^{whole}$ implies that SCC-DFTB agree very well with MP2/Def2TZVP for cluster (H$_2$O)$_{10}$NH$_3$ when all the water molecules are regarded as a whole part. \subsubsection{Properties of (H$_2$O)$_{20}${NH$_4$}$^+$ Cluster} For cluster (H$_2$O)$_{20}${NH$_4$}$^+$, the lowest-energy structure shown in Figure \ref{fig:nh3-nh4-20w} (a) was obtained with the combination of SCC-DFTB and PTMD which is consistent with that of previous study.\cite{Kazimirski2003, Douady2009, Bandow2006} -Microcanonical and canonical caloric curves were obtained using exchange Monte Carlo simulations by Spiegelman’s group.\cite{Douady2009} -We also calculated the canonical heat capacities of cluster (H$_2$O)$_{20}${NH$_4$}$^+$ using the combination of SCC-DFTB and PTMD depicted in Figure. +Microcanonical and canonical caloric curves were obtained using exchange Monte Carlo simulations by F. Spiegelman’s group.\cite{Douady2009} +I also calculated the canonical heat capacities of cluster (H$_2$O)$_{20}${NH$_4$}$^+$ using the combination of SCC-DFTB and PTMD depicted in Figure. \begin{figure}[h!] \includegraphics[width=0.6\linewidth]{nh3-nh4-20w.jpeg} \centering - \caption{The first five low-energy isomers of cluster (H$_2$O)$_{20}${NH$_4$}$^{+}$ (a) and (H$_2$O)$_{20}${NH$_3$} (b) at SCC-DFTB level.} + \caption{The five low-energy isomers of cluster (H$_2$O)$_{20}${NH$_4$}$^{+}$ (a) and (H$_2$O)$_{20}${NH$_3$} (b) at SCC-DFTB level.} \label{fig:nh3-nh4-20w} \end{figure} @@ -511,7 +502,7 @@ We also calculated the canonical heat capacities of cluster (H$_2$O)$_{20}${NH$_ The low-energy isomers reported for (H$_2$O)$_{1-10, 20}${NH$_4$}$^+$ and (H$_2$O)$_{1-10, 20}$NH$_3$ clusters are obtained with a combination of SCC-DFTB (0.12/1.16) and PTMD. Binding energies as a function of the N---O distance in (H$_2$O){NH$_4$}$^+$ and (H$_2$O)NH$_3$ demonstrate -that the improve parameters we propose are in much better agreement with reference calculations than the original SCC-DFTB parameters. +that the improve parameters I proposed are in much better agreement with reference calculations than the original SCC-DFTB parameters. The low-energy isomers of clusters (H$_2$O)$_{1-10}${NH$_4$}$^+$ and (H$_2$O)$_{1-10}$NH$_3$ at the SCC-DFTB (0.12/1.16) level agree well with those at MP2/Def2TZVP level and the corresponding results in the literature. The SCC-DFTB binding energies also agree well with those calculated with MP2/Def2TZVP method with BSSE correction. This demonstrate that SCC-DFTB (0.12/1.16) approach is good @@ -536,9 +527,9 @@ The gas phase study needs to be extended towards more realistic biomolecular sys The nucleobases in DNA and RNA play a significant role in the encoding and expression of genetic information in living systems while water is a natural medium of many reactions in living organisms. The study of the interaction between nucleobase molecules and aqueous environment has attracted a lot of interests among biologists and chemists. Exploring the clusters composed of nucleobase molecules with water is a good workbench to observe how the properties of nucleobase molecules change when going from isolated gas-phase to hydrated species. The radiation can cause damages on RNA and DNA molecules, which is proficiently applied in radiotherapy for cancer treatment. The major drawback in radiotherapy is the unselective damage in both healthy and tumor cells, which has a big side effect. This makes it particularly important to explore the radiation fragments. -Uracil (U), C$_4$H$_4$N$_2$O$_2$, is one of the four nucleobases of RNA, has been paid attention concerning radiation damage. Protonated uracil UH$^+$ can be generated by radiation damages.\cite{Wincel2009} -The reasons for such degradation can be due to the interaction with slow electrons, as shown by the work of Boudaiffa \textit{et al.} \cite{Boudaiffa2000} -Several studies have been devoted to the effect of hydration on the electron affinity of DNA nucleobases. \cite{Smyth2011, Siefermann2011, Alizadeh2013} For instance, Rasmussen \textit{et al.} found that a water molecule is more likely to interact with a charged species than with a neutral one though the study of hydration effects on the lowest triplet states of cytosine, uracil, and thymine by including one or two water molecules explicitly, \cite{Rasmussen2010} +Uracil , C$_4$H$_4$N$_2$O$_2$, is one of the four nucleobases of RNA, has been paid attention concerning radiation damage. Protonated uracil UH$^+$ can be generated by radiation damages.\cite{Wincel2009} +The reasons for such degradation can be due to the interaction with slow electrons, as shown by the work of B. Boudaiffa \textit{et al.} \cite{Boudaiffa2000} +Several studies have been devoted to the effect of hydration on the electron affinity of DNA nucleobases. \cite{Smyth2011, Siefermann2011, Alizadeh2013} For instance, A. Rasmussen \textit{et al.} found that a water molecule is more likely to interact with a charged species than with a neutral one though the study of hydration effects on the lowest triplet states of cytosine, uracil, and thymine by including one or two water molecules explicitly, \cite{Rasmussen2010} However, a lot of work is still needed to be performed to understand the role of aqueous environment on charged nucleobases of DNA and RNA. Collision experiments is a useful tool that can be applied to understand the reactivity of molecules and provide access to structural information.\cite{Coates2018} @@ -547,47 +538,46 @@ however, there are only few studies available concerning the effect of hydration hydrated protonated uracil shows that the most stable tautomeric form of the neutral uracil (diketo) differs from the most stable one for bare protonated uracil (keto-enol).\cite{Bakker2008} %Some theoretical studies reported the structures taken by neutral microhydrated uracil, containing up to 15 water molecules.\cite{Shishkin2000, Gadre2000, Gaigeot2001, Danilov2006, Bacchus2015} -However, fragmentation studies of such species under CID conditions have not been performed. \textbf{S. Zamith and J.-M. l'Hermite conducted such CID +However, fragmentation studies of such species under CID conditions have not been performed. \textbf{S. Zamith and J.-M. L'Hermite conducted such CID experiments on protonated uracil water species (H$_2$O)$_{1-15}$UH$^+$ during my thesis and I collaborated with them in order to provide a theoretical support to their measurements}. -%The dissociation of mass selected (H$_2$O)$_{1-15}$UH$^+$ clusters is induced by collisions with target rare gas atoms (Ne, Ar) or water molecules (H$_2$O, D$_2$O) at a controlled center of mass collision energy 7.2 eV which is chosen high enough so that a large number of fragmentation channels are explored. After the collisions, the remaining charged species, which have lost one or several neutral subunits, are detected. We find essentially the same results whatever the nature of target atoms of molecules is. The resulting inter-molecular dissociation patterns of the (H$_2$O)$_{1-15}$UH$^+$ clusters show that below n = 5 only water molecules are evaporated whereas, for n $\geq$ 5, a new fragmentation channel appears that corresponds to the loss of neutral uracil. +%The dissociation of mass selected (H$_2$O)$_{1-15}$UH$^+$ clusters is induced by collisions with target rare gas atoms (Ne, Ar) or water molecules (H$_2$O, D$_2$O) at a controlled center of mass collision energy 7.2 eV which is chosen high enough so that a large number of fragmentation channels are explored. After the collisions, the remaining charged species, which have lost one or several neutral subunits, are detected. We find essentially the same results whatever the nature of target atoms of molecules is. The resulting inter-molecular dissociation patterns of the (H$_2$O)$_{1-15}$UH$^+$ clusters show that below $n$ = 5 only water molecules are evaporated whereas, for n $\geq$ 5, a new fragmentation channel appears that corresponds to the loss of neutral uracil. Theoretical studies have already been devoted to mixed uracil-water clusters and intended to describe the lowest energy structures. However, only neutral species ((H$_2$O)$_{n}$U) were considered.\cite{Shishkin2000, Gadre2000, Van2001diffu, Gaigeot2001, Danilov2006, Bacchus2015} Those studies showed that for sizes up to with $n$ = 3, the water molecules arrange in monomers or dimers in the plane of the uracil molecule \cite{Gadre2000, Van2001diffu, Gaigeot2001, Danilov2006, Bacchus2015} with no trimer formation. But for $n$ \textgreater~3, very different structures -were predicted depending on the considered study. For instance, Ghomi predicted that for $n$ = 7,\cite{Gaigeot2001} water molecules arrang - in dimers and trimers in the plane of the uracil molecule, whereas for n = 11, water molecules form locked chains.\cite{Shishkin2000} 3D configurations were also proposed. For instance, all water molecules lie above the uracil plane for $n$ = 4, 5 reported by Calvo \textit{et al.}.\cite{Bacchus2015} Similarly, for $n$ = 11, Danilov \textit{et al.} also obtained a - structure that consists of a water cluster above the uracil molecule.\cite{Danilov2006} Such structures are predicted to start with 4 water molecules - reported by Calvo and collaborator \cite{Bacchus2015} or with 6 water molecules (though 5 have not been calculated) reported by Gadre \textit{et al.}.\cite{Gadre2000} +were predicted depending on the considered study. For instance, M. Ghomi predicted that for $n$ = 7,\cite{Gaigeot2001} water molecules arrange + in dimers and trimers in the plane of the uracil molecule, whereas for $n$ = 11, water molecules form locked chains.\cite{Shishkin2000} 3D configurations were also proposed. For instance, all water molecules lie above the uracil plane for $n$ = 4, 5 reported by F. Calvo \textit{et al.}.\cite{Bacchus2015} Similarly, for $n$ = 11, V. Danilov \textit{et al.} also obtained a structure that consists of a water cluster above the uracil molecule.\cite{Danilov2006} Such structures are predicted to start with 4 water molecules + reported by F. Calvo and collaborator \cite{Bacchus2015} or with 6 water molecules (though 5 have not been calculated) reported by S. Gadre \textit{et al.}.\cite{Gadre2000} Those studies may suggest that for few water molecules (up to two), the proton should be located on the uracil molecule, whereas when a large number of water molecules surround the uracil, the charge is expected to be located on the water molecules. Of course, the excess proton is expected to strongly influence the structure of the lowest energy isomers of each species, as observed for pure water clusters, so the size at which the proton is transferred from uracil to water cannot be deduced from the aforementioned studies. Moreover, all those theoretical studies do not lead to the same low-energy - structures as highlighted by Danilov and Calvo.\cite{Danilov2006, Bacchus2015} Consequently, although it is instructive from a qualitative point - of view, the analysis of the experimental data by S. Zamith and J.-M. l'Hermite cannot be based on those studies. We have therefore undertaken a + structures as highlighted by V. Danilov and F. Calvo.\cite{Danilov2006, Bacchus2015} Consequently, although it is instructive from a qualitative point + of view, the analysis of the experimental data by S. Zamith and J.-M. L'Hermite cannot be based on those studies. I have therefore undertaken a theoretical simulation of hydrated protonated uracil clusters (H$_2$O)$_{1-7, 11, 12}$UH$^+$ to determine their lowest-energy structures to - complete the experiments by S. Zamith and J.-M. l'Hermite at the \textit{Laboratoire Collisions Agr\'egats R\'eactivit\'e }(LCAR). This work has + complete the experiments by S. Zamith and J.-M. L'Hermite at the \textit{Laboratoire Collisions Agr\'egats R\'eactivit\'e }(LCAR). This work has been published in 2019 in the \textit{The Journal of Chemical Physics}.\cite{Braud2019} \subsection{Results and Discussion} -In the following section, section~\ref{exp_ur}, I present in details the results obtained from the CID experiments of S. Zamith and J.-M. l'Hermite +In the following section, section~\ref{exp_ur}, I present in details the results obtained from the CID experiments of S. Zamith and J.-M. L'Hermite and the main concepts used to interpret the data. The following section, section~\ref{calcul_ur}, is devoted to the theoretical determination of the low-energy isomers of the (H$_2$O)$_{1-7,11,12}$UH$^+$ clusters. A more detailed presentation of CID experiments is also provided in section~\ref{exp_cid} of chapter~4, where these details are important to explicitly model CID experiments. \subsubsection{Experimental Results} \label{exp_ur} -\textbf{Time of flight of mass spectrum(TOFMS).} +\textbf{Time-of-flight of mass spectrum.} A typical fragmentation mass spectrum obtained by colliding (H$_2$O)$_{7}$UH$^+$ with neon at a center of mass collision energy of 7.2 eV is shown in Figure \ref{mass7w}. The more intense peak on the right comes from the parent cluster (H$_2$O)$_{7}$UH$^+$, the next 7 peaks at the left of the parent peak correspond to the loss of 1-7 water molecules of parent cluster, and the next 5 peaks to the left results from the evaporation of the uracil molecule and several water molecules from parent cluster. This mass spectrum is obtained at the highest pressure explored in the present experiments. This is still true for the largest size investigated here, namely, (H$_2$O)$_{15}$UH$^+$. From the result of the fragmentation mass spectrum displayed in Figure \ref{mass7w}, it indicates multiple collisions are possible, which allows the evaporation of all water molecules. Moreover, the intensity of evaporation of water molecules is bigger than the one of evaporation of U. -In our study, we are interested in two specific channels. Channel 1 corresponds to the loss of only neutral water molecules, whereas channel 2 corresponds to the loss of neutral uracil and one or several water molecules, +In the study, mainly focus on two specific channels. Channel 1 corresponds to the loss of only neutral water molecules, whereas channel 2 corresponds to the loss of neutral uracil and one or several water molecules, \begin{align} \mathrm{Channel~1, ~(H_2O)_nUH^+} & \rightarrow ~ \mathrm{(H_2O)_{n-x}UH^+ + xH_2O } \\ \mathrm{Channel~2, ~(H_2O)_nUH^+} & \rightarrow ~ \mathrm{ (H_2O)_{n-x}H^+ + xH_2O + U} \end{align} -\figuremacro{mass7w}{Time of flight of mass spectrum obtained by colliding (H$_2$O)$_{7}$UH$^+$ with Ne +\figuremacro{mass7w}{Time-of-flight of mass spectrum obtained by colliding (H$_2$O)$_{7}$UH$^+$ with Ne at 7.2 eV center of mass collision energy (93.5 eV in the laboratory frame).} \textbf{Fragmentation cross section.} @@ -603,33 +593,32 @@ The main differences between the curves in Figure \ref{fragcrosssec} can be rat fragmentation cross sections increase with the size and seem to tend toward the geometrical one. The cross sections measured for clusters containing uracil colliding with water molecules (black squares) are of the same magnitude as the ones previously obtained for deuterated pure water clusters (green full circles) at a similar collision energy.\cite{Zamith2012} For clusters containing uracil, fragmentation cross sections are systematically larger than the one for pure water clusters by an amount of the same magnitude as the one predicted by the geometrical cross sections. For instance, the difference between red squares and blue stars, and the difference between red full line and blue dashed line has the same magnitude. -The fragmentation cross sections obtained by Dalleska -and coworkers \cite{Dalleska1993} for protonated water clusters are within our error bars for n = 5, 6 and about a factor of 2 lower for n = 3, 4. However their cross section is notably lower for (H$_2$O)$_2$H$^+$ as compared to our measurement for (H$_2$O)UH$^+$. This difference may be explained by the fact that UH$^+$ forms a weaker bond with water than H$_2$OH$^+$ does. Indeed the dissociation energy D[H$_2$OH$^+$–H$_2$O] is 1.35 eV \cite{Dalleska1993, Hansen2009} whereas the value for D[UH$^+$–H$_2$O] is estimated between 0.54 \cite{Wincel2009} and 0.73 eV. \cite{Bakker2008} The same behavior is observed for n = 3, and the dissociation energy D[(H$_2$O)$_2$H$^+$–H$_2$O] = 0.86 eV \cite{Dalleska1993, Hansen2009} is greater than the dissociation energy D[U(H$_2$O)H$^+$–H$_2$O] = 0.49 eV.\cite{Wincel2009} Hence the dissociation of water molecules is more favored in the protonated uracil cluster than in the pure water clusters. +The fragmentation cross sections obtained by N. Dalleska and coworkers \cite{Dalleska1993} for protonated water clusters are within our error bars for $n$ = 5, 6 and about a factor of 2 lower for $n$ = 3, 4. However their cross section is notably lower for (H$_2$O)$_2$H$^+$ as compared to our measurement for (H$_2$O)UH$^+$. This difference may be explained by the fact that UH$^+$ forms a weaker bond with water than H$_2$OH$^+$ does. Indeed the dissociation energy D[H$_2$OH$^+$–H$_2$O] is 1.35 eV \cite{Dalleska1993, Hansen2009} whereas the value for D[UH$^+$–H$_2$O] is estimated between 0.54 \cite{Wincel2009} and 0.73 eV. \cite{Bakker2008} The same behavior is observed for $n$ = 3, and the dissociation energy D[(H$_2$O)$_2$H$^+$–H$_2$O] = 0.86 eV \cite{Dalleska1993, Hansen2009} is greater than the dissociation energy D[U(H$_2$O)H$^+$–H$_2$O] = 0.49 eV.\cite{Wincel2009} Hence the dissociation of water molecules is more favored in the protonated uracil cluster than in the pure water clusters. -\figuremacro{fragcrosssec}{Fragmentation cross sections of clusters (H$_2$O)$_{n-1}$UH$^+$ at a collision energy of 7.2 eV plotted as a function of the total number n of molecules in the clusters. The experimental results and geometrical cross sections are shown for collision with H$_2$O and Ne. The results from Dalleska et al.\cite{Dalleska1993} using Xe as target atoms on pure protonated water clusters (H$_2$O)$_{2-6}$H$^+$ and from Zamith \textit{et al.} \cite{Zamith2012} using water as target molecules on deuterated water clusters (D$_2$O)$_{5,10}$H$^+$ are also shown. The geometrical collision cross sections of water clusters in collision with Xe atoms and water molecules are also plotted. Error bars represent one standard deviation.} +\figuremacro{fragcrosssec}{Fragmentation cross sections of clusters (H$_2$O)$_{n-1}$UH$^+$ at a collision energy of 7.2 eV plotted as a function of the total number n of molecules in the clusters. The experimental results and geometrical cross sections are shown for collision with H$_2$O and Ne. The results from N. Dalleska et al.\cite{Dalleska1993} using Xe as target atoms on pure protonated water clusters (H$_2$O)$_{2-6}$H$^+$ and from S. Zamith \textit{et al.} \cite{Zamith2012} using water as target molecules on deuterated water clusters (D$_2$O)$_{5,10}$H$^+$ are also shown. The geometrical collision cross sections of water clusters in collision with Xe atoms and water molecules are also plotted. Error bars represent one standard deviation.} \textbf{Intermolecular fragmentation.} -Figure \ref{Uloss} displays the percentage of the fragments that have lost a neutral uracil molecule over all the fragments, plotted as a function of the number of water molecules in the parent cluster (H$_2$O)$_{n}$UH$^+$. It shows that for the cluster (H$_2$O)$_{n}$UH$^+$ with a small number of water molecules, almost no neutral uracil is evaporated. From n = 5 and more clearly from n = 6, the loss of neutral uracil molecule increases up to about 20\% for (H$_2$O)$_{9}$UH$^+$. +Figure \ref{Uloss} displays the percentage of the fragments that have lost a neutral uracil molecule over all the fragments, plotted as a function of the number of water molecules in the parent cluster (H$_2$O)$_{n}$UH$^+$. It shows that for the cluster (H$_2$O)$_{n}$UH$^+$ with a small number of water molecules, almost no neutral uracil is evaporated. From $n$ = 5 and more clearly from $n$ = 6, the loss of neutral uracil molecule increases up to about 20\% for (H$_2$O)$_{9}$UH$^+$. \figuremacro{Uloss}{Proportion of neutral uracil molecule loss plotted as a function of the number of water molecules n in the parent cluster (H$_2$O)$_{n}$UH$^+$. Results obtained for collisions with Ne atoms at 7.2 eV center of mass collision energy.} -The fragmentation can arise from two distinct mechanisms (direct and statistical fragmentation processes) depending on the life time of the collision complex. On the one hand, if the fragmentation occurs in a very short time after collision, the dissociation is impulsive (direct). In this case, we thus assume that the nature of the collision products is partly determined by the nature of the lowest-energy isomers of parent clusters and especially by the location of the excess proton in the structure. In other words, the lowest-energy isomer of the parent cluster obviously plays a major role in determining the fragmentation channels. On the other hand, in the case of long-lived collision complexes, collision energy is transferred to the parent cluster and is redistributed among all degrees of freedom. This is a slow process, and the structures involved during the fragmentation are no longer the lowest-energy isomer, \textit{i.e.}, the structure of the cluster can undergo structural reorganizations before evaporation. Furthermore, the excess proton can also diffuse in the structure and for instance, recombine with the uracil. Then the role of the initial structure of the parent clusters is strongly reduced in determining the fragmentation channels. +The fragmentation can arise from two distinct mechanisms (direct and statistical fragmentation processes) depending on the life time of the collision complex. On the one hand, if the fragmentation occurs in a very short time after collision, the dissociation is impulsive (direct). In this case, I thus assume that the nature of the collision products is partly determined by the nature of the lowest-energy isomers of parent clusters and especially by the location of the excess proton in the structure. In other words, the lowest-energy isomer of the parent cluster obviously plays a major role in determining the fragmentation channels. On the other hand, in the case of long-lived collision complexes, collision energy is transferred to the parent cluster and is redistributed among all degrees of freedom. This is a slow process, and the structures involved during the fragmentation are no longer the lowest-energy isomer, \textit{i.e.}, the structure of the cluster can undergo structural reorganizations before evaporation. Furthermore, the excess proton can also diffuse in the structure and for instance, recombine with the uracil. Then the role of the initial structure of the parent clusters is strongly reduced in determining the fragmentation channels. -In Figure \ref{Uloss}, we focus on the loss of the neutral uracil molecule in the detected fragments since it indicates where the proton lies after collision, namely, on the uracil or on a water cluster. A transition in the nature of fragmentation product is clearly seen from n = 5-6. To account for this transition, we consider that evaporation originates from a direct fragmentation process. A short discussion about the implications of possible structural rearrangement prior to dissociation, which occurs in a statistical process, will be provided in section~\ref{calcul_ur}. +In Figure \ref{Uloss}, I focus on the loss of the neutral uracil molecule in the detected fragments since it indicates where the proton lies after collision, namely, on the uracil or on a water cluster. A transition in the nature of fragmentation product is clearly seen from $n$ = 5-6. To account for this transition, the evaporation originates from a direct fragmentation process is considered. A short discussion about the implications of possible structural rearrangement prior to dissociation, which occurs in a statistical process, will be provided in section~\ref{calcul_ur}. The relative proton affinities of each component of the -mixed clusters gives a first estimate of which molecule, uracil or water, is more likely to carry the positive charge prior to collisions. Experimentally, the gas phase proton affinity of uracil is bracketed to 9 $\pm$ 0.12 eV.\cite{Kurinovich2002} For the proton affinity of water molecule, an experimental value is reported at 7.31 eV \cite{Magnera1991} and a theoretical one at 7.5 eV.\cite{Cheng1998} In the work of Cheng, it shows that the proton affinity of water clusters increases with their size.\cite{Cheng1998} The proton affinities extracted from the different studies for the uracil molecule and for water clusters as a function of the number of water molecules are displayed in Figure~\ref{protonAffinity}. +mixed clusters gives a first estimate of which molecule, uracil or water, is more likely to carry the positive charge prior to collisions. Experimentally, the gas phase proton affinity of uracil is bracketed to 9 $\pm$ 0.12 eV.\cite{Kurinovich2002} For the proton affinity of water molecule, an experimental value is reported at 7.31 eV \cite{Magnera1991} and a theoretical one at 7.5 eV.\cite{Cheng1998} In the work of H. Cheng, it shows that the proton affinity of water clusters increases with their size.\cite{Cheng1998} The proton affinities extracted from the different studies for the uracil molecule and for water clusters as a function of the number of water molecules are displayed in Figure~\ref{protonAffinity}. \figuremacro{protonAffinity}{The proton affinities of water clusters as a function of the number of water -molecules n, which are taken from the work of Magnera (black circles) \cite{Magnera1991} and from the work of Cheng (blue squares).\cite{Cheng1998} The value of the proton affinity of uracil (red dotted dashed line) is also plotted.\cite{Kurinovich2002}} +molecules n, which are taken from the work of T. Magnera (black circles) \cite{Magnera1991} and from the work of Cheng (blue squares).\cite{Cheng1998} The value of the proton affinity of uracil (red dotted dashed line) is also plotted.\cite{Kurinovich2002}} -It clearly shows that the proton affinity of uracil, PA[U], is larger than the one of water monomer PA[H$_2$O]. Thus, for the mono-hydrated uracil, from the energetic point of view, the proton is on the uracil molecule and the only observed fragments are indeed protonated uracil molecules. Moreover, an experimental work \cite{Bakker2008} confirms that there is no proton transfer from the uracil to the water molecule in mono-hydrated clusters. Proton affinity of the uracil molecule is also larger than that of the water dimer, or even the trimer: PA[U] $>$ PA[(H$_2O$)$_n$], n = 2 or 3 depending on the considered data for water. This is still consistent with our experimental observation of no neutral uracil molecule loss for n = 2 and 3. However from the PA values, one would predict that the appearance of neutral uracil should occur for n $\approx$ 3-4. For instance, for n = 4, assuming a statistical fragmentation for which the energies of final products are expected to be of relevance, the channel U + (H$_2$O)$_4$H$^+$ is energetically favorable. If one now assumes a direct dissociation, where the parent protonation state remains unchanged, one also expects that neutral uracil evaporates. However, experimentally, for n = 4, no neutral uracil evaporation is observed. The loss of neutral uracil starts at n = 5 and becomes significant only at n = 6. +It clearly shows that the proton affinity of uracil, PA[U], is larger than the one of water monomer PA[H$_2$O]. Thus, for the mono-hydrated uracil, from the energetic point of view, the proton is on the uracil molecule and the only observed fragments are indeed protonated uracil molecules. Moreover, an experimental work \cite{Bakker2008} confirms that there is no proton transfer from the uracil to the water molecule in mono-hydrated clusters. Proton affinity of the uracil molecule is also larger than that of the water dimer, or even the trimer: PA[U] $>$ PA[(H$_2O$)$_n$], $n$ = 2 or 3 depending on the considered data for water. This is still consistent with our experimental observation of no neutral uracil molecule loss for $n$ = 2 and 3. However from the PA values, one would predict that the appearance of neutral uracil should occur for n $\approx$ 3-4. For instance, for $n$ = 4, assuming a statistical fragmentation for which the energies of final products are expected to be of relevance, the channel U + (H$_2$O)$_4$H$^+$ is energetically favorable. If one now assumes a direct dissociation, where the parent protonation state remains unchanged, one also expects that neutral uracil evaporates. However, experimentally, for $n$ = 4, no neutral uracil evaporation is observed. The loss of neutral uracil starts at $n$ = 5 and becomes significant only at $n$ = 6. This analysis based on PA is however quite crude. Indeed, it assumes that the protonated uracil cluster would be composed of a uracil molecule attached to an intact water cluster. However, one expects that the hydration of uracil may be more complicated than this simple picture. Therefore, the uracil hydration is explored theoretically in the next Section, Section~\ref{calcul_ur}, in order to determine the proton location more realistically. \subsubsection{Calculated Structures of Protonated Uracil Water Clusters} \label{calcul_ur} -As discussed in section~\ref{sec:ammoniumwater}, we have proposed a modified set of NH parameters to describe sp$^3$ nitrogen atoms. For, +As discussed in section~\ref{sec:ammoniumwater}, I have proposed a modified set of NH parameters to describe sp$^3$ nitrogen atoms. For, sp$^2$ nitrogen atoms there is no need to modified the integral parameters as SCC-DFTB describe them rather correctly. Consequently, only the $D_{NH}$ parameter needs to be defined for the present calculations. Table~\ref{tab:DNH} present the binding energy of the two (H$_2$O)U isomers represented in Figure~\ref{uracil_i} at MP2/Def2TZVP and SCC-DFTB levels of theory. Both $D_\textrm{NH}$ = 0.12 and @@ -672,33 +661,33 @@ have used $D_\textrm{NH}$ = 0.12 in the following. %\figuremacro{a-b}{The structure of isomer a and b of cluster (H$_2$O)U.} The lowest-energy isomers determined theoretically for -hydrated uracil protonated clusters (H$_2$O)$_{1-7, 11, 12}$UH$^+$ are shown in Figures \ref{1a-f}-\ref{12a-f}. In the experiments, clusters are produced at a temperature of about 25 K, so only a very few isomers are likely to be populated. Indeed, the clusters are produced in the canonical ensemble at the temperature $T_\mathrm c \approx$ 25 K, so only isomers for which the Boltzmann factor exp(-$\Delta E k_\mathrm{B} T_\mathrm{c}$) is larger than 10$^{-7}$ are considered here. In this formula, $\Delta E$ represents the relative energy of a considered isomer with respect to the lowest-energy one. Thus for each isomer, only the first six lowest-energy structures of U(H$_2$O)$_{1-7, 11, 12}$UH$^+$ obtained from the PES exploration will be discussed. +hydrated uracil protonated clusters (H$_2$O)$_{1-7, 11, 12}$UH$^+$ are shown in Figures \ref{1a-f}-\ref{12a-f}. In the experiments, clusters are produced at a temperature of about 25 K, so only a very few isomers are likely to be populated. Indeed, the clusters are produced in the canonical ensemble at the temperature $T_\mathrm c \approx$ 25 K, so only isomers for which the Boltzmann factor exp(-$\Delta E k_\mathrm{B} T_\mathrm{c}$) is larger than 10$^{-7}$ are considered here. In this formula, $\Delta E$ represents the relative energy of a considered isomer with respect to the lowest-energy one. Thus for each isomer, only the six lowest-energy structures of U(H$_2$O)$_{1-7, 11, 12}$UH$^+$ obtained from the PES exploration will be discussed. Figure \ref{1a-f} displays the six lowest-energy isomers obtained for (H$_2$O)UH$^+$. Two (1a and 1b) of them contain the u138-like isomer of U (each one with a different orientation of the hydroxyl hydrogen). Three of them (1c, 1d, and 1e) contain the u178 isomer and 1f contains the u137\cite{Wolken2000} isomer with a reverse orientation of the hydroxyl hydrogen. From those isomers, different sites are possible for the water molecule attachment which leads to variety of isomers even for such small size system. To the best of our knowledge, (H$_2$O)UH$^+$ is the most studied protonated uracil water cluster and our results are consistent with previous -published studies. Indeed, Pedersen and co-workers \cite{Pedersen2014} conducted ultraviolet action spectroscopy on (H$_2$O)UH$^+$ and discussed their measurements in the light of theoretical calculations performed on two isomers: ur138w8 (1a in the present study) and ur178w7 (1c).\cite{Pedersen2014} Their energy ordering at 0 K is the same whatever the computational method they used: B3LYP/6-311++G(3df,2p), M06-2X/6-311++G(3df,2p), MP2/6-311++G(3df,2p), CCSD(T)/6-311++G(3df,2p), and CCSD(T)/augcc-pVTZ and is similar to what we obtain. Similarly, Bakker and co-workers\cite{Bakker2008} considered three isomers: U(DK)H$^+_W$ (1a), U(KE)H$^+_{Wa}$ (1c), and U(KE)H$^+_{Wb}$ (1e) at the B3LYP/6-311++G(3df,2p) level of theory and obtained the same energy ordering as we do. Our methodology has thus allowed us to retrieve those isomers and to locate two new low-energy structures (1b and 1d). 1f is too high in energy to be considered in low-temperature experiments that are in the same range of relative energies but have never been discussed. To ensure that they are not artificially favored in our computational method, calculations were also performed at the B3LYP/6-311++G(3df,2p) level of theory. The results are presented in Figure \ref{1a-f-b3lyp}, which are consistent with the MP2/Def2TZVP ones. This makes us confident in the ability of the present methodology to locate meaningful low energy structures. Importantly, no isomer with the proton on the water molecule was obtained, neither at the DFTB or MP2 levels. +published studies. Indeed, S. Pedersen and co-workers \cite{Pedersen2014} conducted ultraviolet action spectroscopy on (H$_2$O)UH$^+$ and discussed their measurements in the light of theoretical calculations performed on two isomers: ur138w8 (1a in the present study) and ur178w7 (1c).\cite{Pedersen2014} Their energy ordering at 0 K is the same whatever the computational method they used: B3LYP/6-311++G(3df,2p), M06-2X/6-311++G(3df,2p), MP2/6-311++G(3df,2p), CCSD(T)/6-311++G(3df,2p), and CCSD(T)/augcc-pVTZ and is similar to what I obtained. Similarly, J. Bakker and co-workers\cite{Bakker2008} considered three isomers: U(DK)H$^+_W$ (1a), U(KE)H$^+_{Wa}$ (1c), and U(KE)H$^+_{Wb}$ (1e) at the B3LYP/6-311++G(3df,2p) level of theory and obtained the same energy ordering as I did. Our methodology has thus allowed us to retrieve those isomers and to locate two new low-energy structures (1b and 1d). 1f is too high in energy to be considered in low-temperature experiments that are in the same range of relative energies but have never been discussed. To ensure that they are not artificially favored in our computational method, calculations were also performed at the B3LYP/6-311++G(3df,2p) level of theory. The results are presented in Figure \ref{1a-f-b3lyp}, which are consistent with the MP2/Def2TZVP ones. This makes us confident in the ability of the present methodology to locate meaningful low energy structures. Importantly, no isomer with the proton on the water molecule was obtained, neither at the DFTB or MP2 levels. \figuremacrob{1a-f}{Lowest-energy structures of (H$_2$O)UH$^+$ obtained at the MP2/Def2TZVP level of theory. Relative ($E_\textrm{rel}$) and binding energies ($E_\textrm{bind}$) are given in kcal.mol$^{-1}$. Important hydrogen-bond distances are indicated in bold and are given in \AA.} \figuremacrob{1a-f-b3lyp}{Lowest-energy structures of (H$_2$O)UH$^+$ obtained at the B3LYP/6-311++G(3df,2p) level of theory. Relative ($E_\textrm{rel}$) and binding energies ($E_\textrm{bind}$) are given in kcal.mol$^{-1}$. The corresponding values with ZPVE corrections are provided in brackets. Important hydrogen-bond distances are indicated in bold and are given in \AA.} -Figures \ref{2a-f} and \ref{3a-f} display the first six lowest-energy isomers obtained for (H$_2$O)$_2$UH$^+$ and (H$_2$O)$_3$UH$^+$, respectively. For (H$_2$O)$_2$UH$^+$, the lowest energy structure, 2a contains the u138 isomer of uracil. 2b, 2d, and 2e contain u178 and 2c contains u138 with reverse orientation of the hydroxyl hydrogen. 2f contains u178 with reverse orientation of the hydroxyl hydrogen. This demonstrates that, similarly to (H$_2$O)UH$^+$, a diversity of uracil isomers are present in the low-energy structures of (H$_2$O)$_2$UH$^+$ which makes an exhaustive exploration of its PES more difficult. The same behavior is observed for (H$_2$O)$_3$UH$^+$. The configuration of u138 does not allow for the formation of a water dimer which leads to two unbound water molecules in 2a. By contrast, a water-water hydrogen bond is observed for 2b and 2c. The existence of a water dimer was not encountered in the low-energy isomers of the unprotonated (H$_2$O)$_2$U species due to the absence of the hydroxyl group on U. It is worth pointing out that 2a, 2b, 2c, and 2d are very close in energy which makes their exact energy ordering difficult to determine. However, no isomer displaying an unprotonated uracil in the low-energy isomers of (H$_2$O)$_2$UH$^+$ was located. The lowest-energy structure of (H$_2$O)$_3$UH$^+$, 3a, is characterized by two water-water hydrogen bond that forms a linear water trimer. Higher energy isomers display only one (3b, 3d, and 3e) or zero (3c and 3f) water-water bond (see Figure \ref{3a-f}). Similarly to (H$_2$O)$_2$UH$^+$, no isomer displaying an unprotonated uracil was located for (H$_2$O)$_3$UH$^+$. +Figures \ref{2a-f} and \ref{3a-f} display the six lowest-energy isomers obtained for (H$_2$O)$_2$UH$^+$ and (H$_2$O)$_3$UH$^+$, respectively. For (H$_2$O)$_2$UH$^+$, the lowest energy structure, 2a contains the u138 isomer of uracil. 2b, 2d, and 2e contain u178 and 2c contains u138 with reverse orientation of the hydroxyl hydrogen. 2f contains u178 with reverse orientation of the hydroxyl hydrogen. This demonstrates that, similarly to (H$_2$O)UH$^+$, a diversity of uracil isomers are present in the low-energy structures of (H$_2$O)$_2$UH$^+$ which makes an exhaustive exploration of its PES more difficult. The same behavior is observed for (H$_2$O)$_3$UH$^+$. The configuration of u138 does not allow for the formation of a water dimer which leads to two unbound water molecules in 2a. By contrast, a water-water hydrogen bond is observed for 2b and 2c. The existence of a water dimer was not encountered in the low-energy isomers of the unprotonated (H$_2$O)$_2$U species due to the absence of the hydroxyl group on U. It is worth pointing out that 2a, 2b, 2c, and 2d are very close in energy which makes their exact energy ordering difficult to determine. However, no isomer displaying an unprotonated uracil in the low-energy isomers of (H$_2$O)$_2$UH$^+$ was located. The lowest-energy structure of (H$_2$O)$_3$UH$^+$, 3a, is characterized by two water-water hydrogen bond that forms a linear water trimer. Higher energy isomers display only one (3b, 3d, and 3e) or zero (3c and 3f) water-water bond (see Figure \ref{3a-f}). Similarly to (H$_2$O)$_2$UH$^+$, no isomer displaying an unprotonated uracil was located for (H$_2$O)$_3$UH$^+$. \figuremacrob{2a-f}{Lowest-energy structures of (H$_2$O)$_2$UH$^+$ obtained at the MP2/Def2TZVP level of theory. Relative ($E_\textrm{rel}$) and binding energies ($E_\textrm{bind}$) are given in kcal.mol$^{-1}$. Important hydrogen-bond distances are indicated in bold and are given in \AA.} \figuremacrob{3a-f}{(H$_2$O)$_3$UH$^+$ lowest-energy structures obtained at the MP2/Def2TZVP level of theory. Relative ($E_\textrm{rel}$) and binding energies ($E_\textrm{bind}$) are given in kcal.mol$^{-1}$. Important hydrogen-bond distances are indicated in bold and are given in \AA.} -The first six lowest-energy isomers obtained for (H$_2$O)$_4$UH$^+$ and (H$_2$O)$_5$UH$^+$ are displayed in Figures \ref{4a-f} and \ref{5a-f}, which constitute a transition in the behavior of the proton. Indeed, in (H$_2$O)$_4$UH$^+$, two kind of low-lying energy structures appear: (i) structures composed of UH$^+$, one water trimer, and one isolated water molecule (4b, 4d, 4e, and 4f); (ii) structures composed of U and a protonated water tetramer (4a and 4c). In the latter case, the hydronium ion is always bounded to an uracil oxygen atom. The U–H$_2$OH$^+$ bond is always rather strong as compared to U–H$_2$O bonds as highlighted by the corresponding short oxygen-hydrogen distance. Furthermore, speaking of distances, the difference between the U–H$_2$OH$^+$ and UH$^+$–H$_2$O forms is rather fuzzy and might be sensitive to computational parameters and also to quantum fluctuations of the hydrogen. This suggests that collision with (H$_2$O)$_4$UH$^+$ is more likely to induce evaporation of H$_2$O rather than H$_2$OH$^+$ or a protonated water cluster. The picture is significantly different in (H$_2$O)$_5$UH$^+$ where the lowest-energy structure displays a hydronium ion separated by one water molecule from U. Such structures do not appear in (H$_2$O)$_4$UH$^+$ due to the limited number of water molecules available to separate H$_2$OH$^+$ from U. Such separation suggests that, if considering a direct dissociation process, evaporation of neutral uracil can now occurs in agreement with the experimental observations (see discussion above). One can see that 5b, which is only 0.3 kcal.mol$^{-1}$ higher in energy than 5a, still displays a U–H$_2$OH$^+$ link. This is in line with the low amount of neutral uracil that is evaporated in the experiment (see Figure \ref{Uloss}). +The six lowest-energy isomers obtained for (H$_2$O)$_4$UH$^+$ and (H$_2$O)$_5$UH$^+$ are displayed in Figures \ref{4a-f} and \ref{5a-f}, which constitute a transition in the behavior of the proton. Indeed, in (H$_2$O)$_4$UH$^+$, two kind of low-lying energy structures appear: (i) structures composed of UH$^+$, one water trimer, and one isolated water molecule (4b, 4d, 4e, and 4f); (ii) structures composed of U and a protonated water tetramer (4a and 4c). In the latter case, the hydronium ion is always bounded to an uracil oxygen atom. The U–H$_2$OH$^+$ bond is always rather strong as compared to U–H$_2$O bonds as highlighted by the corresponding short oxygen-hydrogen distance. Furthermore, speaking of distances, the difference between the U–H$_2$OH$^+$ and UH$^+$–H$_2$O forms is rather fuzzy and might be sensitive to computational parameters and also to quantum fluctuations of the hydrogen. This suggests that collision with (H$_2$O)$_4$UH$^+$ is more likely to induce evaporation of H$_2$O rather than H$_2$OH$^+$ or a protonated water cluster. The picture is significantly different in (H$_2$O)$_5$UH$^+$ where the lowest-energy structure displays a hydronium ion separated by one water molecule from U. Such structures do not appear in (H$_2$O)$_4$UH$^+$ due to the limited number of water molecules available to separate H$_2$OH$^+$ from U. Such separation suggests that, if considering a direct dissociation process, evaporation of neutral uracil can now occurs in agreement with the experimental observations (see discussion above). One can see that 5b, which is only 0.3 kcal.mol$^{-1}$ higher in energy than 5a, still displays a U–H$_2$OH$^+$ link. This is in line with the low amount of neutral uracil that is evaporated in the experiment (see Figure \ref{Uloss}). \figuremacrob{4a-f}{Lowest-energy structures of (H$_2$O)$_4$UH$^+$ obtained at the MP2/Def2TZVP level of theory. Relative ($E_\textrm{rel}$) and binding energies ($E_\textrm{bind}$) are given in kcal.mol$^{-1}$. Important hydrogen-bond distances are indicated in bold and are given in \AA.} \figuremacrob{5a-f}{Lowest-energy structures of (H$_2$O)$_5$UH$^+$ obtained at the MP2/Def2TZVP level of theory. Relative ($E_\textrm{rel}$) and binding energies ($E_\textrm{bind}$) are given in kcal.mol$^{-1}$. Important hydrogen-bond distances are indicated in bold and are given in \AA.} -Figures \ref{6a-f} and \ref{7a-f} display the first six lowest-energy isomers obtained for (H$_2$O)$_6$UH$^+$ and (H$_2$O)$_7$UH$^+$. Similarly to (H$_2$O)$_5$UH$^+$, the first lowest-energy structure, 6a and 7a, we located for both species (H$_2$O)$_6$UH$^+$ and (H$_2$O)$_7$UH$^+$ has the excess proton on a water molecule that is separated by one water molecule from the uracil. This appears to be common to the clusters with at least 5 water molecules. This is also observed for higher-energy isomers (6c, 6d, 7c, 7e, and 7f). Other characteristics of the proton are also observed: proton in a similar Zundel form \cite{Zundel1968} bounded to the uracil (6b, 6e, and 7d) or H$_2$OH$^+$ still bounded to uracil (6f and 7b). +Figures \ref{6a-f} and \ref{7a-f} display the six lowest-energy isomers obtained for (H$_2$O)$_6$UH$^+$ and (H$_2$O)$_7$UH$^+$. Similarly to (H$_2$O)$_5$UH$^+$, the first lowest-energy structure, 6a and 7a, for both species (H$_2$O)$_6$UH$^+$ and (H$_2$O)$_7$UH$^+$ have the excess proton on a water molecule that is separated by one water molecule from the uracil. This appears to be common to the clusters with at least 5 water molecules. This is also observed for higher-energy isomers (6c, 6d, 7c, 7e, and 7f). Other characteristics of the proton are also observed: proton in a similar Zundel form \cite{Zundel1968} bounded to the uracil (6b, 6e, and 7d) or H$_2$OH$^+$ still bounded to uracil (6f and 7b). -Finally, due to the neutral uracil loss proportion starts to decrease from $n$=9 (see Figure \ref{Uloss}), which attracted us to perform the optimization of big cluster (H$_2$O)$_{11, 12}$UH$^+$ as examples to explore why it has this change. The first six low-lying energy isomers obtained for cluster (H$_2$O)$_{11, 12}$UH$^+$ are shown in Figures \ref{11a-f} and \ref{12a-f}. +Finally, due to the neutral uracil loss proportion starts to decrease from $n$=9 (see Figure \ref{Uloss}), which attracted us to perform the optimization of big cluster (H$_2$O)$_{11, 12}$UH$^+$ as examples to explore why it has this change. The six low-lying energy isomers obtained for cluster (H$_2$O)$_{11, 12}$UH$^+$ are shown in Figures \ref{11a-f} and \ref{12a-f}. In all isomers (11a to 11f) of cluster (H$_2$O)$_{11}$UH$^+$, the excess is on the water cluster and was separated by water molecule from uracil. -For 12a, 12b, 12c, and 12d, it is obvious that the excess proton is not directly bounded to the uracil. The uracil in 12a and 12d belongs to the di-keto form (there is a hydrogen atom on each nitrogen of uracil), and the excess proton was separated by one water molecule from uracil, additionally, the uracil is surrounded by the water cluster, all of these may lead the excess proton to go to the near oxygen atom of uracil. For 12b, the excess proton is on the water cluster and is very far from the uracil. For 12c, the excess proton was separately by one water molecule from uracil. For isomers 12e and 12f, the excess proton is between the uracil and a water molecule. The uracil is surrounded by the water cluster in 12e but it is not in 12f. Of course, for (H$_2$O)$_{11}$UH$^+$, (H$_2$O)$_{12}$UH$^+$, (H$_2$O)$_6$UH$^+$ and (H$_2$O)$_7$UH$^+$ and also (H$_2$O)$_4$UH$^+$ and (H$_2$O)$_5$UH$^+$, the amount of low-energy isomers is expected to be very large and we do not intended to find them all. Furthermore, due to the limited number of MP2 geometry optimization we performed, there is few chances that we located the global energy minima for (H$_2$O)$_6$UH$^+$, (H$_2$O)$_7$UH$^+$, (H$_2$O)$_{11}$UH$^+$ and (H$_2$O)$_{12}$UH$^+$. However, the general picture we are able to draw from the present discussed structures fully supports the experimental results: from (H$_2$O)$_5$UH$^+$, it exists low-energy structures populated at very low temperature in which the excess proton is not directly bound to the uracil molecule. Upon fragmentation, this allows the proton to remain bounded to the water molecules. +For 12a, 12b, 12c, and 12d, it is obvious that the excess proton is not directly bounded to the uracil. The uracil in 12a and 12d belongs to the di-keto form (there is a hydrogen atom on each nitrogen of uracil), and the excess proton was separated by one water molecule from uracil, additionally, the uracil is surrounded by the water cluster, all of these may lead the excess proton to go to the near oxygen atom of uracil. For 12b, the excess proton is on the water cluster and is very far from the uracil. For 12c, the excess proton was separately by one water molecule from uracil. For isomers 12e and 12f, the excess proton is between the uracil and a water molecule. The uracil is surrounded by the water cluster in 12e but it is not in 12f. Of course, for (H$_2$O)$_{11}$UH$^+$, (H$_2$O)$_{12}$UH$^+$, (H$_2$O)$_6$UH$^+$ and (H$_2$O)$_7$UH$^+$ and also (H$_2$O)$_4$UH$^+$ and (H$_2$O)$_5$UH$^+$, the amount of low-energy isomers is expected to be very large and do not intended to find them all. Furthermore, due to the limited number of MP2 geometry optimization I performed, there are few chances that I located the global energy minima for (H$_2$O)$_6$UH$^+$, (H$_2$O)$_7$UH$^+$, (H$_2$O)$_{11}$UH$^+$ and (H$_2$O)$_{12}$UH$^+$. However, the general picture I am able to draw from the present discussed structures fully supports the experimental results: from (H$_2$O)$_5$UH$^+$, it exists low-energy structures populated at very low temperature in which the excess proton is not directly bound to the uracil molecule. Upon fragmentation, this allows the proton to remain bounded to the water molecules. \figuremacrob{6a-f}{Lowest-energy structures of (H$_2$O)$_6$UH$^+$ obtained at the MP2/Def2TZVP level of theory. Relative ($E_\textrm{rel}$) and binding energies ($E_\textrm{bind}$) are given in kcal.mol$^{-1}$. Important hydrogen-bond distances are indicated in bold and are given in \AA.} @@ -708,21 +697,21 @@ For 12a, 12b, 12c, and 12d, it is obvious that the excess proton is not directly \figuremacrob{12a-f}{Lowest-energy structures of (H$_2$O)$_{12}$UH$^+$ obtained at the MP2/Def2TZVP level of theory. Relative ($E_\textrm{rel}$) and binding energies ($E_\textrm{bind}$) are given in kcal.mol$^{-1}$. Important hydrogen-bond distances are indicated in bold and are given in \AA.} -All the aforementioned low-lying energy structures are relevant to describe the \newline (H$_2$O)$_{1-7, 11, 12}$UH$^+$ species at low temperature and to understand the relation between the parent cluster size and the amount of evaporated neutral uracil in the case of direct dissociation. However, as already stated, one has to keep in mind that upon collision statistical dissociation can also occur. In that case, structural rearrangements are expected to occur which are important to understand each individual mass spectra of the (H$_2$O)$_{1-15}$UH$^+$ clusters and the origin of each collision product. For instance, the fragment UH$^+$ is detected for all cluster sizes in experiment. This means that for the largest sizes, for which we have shown from the calculation that the proton is located away from the uracil, proton transfer does occur prior to dissociation. One possible scenario is that after collision, water molecules sequentially evaporates. When the number of water molecules is small enough, the proton affinity of uracil gets larger than the one of the remaining attached water cluster. Proton transfer is then likely and therefore protonated uracil can be obtained at the end. +All the aforementioned low-lying energy structures are relevant to describe the \newline (H$_2$O)$_{1-7, 11, 12}$UH$^+$ species at low temperature and to understand the relation between the parent cluster size and the amount of evaporated neutral uracil in the case of direct dissociation. However, as already stated, one has to keep in mind that upon collision statistical dissociation can also occur. In that case, structural rearrangements are expected to occur which are important to understand each individual mass spectra of the (H$_2$O)$_{1-15}$UH$^+$ clusters and the origin of each collision product. For instance, the fragment UH$^+$ is detected for all cluster sizes in experiment. This means that for the largest sizes, for which I have shown from the calculation that the proton is located away from the uracil, proton transfer does occur prior to dissociation. One possible scenario is that after collision, water molecules sequentially evaporates. When the number of water molecules is small enough, the proton affinity of uracil gets larger than the one of the remaining attached water cluster. Proton transfer is then likely and therefore protonated uracil can be obtained at the end. -If one turns to the neutral uracil evaporation channel, it appears that the smaller clusters H$_2$OH$^+$ and (H$_2$O)$_2$H$^+$ are not present in the time of flight mass spectra. This absence might have two origins. First, the dissociation energies of the protonated water monomers and dimers are substantially higher than larger sizes, and they are therefore less prone to evaporation. Second, as already mentioned, for such small sizes, the proton affinity of uracil gets larger than the one of the water dimer or trimer and proton transfer to the uracil is likely to occur. +If one turns to the neutral uracil evaporation channel, it appears that the smaller clusters H$_2$OH$^+$ and (H$_2$O)$_2$H$^+$ are not present in the time-of-flight mass spectra. This absence might have two origins. First, the dissociation energies of the protonated water monomers and dimers are substantially higher than larger sizes, and they are therefore less prone to evaporation. Second, as already mentioned, for such small sizes, the proton affinity of uracil gets larger than the one of the water dimer or trimer and proton transfer to the uracil is likely to occur. In order to confirm the above scenarios, simulations -and/or evaporation rate calculation would have to be conducted to describe the fragmentation channels in details. MD simulations of protonated uracil have already been performed by Spezia and co-workers to understand the collision-induced dissociation.\cite{Molina2015, Molina2016} Although, in the present case, the initial position of the excess proton appears as a key parameter to explain the evaporation of neutral uracil, such MD simulations could be additionally conducted to provide a clearer picture on the various evaporation pathways, which will be shown in section \ref{sec:collisionwUH}. +and/or evaporation rate calculation would have to be conducted to describe the fragmentation channels in details. MD simulations of protonated uracil have already been performed by R. Spezia and co-workers to understand the collision-induced dissociation.\cite{Molina2015, Molina2016} Although, in the present case, the initial position of the excess proton appears as a key parameter to explain the evaporation of neutral uracil, such MD simulations could be additionally conducted to provide a clearer picture on the various evaporation pathways, which will be shown in section \ref{sec:collisionwUH}. \subsection{Conclusions on (H$_2$O)$_{n}$UH$^+$ clusters} The work in this section presents the collision-induced dissociation of hydrated protonated uracil (H$_2$O)$_{1-15}$UH$^+$ clusters and their experimental -absolute fragmentation cross sections. The experiments demonstrate that the evaporation channels evolve with size: Below n = 5, the observed charged fragments -always contain the uracil molecule, whereas from n = 5, the loss of a neutral uracil molecule becomes significant. To understand this transition, I conducted an +absolute fragmentation cross sections. The experiments demonstrate that the evaporation channels evolve with size: Below $n$ = 5, the observed charged fragments +always contain the uracil molecule, whereas from $n$ = 5, the loss of a neutral uracil molecule becomes significant. To understand this transition, I conducted an exhaustive exploration of the potential energy surface of (H$_2$O)$_{1-7, 11, 12}$UH$^+$ clusters combining a rough exploration at the SCC-DFTB level with -fine geometry optimizations at the MP2 level of theory. Those calculations show that below n = 5, the excess proton is either on the uracil or on a water molecule -directly bound to uracil, \textit{i.e.}, forming a strongly bound U–H$_2$OH$^+$ complex. From n = 5 and above, clusters contain enough water molecules to allow +fine geometry optimizations at the MP2 level of theory. Those calculations show that below $n$ = 5, the excess proton is either on the uracil or on a water molecule +directly bound to uracil, \textit{i.e.}, forming a strongly bound U–H$_2$OH$^+$ complex. From $n$ = 5 and above, clusters contain enough water molecules to allow for a net separation between uracil and the excess proton: The latter is often found bound to a water molecule which is separated from uracil by at least one other water molecule. Upon direct dissociation, the excess proton and the uracil can thus belong to different fragments. This study demonstrates that combination of collision-induced dissociation experiments and theoretical calculation allows to probe the solvation and protonation properties of organic molecules such as nucleobases. diff --git a/thesis/4/collision.aux b/thesis/4/collision.aux index ad88d22..49e0ea9 100644 --- a/thesis/4/collision.aux +++ b/thesis/4/collision.aux @@ -3,18 +3,18 @@ \FN@pp@footnotehinttrue \citation{Brechignac1989,Brechignac1994} \citation{Wong2004,Bush2008} -\citation{Holm2010,Gatchell2014,Gatchell2017} +\citation{Holm2010,M. Gatchell2014,Gatchell2017} \citation{Boering1992,Wells2005,Zamith2019thermal} -\@writefile{toc}{\contentsline {chapter}{\numberline {4}Dynamical Simulation of Collision-Induced Dissociation}{99}{chapter.4}\protected@file@percent } +\@writefile{toc}{\contentsline {chapter}{\numberline {4}Dynamical Simulation of Collision-Induced Dissociation}{97}{chapter.4}\protected@file@percent } \@writefile{lof}{\addvspace {10\p@ }} \@writefile{lot}{\addvspace {10\p@ }} -\newlabel{chap:collision}{{4}{99}{Dynamical Simulation of Collision-Induced Dissociation}{chapter.4}{}} -\@writefile{toc}{\contentsline {section}{\numberline {4.1}Experimental Methods}{99}{section.4.1}\protected@file@percent } -\newlabel{exp_cid}{{4.1}{99}{Experimental Methods}{section.4.1}{}} -\@writefile{brf}{\backcite{Brechignac1989}{{99}{4.1}{section.4.1}}} -\@writefile{brf}{\backcite{Brechignac1994}{{99}{4.1}{section.4.1}}} -\@writefile{brf}{\backcite{Wong2004}{{99}{4.1}{section.4.1}}} 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Impact parameters $b$ are (a) 2, (b) 3, (c) 0, (d) 2.5, (e) 2, and (f) 2~\r A{}. In cases (a) and (b) dissociation takes place whereas in the other cases the dimer remains undissociated at the end of the MD simulation. In (c) to (f) the lower panel is a vertical zoom of the corresponding intramolecular parts in upper panel.}}{152}{figure.caption.80}\protected@file@percent } +\newlabel{T-time-zoom_abcdef}{{4.36}{152}{Instantaneous kinetic temperatures as a function of time for intra and intermolecular modes of the pyrene dimer at a collision energy of 22.5~eV. Impact parameters $b$ are (a) 2, (b) 3, (c) 0, (d) 2.5, (e) 2, and (f) 2~\AA {}. In cases (a) and (b) dissociation takes place whereas in the other cases the dimer remains undissociated at the end of the MD simulation. 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In cases (a) and (b), dissociation takes place whereas in the other cases the dimer remains undissociated at the end of the MD simulation}{figure.caption.81}{}} +\@writefile{toc}{\contentsline {subsection}{\numberline {4.4.5}Conclusions about CID of Py$_2^+$}{154}{subsection.4.4.5}\protected@file@percent } \citation{Chen2014,Gatchell2016knockout} -\@writefile{brf}{\backcite{Gatchell2016knockout}{{157}{4.4.5}{subsection.4.4.5}}} -\@writefile{brf}{\backcite{Chen2014}{{157}{4.4.5}{subsection.4.4.5}}} +\@writefile{brf}{\backcite{Gatchell2016knockout}{{155}{4.4.5}{subsection.4.4.5}}} +\@writefile{brf}{\backcite{Chen2014}{{155}{4.4.5}{subsection.4.4.5}}} \FN@pp@footnotehinttrue \@setckpt{4/collision}{ -\setcounter{page}{159} +\setcounter{page}{157} \setcounter{equation}{14} \setcounter{enumi}{5} \setcounter{enumii}{0} diff --git a/thesis/4/collision.blg b/thesis/4/collision.blg index ff9e07e..5908000 100644 --- a/thesis/4/collision.blg +++ b/thesis/4/collision.blg @@ -1,11 +1,15 @@ This is BibTeX, Version 0.99d (TeX Live 2019) Capacity: max_strings=100000, hash_size=100000, hash_prime=85009 The top-level auxiliary file: collision.aux +White space in argument---line 6 of file collision.aux + : \citation{Holm2010,M. + : Gatchell2014,Gatchell2017} +I'm skipping whatever remains of this command I found no \bibdata command---while reading file collision.aux I found no \bibstyle command---while reading file collision.aux -You've used 141 entries, +You've used 107 entries, 0 wiz_defined-function locations, - 364 strings with 3525 characters, + 297 strings with 2816 characters, and the built_in function-call counts, 0 in all, are: = -- 0 > -- 0 @@ -44,4 +48,4 @@ warning$ -- 0 while$ -- 0 width$ -- 0 write$ -- 0 -(There were 2 error messages) +(There were 3 error messages) diff --git a/thesis/4/collision.log b/thesis/4/collision.log index c8d6474..eec54b9 100644 --- a/thesis/4/collision.log +++ b/thesis/4/collision.log @@ -1,11 +1,10 @@ -This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex 2018.9.24) 13 JUN 2021 21:35 +This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019) (preloaded format=pdflatex 2019.10.4) 15 JUN 2021 00:34 entering extended mode restricted \write18 enabled. %&-line parsing enabled. **collision.tex (./collision.tex -LaTeX2e <2018-04-01> patch level 2 -Babel <3.18> and hyphenation patterns for 84 language(s) loaded. +LaTeX2e <2018-12-01> ! 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-Missing character: There is no c in font nullfont! -Missing character: There is no u in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no d in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no h in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no l in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no l in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no f in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no h in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no x in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no p in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no , in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no z in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no f in font nullfont! -Missing character: There is no f in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no h in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no l in font nullfont! -Missing character: There is no l in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no u in font nullfont! -Missing character: There is no l in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no d in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no h in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no d in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no m in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no h in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no m in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no h in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no m in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no l in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no . in font nullfont! -Missing character: There is no F in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no h in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no p in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no b in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no u in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no p in font nullfont! -Missing character: There is no y in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no d in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no m in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no , in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no d in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no h in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no l in font nullfont! -Missing character: There is no l in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no g in font nullfont! -Missing character: There is no y in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no f in font nullfont! -Missing character: There is no f in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no h in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no l in font nullfont! -Missing character: There is no l in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no u in font nullfont! -Missing character: There is no l in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no , in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no h in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no g in font nullfont! -Missing character: There is no y in font nullfont! -Missing character: There is no p in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no f in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no l in font nullfont! -Missing character: There is no l in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no b in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no h in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no h in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no d in font nullfont! -Missing character: There is no l in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no g in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no m in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no l in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no d in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no h in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no g in font nullfont! -Missing character: There is no y in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no f in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no f in font nullfont! -Missing character: There is no f in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no y in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no f in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no l in font nullfont! -Missing character: There is no l in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no n in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no d in font nullfont! -Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! -Missing character: There is no t in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! -Missing character: There is no , in font nullfont! +Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! -Missing character: There is no u in font nullfont! -Missing character: There is no l in font nullfont! -Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! -Missing character: There is no , in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no d in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no l in font nullfont! -Missing character: There is no u in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! @@ -1517,55 +499,600 @@ Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no o in font nullfont! +Missing character: There is no s in font nullfont! Missing character: There is no t in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no v in font nullfont! Missing character: There is no o in font nullfont! -Missing character: There is no p in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no v in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no y in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no c in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no l in font nullfont! Missing character: There is no s in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no Q in font nullfont! +Missing character: There is no M in font nullfont! +Missing character: There is no / in font nullfont! +Missing character: There is no M in font nullfont! +Missing character: There is no M in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no v in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no l in font nullfont! Missing character: There is no w in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! Missing character: There is no i in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! -Missing character: There is no l in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no a in font nullfont! Missing character: There is no b in font nullfont! +Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no i in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no r in font nullfont! +Missing character: There is no M in font nullfont! +Missing character: There is no M in font nullfont! Missing character: There is no p in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no w in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no - in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no y in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no g in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no ( in font nullfont! +Missing character: There is no H in font nullfont! +Missing character: There is no O in font nullfont! +Missing character: There is no ) in font nullfont! +Missing character: There is no U in font nullfont! +Missing character: There is no H in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no P in font nullfont! +Missing character: There is no y in font nullfont! +Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no S in font nullfont! +Missing character: There is no C in font nullfont! +Missing character: There is no C in font nullfont! +Missing character: There is no - in font nullfont! +Missing character: There is no D in font nullfont! +Missing character: There is no F in font nullfont! +Missing character: There is no T in font nullfont! +Missing character: There is no B in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no v in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no . in font nullfont! +Missing character: There is no T in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no y in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no f in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no w in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no u in font nullfont! Missing character: There is no d in font nullfont! +Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no p in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no w in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no v in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no d in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! 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Undefined control sequence. -l.25 \section +l.27 \section {Experimental Methods} \label{exp_cid} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -1580,7 +1107,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.25 \section{E +l.27 \section{E xperimental Methods} \label{exp_cid} You're in trouble here. Try typing to proceed. If that doesn't work, type X to quit. @@ -1605,7 +1132,7 @@ Missing character: There is no o in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no s in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 25--26 +Overfull \hbox (20.0pt too wide) in paragraph at lines 27--28 [] [] @@ -1616,7 +1143,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.27 T +l.29 T he stability of cluster can be investigated from dissociation experime... You're in trouble here. Try typing to proceed. @@ -1945,7 +1472,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.28 ...urce.\cite{Brechignac1989, Brechignac1994} +l.30 ...urce.\cite{Brechignac1989, Brechignac1994} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -1954,14 +1481,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Brechignac1989' on page undefined on input line 28. +LaTeX Warning: Citation `Brechignac1989' on page undefined on input line 30. Missing character: There is no , in font nullfont! \citation{Brechignac1994} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.28 ...urce.\cite{Brechignac1989, Brechignac1994} +l.30 ...urce.\cite{Brechignac1989, Brechignac1994} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -1970,7 +1497,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Brechignac1994' on page undefined on input line 28. +LaTeX Warning: Citation `Brechignac1994' on page undefined on input line 30. Missing character: There is no ] in font nullfont! Missing character: There is no G in font nullfont! @@ -2076,7 +1603,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.29 ...sociation (BIRD).\cite{Wong2004, Bush2008} +l.31 ...sociation (BIRD).\cite{Wong2004, Bush2008} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -2085,14 +1612,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Wong2004' on page undefined on input line 29. +LaTeX Warning: Citation `Wong2004' on page undefined on input line 31. Missing character: There is no , in font nullfont! \citation{Bush2008} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.29 ...sociation (BIRD).\cite{Wong2004, Bush2008} +l.31 ...sociation (BIRD).\cite{Wong2004, Bush2008} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -2101,7 +1628,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Bush2008' on page undefined on input line 29. +LaTeX Warning: Citation `Bush2008' on page undefined on input line 31. Missing character: There is no ] in font nullfont! Missing character: There is no T in font nullfont! @@ -2264,10 +1791,6 @@ Missing character: There is no e in font nullfont! Missing character: There is no V in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no r in font nullfont! -LaTeX Font Info: External font `cmex10' loaded for size -(Font) <7> on input line 31. -LaTeX Font Info: External font `cmex10' loaded for size -(Font) <5> on input line 31. Missing character: There is no , in font nullfont! Missing character: There is no 2 in font nullfont! Missing character: There is no 2 in font nullfont! @@ -2325,6 +1848,8 @@ Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! +Missing character: There is no A in font nullfont! +Missing character: There is no . in font nullfont! Missing character: There is no H in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! @@ -2335,7 +1860,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.31 ...cite{Holm2010, Gatchell2014, Gatchell2017} +l.33 ...e{Holm2010, M. Gatchell2014, Gatchell2017} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -2344,14 +1869,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Holm2010' on page undefined on input line 31. +LaTeX Warning: Citation `Holm2010' on page undefined on input line 33. Missing character: There is no , in font nullfont! -\citation{Gatchell2014} +\citation{M. Gatchell2014} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.31 ...cite{Holm2010, Gatchell2014, Gatchell2017} +l.33 ...e{Holm2010, M. Gatchell2014, Gatchell2017} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -2360,14 +1885,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Gatchell2014' on page undefined on input line 31. +LaTeX Warning: Citation `M. Gatchell2014' on page undefined on input line 33. Missing character: There is no , in font nullfont! \citation{Gatchell2017} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.31 ...cite{Holm2010, Gatchell2014, Gatchell2017} +l.33 ...e{Holm2010, M. Gatchell2014, Gatchell2017} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -2376,7 +1901,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Gatchell2017' on page undefined on input line 31. +LaTeX Warning: Citation `Gatchell2017' on page undefined on input line 33. Missing character: There is no ] in font nullfont! Missing character: There is no C in font nullfont! @@ -2559,7 +2084,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.32 ...Boering1992, Wells2005, Zamith2019thermal} +l.34 ...Boering1992, Wells2005, Zamith2019thermal} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -2568,14 +2093,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Boering1992' on page undefined on input line 32. +LaTeX Warning: Citation `Boering1992' on page undefined on input line 34. Missing character: There is no , in font nullfont! \citation{Wells2005} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.32 ...Boering1992, Wells2005, Zamith2019thermal} +l.34 ...Boering1992, Wells2005, Zamith2019thermal} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -2584,14 +2109,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Wells2005' on page undefined on input line 32. +LaTeX Warning: Citation `Wells2005' on page undefined on input line 34. Missing character: There is no , in font nullfont! \citation{Zamith2019thermal} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.32 ...Boering1992, Wells2005, Zamith2019thermal} +l.34 ...Boering1992, Wells2005, Zamith2019thermal} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -2600,72 +2125,72 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Zamith2019thermal' on page undefined on input line 32 +LaTeX Warning: Citation `Zamith2019thermal' on page undefined on input line 34 . Missing character: There is no ] in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 27--33 +Overfull \hbox (20.0pt too wide) in paragraph at lines 29--35 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 27--33 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 29--35 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 27--33 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 29--35 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 27--33 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 29--35 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 27--33 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 29--35 [] [] -Overfull \hbox (6.63892pt too wide) in paragraph at lines 27--33 +Overfull \hbox (6.63892pt too wide) in paragraph at lines 29--35 []$ [] -Overfull \hbox (10.62505pt too wide) in paragraph at lines 27--33 +Overfull \hbox (10.62505pt too wide) in paragraph at lines 29--35 []$ [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 27--33 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 29--35 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 27--33 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 29--35 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 27--33 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 29--35 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 27--33 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 29--35 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 27--33 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 29--35 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 27--33 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 29--35 [] [] @@ -2676,7 +2201,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.34 B +l.36 B y colliding a molecule, or a molecular aggregate, with a non-reactive ... You're in trouble here. Try typing to proceed. @@ -2902,7 +2427,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.34 ...metry (MS/MS).\cite{Ma1997, Chowdhury2009} +l.36 ...metry (MS/MS).\cite{Ma1997, Chowdhury2009} The resulting mass spectr... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -2911,14 +2436,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Ma1997' on page undefined on input line 34. +LaTeX Warning: Citation `Ma1997' on page undefined on input line 36. Missing character: There is no , in font nullfont! \citation{Chowdhury2009} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.34 ...metry (MS/MS).\cite{Ma1997, Chowdhury2009} +l.36 ...metry (MS/MS).\cite{Ma1997, Chowdhury2009} The resulting mass spectr... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -2927,7 +2452,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Chowdhury2009' on page undefined on input line 34. +LaTeX Warning: Citation `Chowdhury2009' on page undefined on input line 36. Missing character: There is no ] in font nullfont! Missing character: There is no T in font nullfont! @@ -3082,7 +2607,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.34 ...n mechanisms \cite{Nelson1994, Molina2015} +l.36 ...n mechanisms \cite{Nelson1994, Molina2015} or bond and hydration ent... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -3091,14 +2616,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Nelson1994' on page undefined on input line 34. +LaTeX Warning: Citation `Nelson1994' on page undefined on input line 36. Missing character: There is no , in font nullfont! \citation{Molina2015} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.34 ...n mechanisms \cite{Nelson1994, Molina2015} +l.36 ...n mechanisms \cite{Nelson1994, Molina2015} or bond and hydration ent... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -3107,7 +2632,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Molina2015' on page undefined on input line 34. +LaTeX Warning: Citation `Molina2015' on page undefined on input line 36. Missing character: There is no ] in font nullfont! Missing character: There is no o in font nullfont! @@ -3143,7 +2668,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.34 ...d and hydration enthalpies \cite{Carl2007} +l.36 ...d and hydration enthalpies \cite{Carl2007} . The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -3152,47 +2677,47 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Carl2007' on page undefined on input line 34. +LaTeX Warning: Citation `Carl2007' on page undefined on input line 36. Missing character: There is no ] in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 34--35 +Overfull \hbox (20.0pt too wide) in paragraph at lines 36--37 [] [] -Overfull \hbox (4.48613pt too wide) in paragraph at lines 34--35 +Overfull \hbox (4.48613pt too wide) in paragraph at lines 36--37 []$ [] -Overfull \hbox (4.48613pt too wide) in paragraph at lines 34--35 +Overfull \hbox (4.48613pt too wide) in paragraph at lines 36--37 []$ [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 34--35 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 36--37 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 34--35 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 36--37 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 34--35 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 36--37 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 34--35 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 36--37 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 34--35 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 36--37 [] [] @@ -3203,7 +2728,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.36 T +l.38 T he overall process of collisional activation followed by dissociation/... You're in trouble here. Try typing to proceed. @@ -3580,7 +3105,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.36 ...n pathways. \cite{Sleno2004ion, Wells2005} +l.38 ...n pathways. \cite{Sleno2004ion, Wells2005} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -3589,14 +3114,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Sleno2004ion' on page undefined on input line 36. +LaTeX Warning: Citation `Sleno2004ion' on page undefined on input line 38. Missing character: There is no , in font nullfont! \citation{Wells2005} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.36 ...n pathways. \cite{Sleno2004ion, Wells2005} +l.38 ...n pathways. \cite{Sleno2004ion, Wells2005} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -3605,7 +3130,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Wells2005' on page undefined on input line 36. +LaTeX Warning: Citation `Wells2005' on page undefined on input line 38. Missing character: There is no ] in font nullfont! Missing character: There is no T in font nullfont! @@ -3805,7 +3330,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.37 ...ssentially a mass spectrum.\cite{Cody1982} +l.39 ...ssentially a mass spectrum.\cite{Cody1982} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -3814,7 +3339,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Cody1982' on page undefined on input line 37. +LaTeX Warning: Citation `Cody1982' on page undefined on input line 39. Missing character: There is no ] in font nullfont! Missing character: There is no T in font nullfont! @@ -4006,7 +3531,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.39 ... the trap \cite{Olsen2007higher, Hart2011} +l.41 ... the trap \cite{Olsen2007higher, Hart2011} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -4015,14 +3540,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Olsen2007higher' on page undefined on input line 39. +LaTeX Warning: Citation `Olsen2007higher' on page undefined on input line 41. Missing character: There is no , in font nullfont! \citation{Hart2011} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.39 ... the trap \cite{Olsen2007higher, Hart2011} +l.41 ... the trap \cite{Olsen2007higher, Hart2011} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -4031,7 +3556,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Hart2011' on page undefined on input line 39. +LaTeX Warning: Citation `Hart2011' on page undefined on input line 41. Missing character: There is no ] in font nullfont! Missing character: There is no S in font nullfont! @@ -4291,7 +3816,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.40 ...lision gas.\cite{Gauthier1991, Laskin2005} +l.42 ...lision gas.\cite{Gauthier1991, Laskin2005} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -4300,14 +3825,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Gauthier1991' on page undefined on input line 40. +LaTeX Warning: Citation `Gauthier1991' on page undefined on input line 42. Missing character: There is no , in font nullfont! \citation{Laskin2005} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.40 ...lision gas.\cite{Gauthier1991, Laskin2005} +l.42 ...lision gas.\cite{Gauthier1991, Laskin2005} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -4316,46 +3841,46 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Laskin2005' on page undefined on input line 40. +LaTeX Warning: Citation `Laskin2005' on page undefined on input line 42. Missing character: There is no ] in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 36--42 +Overfull \hbox (20.0pt too wide) in paragraph at lines 38--44 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 36--42 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 38--44 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 36--42 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 38--44 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 36--42 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 38--44 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 36--42 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 38--44 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 36--42 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 38--44 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 36--42 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 38--44 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 36--42 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 38--44 [] [] @@ -4366,7 +3891,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.43 C +l.45 C ID and the dissociated/fragmented ions produced by CID are used for se... You're in trouble here. Try typing to proceed. @@ -4758,7 +4283,7 @@ Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 43--44 +Overfull \hbox (20.0pt too wide) in paragraph at lines 45--46 [] [] @@ -4769,7 +4294,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.45 C +l.47 C ID has been applied to a variety of systems, in particular hydrated at... You're in trouble here. Try typing to proceed. @@ -4847,7 +4372,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.45 ...3, Hofstetter2013, Coates2017, Coates2018} +l.47 ...3, Hofstetter2013, Coates2017, Coates2018} and molecular ions \cite{... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -4856,14 +4381,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Mcquinn2009' on page undefined on input line 45. +LaTeX Warning: Citation `Mcquinn2009' on page undefined on input line 47. Missing character: There is no , in font nullfont! \citation{Carl2013} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.45 ...3, Hofstetter2013, Coates2017, Coates2018} +l.47 ...3, Hofstetter2013, Coates2017, Coates2018} and molecular ions \cite{... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -4872,14 +4397,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Carl2013' on page undefined on input line 45. +LaTeX Warning: Citation `Carl2013' on page undefined on input line 47. Missing character: There is no , in font nullfont! \citation{Hofstetter2013} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.45 ...3, Hofstetter2013, Coates2017, Coates2018} +l.47 ...3, Hofstetter2013, Coates2017, Coates2018} and molecular ions \cite{... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -4888,14 +4413,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Hofstetter2013' on page undefined on input line 45. +LaTeX Warning: Citation `Hofstetter2013' on page undefined on input line 47. Missing character: There is no , in font nullfont! \citation{Coates2017} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.45 ...3, Hofstetter2013, Coates2017, Coates2018} +l.47 ...3, Hofstetter2013, Coates2017, Coates2018} and molecular ions \cite{... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -4904,14 +4429,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Coates2017' on page undefined on input line 45. +LaTeX Warning: Citation `Coates2017' on page undefined on input line 47. Missing character: There is no , in font nullfont! \citation{Coates2018} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.45 ...3, Hofstetter2013, Coates2017, Coates2018} +l.47 ...3, Hofstetter2013, Coates2017, Coates2018} and molecular ions \cite{... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -4920,7 +4445,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Coates2018' on page undefined on input line 45. +LaTeX Warning: Citation `Coates2018' on page undefined on input line 47. Missing character: There is no ] in font nullfont! Missing character: There is no a in font nullfont! @@ -4944,7 +4469,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.45 ...raul1989, Wei1991, Goebbert2006, Haag2009} +l.47 ...raul1989, Wei1991, Goebbert2006, Haag2009} . In the second case, it h... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -4953,14 +4478,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Graul1989' on page undefined on input line 45. +LaTeX Warning: Citation `Graul1989' on page undefined on input line 47. Missing character: There is no , in font nullfont! \citation{Wei1991} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.45 ...raul1989, Wei1991, Goebbert2006, Haag2009} +l.47 ...raul1989, Wei1991, Goebbert2006, Haag2009} . In the second case, it h... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -4969,14 +4494,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Wei1991' on page undefined on input line 45. +LaTeX Warning: Citation `Wei1991' on page undefined on input line 47. Missing character: There is no , in font nullfont! \citation{Goebbert2006} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.45 ...raul1989, Wei1991, Goebbert2006, Haag2009} +l.47 ...raul1989, Wei1991, Goebbert2006, Haag2009} . In the second case, it h... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -4985,14 +4510,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Goebbert2006' on page undefined on input line 45. +LaTeX Warning: Citation `Goebbert2006' on page undefined on input line 47. Missing character: There is no , in font nullfont! \citation{Haag2009} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.45 ...raul1989, Wei1991, Goebbert2006, Haag2009} +l.47 ...raul1989, Wei1991, Goebbert2006, Haag2009} . In the second case, it h... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -5001,7 +4526,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Haag2009' on page undefined on input line 45. +LaTeX Warning: Citation `Haag2009' on page undefined on input line 47. Missing character: There is no ] in font nullfont! Missing character: There is no . in font nullfont! @@ -5107,7 +4632,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.45 ... RNA \cite{Liu2006, Nguyen2011, Shuck2014} +l.47 ... RNA \cite{Liu2006, Nguyen2011, Shuck2014} , as well as low-energy co... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -5116,14 +4641,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Liu2006' on page undefined on input line 45. +LaTeX Warning: Citation `Liu2006' on page undefined on input line 47. Missing character: There is no , in font nullfont! \citation{Nguyen2011} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.45 ... RNA \cite{Liu2006, Nguyen2011, Shuck2014} +l.47 ... RNA \cite{Liu2006, Nguyen2011, Shuck2014} , as well as low-energy co... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -5132,14 +4657,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Nguyen2011' on page undefined on input line 45. +LaTeX Warning: Citation `Nguyen2011' on page undefined on input line 47. Missing character: There is no , in font nullfont! \citation{Shuck2014} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.45 ... RNA \cite{Liu2006, Nguyen2011, Shuck2014} +l.47 ... RNA \cite{Liu2006, Nguyen2011, Shuck2014} , as well as low-energy co... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -5148,7 +4673,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Shuck2014' on page undefined on input line 45. +LaTeX Warning: Citation `Shuck2014' on page undefined on input line 47. Missing character: There is no ] in font nullfont! Missing character: There is no , in font nullfont! @@ -5216,7 +4741,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.45 ... interest \cite{Castrovilli2017, Bera2018} +l.47 ... interest \cite{Castrovilli2017, Bera2018} . The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -5225,14 +4750,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Castrovilli2017' on page undefined on input line 45. +LaTeX Warning: Citation `Castrovilli2017' on page undefined on input line 47. Missing character: There is no , in font nullfont! \citation{Bera2018} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.45 ... interest \cite{Castrovilli2017, Bera2018} +l.47 ... interest \cite{Castrovilli2017, Bera2018} . The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -5241,82 +4766,82 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Bera2018' on page undefined on input line 45. +LaTeX Warning: Citation `Bera2018' on page undefined on input line 47. Missing character: There is no ] in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 45--46 +Overfull \hbox (20.0pt too wide) in paragraph at lines 47--48 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 45--46 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 47--48 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 45--46 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 47--48 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 45--46 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 47--48 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 45--46 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 47--48 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 45--46 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 47--48 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 45--46 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 47--48 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 45--46 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 47--48 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 45--46 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 47--48 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 45--46 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 47--48 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 45--46 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 47--48 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 45--46 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 47--48 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 45--46 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 47--48 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 45--46 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 47--48 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 45--46 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 47--48 [] [] @@ -5327,7 +4852,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.47 T +l.49 T heoretical and experimental studies devoted to fragmentation of hydrat... You're in trouble here. Try typing to proceed. @@ -5432,7 +4957,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.47 ... Bakker2008, Markush2016, Castrovilli2017} +l.49 ... Bakker2008, Markush2016, Castrovilli2017} although CID has been app... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -5441,14 +4966,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Li1992' on page undefined on input line 47. +LaTeX Warning: Citation `Li1992' on page undefined on input line 49. Missing character: There is no , in font nullfont! \citation{Bobbert2002} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.47 ... Bakker2008, Markush2016, Castrovilli2017} +l.49 ... Bakker2008, Markush2016, Castrovilli2017} although CID has been app... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -5457,14 +4982,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Bobbert2002' on page undefined on input line 47. +LaTeX Warning: Citation `Bobbert2002' on page undefined on input line 49. Missing character: There is no , in font nullfont! \citation{Liu2006} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.47 ... Bakker2008, Markush2016, Castrovilli2017} +l.49 ... Bakker2008, Markush2016, Castrovilli2017} although CID has been app... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -5473,14 +4998,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Liu2006' on page undefined on input line 47. +LaTeX Warning: Citation `Liu2006' on page undefined on input line 49. Missing character: There is no , in font nullfont! \citation{Bakker2008} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.47 ... Bakker2008, Markush2016, Castrovilli2017} +l.49 ... Bakker2008, Markush2016, Castrovilli2017} although CID has been app... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -5489,14 +5014,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Bakker2008' on page undefined on input line 47. +LaTeX Warning: Citation `Bakker2008' on page undefined on input line 49. Missing character: There is no , in font nullfont! \citation{Markush2016} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.47 ... Bakker2008, Markush2016, Castrovilli2017} +l.49 ... Bakker2008, Markush2016, Castrovilli2017} although CID has been app... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -5505,14 +5030,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Markush2016' on page undefined on input line 47. +LaTeX Warning: Citation `Markush2016' on page undefined on input line 49. Missing character: There is no , in font nullfont! \citation{Castrovilli2017} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.47 ... Bakker2008, Markush2016, Castrovilli2017} +l.49 ... Bakker2008, Markush2016, Castrovilli2017} although CID has been app... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -5521,7 +5046,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Castrovilli2017' on page undefined on input line 47. +LaTeX Warning: Citation `Castrovilli2017' on page undefined on input line 49. Missing character: There is no ] in font nullfont! Missing character: There is no a in font nullfont! @@ -5590,7 +5115,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.47 ...cite{Carl2013, Hofstetter2013, Coates2018} +l.49 ...cite{Carl2013, Hofstetter2013, Coates2018} and on charged water The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -5599,14 +5124,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Carl2013' on page undefined on input line 47. +LaTeX Warning: Citation `Carl2013' on page undefined on input line 49. Missing character: There is no , in font nullfont! \citation{Hofstetter2013} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.47 ...cite{Carl2013, Hofstetter2013, Coates2018} +l.49 ...cite{Carl2013, Hofstetter2013, Coates2018} and on charged water The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -5615,14 +5140,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Hofstetter2013' on page undefined on input line 47. +LaTeX Warning: Citation `Hofstetter2013' on page undefined on input line 49. Missing character: There is no , in font nullfont! \citation{Coates2018} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.47 ...cite{Carl2013, Hofstetter2013, Coates2018} +l.49 ...cite{Carl2013, Hofstetter2013, Coates2018} and on charged water The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -5631,7 +5156,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Coates2018' on page undefined on input line 47. +LaTeX Warning: Citation `Coates2018' on page undefined on input line 49. Missing character: There is no ] in font nullfont! Missing character: There is no a in font nullfont! @@ -5664,7 +5189,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.48 ...1982, Bakker2008, Mcquinn2009, Zamith2012} +l.50 ...1982, Bakker2008, Mcquinn2009, Zamith2012} . This is a real lack as u... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -5673,14 +5198,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Dawson1982' on page undefined on input line 48. +LaTeX Warning: Citation `Dawson1982' on page undefined on input line 50. Missing character: There is no , in font nullfont! \citation{Bakker2008} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.48 ...1982, Bakker2008, Mcquinn2009, Zamith2012} +l.50 ...1982, Bakker2008, Mcquinn2009, Zamith2012} . This is a real lack as u... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -5689,14 +5214,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Bakker2008' on page undefined on input line 48. +LaTeX Warning: Citation `Bakker2008' on page undefined on input line 50. Missing character: There is no , in font nullfont! \citation{Mcquinn2009} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.48 ...1982, Bakker2008, Mcquinn2009, Zamith2012} +l.50 ...1982, Bakker2008, Mcquinn2009, Zamith2012} . This is a real lack as u... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -5705,14 +5230,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Mcquinn2009' on page undefined on input line 48. +LaTeX Warning: Citation `Mcquinn2009' on page undefined on input line 50. Missing character: There is no , in font nullfont! \citation{Zamith2012} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.48 ...1982, Bakker2008, Mcquinn2009, Zamith2012} +l.50 ...1982, Bakker2008, Mcquinn2009, Zamith2012} . This is a real lack as u... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -5721,7 +5246,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Zamith2012' on page undefined on input line 48. +LaTeX Warning: Citation `Zamith2012' on page undefined on input line 50. Missing character: There is no ] in font nullfont! Missing character: There is no . in font nullfont! @@ -6120,6 +5645,8 @@ Missing character: There is no d in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! +Missing character: There is no B in font nullfont! +Missing character: There is no . in font nullfont! Missing character: There is no L in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no u in font nullfont! @@ -6271,7 +5798,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.50 ... solvation state of AMP$^-$.\cite{Liu2006} +l.52 ... solvation state of AMP$^-$.\cite{Liu2006} However, to the best of o... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -6280,7 +5807,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Liu2006' on page undefined on input line 50. +LaTeX Warning: Citation `Liu2006' on page undefined on input line 52. Missing character: There is no ] in font nullfont! Missing character: There is no H in font nullfont! @@ -6403,7 +5930,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.50 ...cite{Carl2013, Hofstetter2013, Coates2018} +l.52 ...cite{Carl2013, Hofstetter2013, Coates2018} . The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -6412,14 +5939,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Carl2013' on page undefined on input line 50. +LaTeX Warning: Citation `Carl2013' on page undefined on input line 52. Missing character: There is no , in font nullfont! \citation{Hofstetter2013} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.50 ...cite{Carl2013, Hofstetter2013, Coates2018} +l.52 ...cite{Carl2013, Hofstetter2013, Coates2018} . The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -6428,14 +5955,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Hofstetter2013' on page undefined on input line 50. +LaTeX Warning: Citation `Hofstetter2013' on page undefined on input line 52. Missing character: There is no , in font nullfont! \citation{Coates2018} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.50 ...cite{Carl2013, Hofstetter2013, Coates2018} +l.52 ...cite{Carl2013, Hofstetter2013, Coates2018} . The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -6444,112 +5971,112 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Coates2018' on page undefined on input line 50. +LaTeX Warning: Citation `Coates2018' on page undefined on input line 52. Missing character: There is no ] in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 47--53 +Overfull \hbox (20.0pt too wide) in paragraph at lines 49--55 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 47--53 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 49--55 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 47--53 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 49--55 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 47--53 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 49--55 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 47--53 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 49--55 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 47--53 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 49--55 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 47--53 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 49--55 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 47--53 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 49--55 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 47--53 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 49--55 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 47--53 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 49--55 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 47--53 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 49--55 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 47--53 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 49--55 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 47--53 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 49--55 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 47--53 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 49--55 [] [] -Overfull \hbox (7.92215pt too wide) in paragraph at lines 47--53 +Overfull \hbox (7.92215pt too wide) in paragraph at lines 49--55 \OT1/cmr/m/it/10 et [] -Overfull \hbox (10.73328pt too wide) in paragraph at lines 47--53 +Overfull \hbox (10.73328pt too wide) in paragraph at lines 49--55 \OT1/cmr/m/it/10 al. [] -Overfull \hbox (6.75002pt too wide) in paragraph at lines 47--53 +Overfull \hbox (6.75002pt too wide) in paragraph at lines 49--55 []$ [] -Overfull \hbox (12.18054pt too wide) in paragraph at lines 47--53 +Overfull \hbox (12.18054pt too wide) in paragraph at lines 49--55 []$[] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 47--53 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 49--55 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 47--53 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 49--55 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 47--53 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 49--55 [] [] @@ -6560,7 +6087,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.58 T +l.60 T hreshold collision-induced dissociation (TCID) method has also been us... You're in trouble here. Try typing to proceed. @@ -6725,8 +6252,8 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.58 ...clusters.\cite{Spasov2000, Armentrout2008} - Zamith \textit{et al.} di... +l.60 ...clusters.\cite{Spasov2000, Armentrout2008} + S. Zamith \textit{et al.}... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct @@ -6734,15 +6261,15 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Spasov2000' on page undefined on input line 58. +LaTeX Warning: Citation `Spasov2000' on page undefined on input line 60. Missing character: There is no , in font nullfont! \citation{Armentrout2008} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.58 ...clusters.\cite{Spasov2000, Armentrout2008} - Zamith \textit{et al.} di... +l.60 ...clusters.\cite{Spasov2000, Armentrout2008} + S. Zamith \textit{et al.}... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct @@ -6750,9 +6277,11 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Armentrout2008' on page undefined on input line 58. +LaTeX Warning: Citation `Armentrout2008' on page undefined on input line 60. Missing character: There is no ] in font nullfont! +Missing character: There is no S in font nullfont! +Missing character: There is no . in font nullfont! Missing character: There is no Z in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! @@ -6868,7 +6397,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.58 ...noble gases, respectively.\cite{Braud2019} +l.60 ...noble gases, respectively.\cite{Braud2019} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -6877,7 +6406,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Braud2019' on page undefined on input line 58. +LaTeX Warning: Citation `Braud2019' on page undefined on input line 60. Missing character: There is no ] in font nullfont! Missing character: There is no I in font nullfont! @@ -6947,7 +6476,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.59 ...luster cations. \cite{Zamith2020threshold} +l.61 ...luster cations. \cite{Zamith2020threshold} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -6957,7 +6486,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Citation `Zamith2020threshold' on page undefined on input line -59. +61. Missing character: There is no ] in font nullfont! Missing character: There is no F in font nullfont! @@ -7222,42 +6751,42 @@ Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 58--63 +Overfull \hbox (20.0pt too wide) in paragraph at lines 60--65 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 58--63 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 60--65 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 58--63 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 60--65 [] [] -Overfull \hbox (7.92215pt too wide) in paragraph at lines 58--63 +Overfull \hbox (7.92215pt too wide) in paragraph at lines 60--65 \OT1/cmr/m/it/10 et [] -Overfull \hbox (10.73328pt too wide) in paragraph at lines 58--63 +Overfull \hbox (10.73328pt too wide) in paragraph at lines 60--65 \OT1/cmr/m/it/10 al. [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 58--63 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 60--65 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 58--63 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 60--65 [] [] ! Undefined control sequence. -l.67 \subsection +l.69 \subsection {Principle of TCID} \label{principleTCID} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -7272,7 +6801,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.67 \subsection{P +l.69 \subsection{P rinciple of TCID} \label{principleTCID} You're in trouble here. Try typing to proceed. If that doesn't work, type X to quit. @@ -7293,7 +6822,7 @@ Missing character: There is no C in font nullfont! Missing character: There is no I in font nullfont! Missing character: There is no D in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 67--68 +Overfull \hbox (20.0pt too wide) in paragraph at lines 69--70 [] [] @@ -7304,7 +6833,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.69 I +l.71 I n usual TCID setups, experiments are done in ion guides, allowing to p... You're in trouble here. Try typing to proceed. @@ -8120,7 +7649,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.69 ...on rates.\cite{Klippenstein1992, Baer1996} +l.71 ...on rates.\cite{Klippenstein1992, Baer1996} Third, the initial therma... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -8129,7 +7658,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Klippenstein1992' on page undefined on input line 69. +LaTeX Warning: Citation `Klippenstein1992' on page undefined on input line 71. Missing character: There is no , in font nullfont! @@ -8137,7 +7666,7 @@ Missing character: There is no , in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.69 ...on rates.\cite{Klippenstein1992, Baer1996} +l.71 ...on rates.\cite{Klippenstein1992, Baer1996} Third, the initial therma... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -8146,7 +7675,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Baer1996' on page undefined on input line 69. +LaTeX Warning: Citation `Baer1996' on page undefined on input line 71. Missing character: There is no ] in font nullfont! Missing character: There is no T in font nullfont! @@ -8327,7 +7856,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.69 ... can be expressed as \cite{Armentrout2008} +l.71 ... can be expressed as \cite{Armentrout2008} : The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -8336,27 +7865,27 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Armentrout2008' on page undefined on input line 69. +LaTeX Warning: Citation `Armentrout2008' on page undefined on input line 71. Missing character: There is no ] in font nullfont! Missing character: There is no : in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 69--70 +Overfull \hbox (20.0pt too wide) in paragraph at lines 71--72 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 69--70 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 71--72 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 69--70 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 71--72 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 69--70 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 71--72 [] [] @@ -8367,18 +7896,18 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.71 \begin{eqnarray} +l.73 \begin{eqnarray} You're in trouble here. Try typing to proceed. If that doesn't work, type X to quit. -Overfull \hbox (20.0pt too wide) in paragraph at lines 71--71 +Overfull \hbox (20.0pt too wide) in paragraph at lines 73--73 [] [] -Overfull \hbox (299.39906pt too wide) in alignment at lines 71--74 +Overfull \hbox (299.39906pt too wide) in alignment at lines 73--76 [][][] [] [] @@ -8389,7 +7918,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.76 w +l.78 w here $\sigma_{_0}$ is the collision cross section, $n$ is the energy d... You're in trouble here. Try typing to proceed. @@ -8746,7 +8275,7 @@ Missing character: There is no q in font nullfont! ! Undefined control sequence. ... Reference `CIDcross' on page \thepage \space undefined\on@line . -l.76 ...ith experimental curves, eq \ref{CIDcross} +l.78 ...ith experimental curves, eq \ref{CIDcross} is further convolved with... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -8755,7 +8284,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `CIDcross' on page undefined on input line 76. +LaTeX Warning: Reference `CIDcross' on page undefined on input line 78. Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! @@ -8940,7 +8469,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.76 ...ncluded.\cite{Rodgers1998, Armentrout2007} +l.78 ...ncluded.\cite{Rodgers1998, Armentrout2007} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -8949,14 +8478,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Rodgers1998' on page undefined on input line 76. +LaTeX Warning: Citation `Rodgers1998' on page undefined on input line 78. Missing character: There is no , in font nullfont! \citation{Armentrout2007} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.76 ...ncluded.\cite{Rodgers1998, Armentrout2007} +l.78 ...ncluded.\cite{Rodgers1998, Armentrout2007} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -8965,61 +8494,61 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Armentrout2007' on page undefined on input line 76. +LaTeX Warning: Citation `Armentrout2007' on page undefined on input line 78. Missing character: There is no ] in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 76--77 +Overfull \hbox (20.0pt too wide) in paragraph at lines 78--79 [] [] -Overfull \hbox (10.11696pt too wide) in paragraph at lines 76--77 +Overfull \hbox (10.11696pt too wide) in paragraph at lines 78--79 \OML/cmm/m/it/10 ^^[[]$ [] -Overfull \hbox (6.00235pt too wide) in paragraph at lines 76--77 +Overfull \hbox (6.00235pt too wide) in paragraph at lines 78--79 \OML/cmm/m/it/10 n$ [] -Overfull \hbox (17.97237pt too wide) in paragraph at lines 76--77 +Overfull \hbox (17.97237pt too wide) in paragraph at lines 78--79 \OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (8.09897pt too wide) in paragraph at lines 76--77 +Overfull \hbox (8.09897pt too wide) in paragraph at lines 78--79 \OML/cmm/m/it/10 g[]$ [] -Overfull \hbox (10.71123pt too wide) in paragraph at lines 76--77 +Overfull \hbox (10.71123pt too wide) in paragraph at lines 78--79 \OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (5.52084pt too wide) in paragraph at lines 76--77 +Overfull \hbox (5.52084pt too wide) in paragraph at lines 78--79 \OML/cmm/m/it/10 k$ [] -Overfull \hbox (5.50348pt too wide) in paragraph at lines 76--77 +Overfull \hbox (5.50348pt too wide) in paragraph at lines 78--79 \OML/cmm/m/it/10 ^^\$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 76--77 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 78--79 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 76--77 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 78--79 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 76--77 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 78--79 [] [] @@ -9030,7 +8559,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.78 I +l.80 I n this method, ion guides are not used. Therefore, it needs to simulat... You're in trouble here. Try typing to proceed. @@ -9265,7 +8794,7 @@ Missing character: There is no q in font nullfont! ! Undefined control sequence. ... Reference `CIDcross' on page \thepage \space undefined\on@line . -l.78 ...e average curve given by eq \ref{CIDcross} +l.80 ...e average curve given by eq \ref{CIDcross} . This approach allows to ... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -9274,7 +8803,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `CIDcross' on page undefined on input line 78. +LaTeX Warning: Reference `CIDcross' on page undefined on input line 80. Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! @@ -9597,17 +9126,17 @@ Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 78--80 +Overfull \hbox (20.0pt too wide) in paragraph at lines 80--82 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 78--80 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 80--82 [] [] ! Undefined control sequence. -l.83 \subsection +l.85 \subsection {Experimental Setup} \label{EXPsetup} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -9622,7 +9151,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.83 \subsection{E +l.85 \subsection{E xperimental Setup} \label{EXPsetup} You're in trouble here. Try typing to proceed. If that doesn't work, type X to quit. @@ -9645,7 +9174,7 @@ Missing character: There is no t in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no p in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 83--84 +Overfull \hbox (20.0pt too wide) in paragraph at lines 85--86 [] [] @@ -9656,7 +9185,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.85 T +l.87 T he experimental setup of Laboratoire Collisions Agr{\'e}gats R{\'e}act... You're in trouble here. Try typing to proceed. @@ -9708,16 +9237,16 @@ Missing character: There is no s in font nullfont! Missing character: There is no A in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no r in font nullfont! -LaTeX Font Info: Try loading font information for +cmr on input line 85. -LaTeX Font Info: No file cmr.fd. on input line 85. +LaTeX Font Info: Try loading font information for +cmr on input line 87. +LaTeX Font Info: No file cmr.fd. on input line 87. LaTeX Font Warning: Font shape `/cmr/m/n' undefined -(Font) using `/cmr/m/n' instead on input line 85. +(Font) using `/cmr/m/n' instead on input line 87. ! Corrupted NFSS tables. wrong@fontshape ...message {Corrupted NFSS tables} error@fontshape else let f... -l.85 ...al setup of Laboratoire Collisions Agr{\'e +l.87 ...al setup of Laboratoire Collisions Agr{\'e }gats R{\'e}activi{\'e} (L... This error message was generated by an \errmessage command, so I can't give any explicit help. @@ -9726,7 +9255,7 @@ and deduce the truth by order and method. LaTeX Font Warning: Font shape `/cmr/m/n' undefined -(Font) using `OT1/cmr/m/n' instead on input line 85. +(Font) using `OT1/cmr/m/n' instead on input line 87. Missing character: There is no g in font nullfont! Missing character: There is no a in font nullfont! @@ -9747,6 +9276,8 @@ Missing character: There is no R in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no y in font nullfont! +Missing character: There is no S in font nullfont! +Missing character: There is no . in font nullfont! Missing character: There is no Z in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! @@ -9857,27 +9388,27 @@ Missing character: There is no w in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no : in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 85--86 +Overfull \hbox (20.0pt too wide) in paragraph at lines 87--88 [] [] -Overfull \hbox (9.44446pt too wide) in paragraph at lines 85--86 +Overfull \hbox (9.44446pt too wide) in paragraph at lines 87--88 \/cmr/m/n/10 ^^Se [] -Overfull \hbox (8.88889pt too wide) in paragraph at lines 85--86 +Overfull \hbox (8.88889pt too wide) in paragraph at lines 87--88 \/cmr/m/n/10 ^^Se^^Se [] -Overfull \hbox (4.59996pt too wide) in paragraph at lines 85--86 +Overfull \hbox (4.59996pt too wide) in paragraph at lines 87--88 \OT1/cmr/m/it/10 e [] ! Undefined control sequence. -l.87 \figuremacrob +l.89 \figuremacrob {experiment-setup}{Schematic view of the experimental setu... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -9892,7 +9423,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.87 \figuremacrob{e +l.89 \figuremacrob{e xperiment-setup}{Schematic view of the experimental setu... You're in trouble here. Try typing to proceed. @@ -10193,17 +9724,17 @@ Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 87--92 +Overfull \hbox (20.0pt too wide) in paragraph at lines 89--94 [] [] -Overfull \hbox (5.00002pt too wide) in paragraph at lines 87--92 +Overfull \hbox (5.00002pt too wide) in paragraph at lines 89--94 \/cmr/m/n/10 { [] -Overfull \hbox (5.00002pt too wide) in paragraph at lines 87--92 +Overfull \hbox (5.00002pt too wide) in paragraph at lines 89--94 \/cmr/m/n/10 { [] @@ -10214,7 +9745,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.93 C +l.95 C lusters are produced in a gas aggregation source \cite{Braud2017}(a) a... You're in trouble here. Try typing to proceed. @@ -10267,7 +9798,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.93 ... a gas aggregation source \cite{Braud2017} +l.95 ... a gas aggregation source \cite{Braud2017} (a) and then thermalized (... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -10276,7 +9807,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Braud2017' on page undefined on input line 93. +LaTeX Warning: Citation `Braud2017' on page undefined on input line 95. Missing character: There is no ] in font nullfont! Missing character: There is no ( in font nullfont! @@ -10792,12 +10323,12 @@ Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 93--94 +Overfull \hbox (20.0pt too wide) in paragraph at lines 95--96 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 93--94 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 95--96 [] [] @@ -10808,7 +10339,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.95 I +l.97 I n the second mode, all the electrodes were used to mass-select the clu... You're in trouble here. Try typing to proceed. @@ -12300,12 +11831,12 @@ Missing character: There is no e in font nullfont! Missing character: There is no V in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 95--97 +Overfull \hbox (20.0pt too wide) in paragraph at lines 97--99 [] [] -Overfull \hbox (5.00002pt too wide) in paragraph at lines 95--97 +Overfull \hbox (5.00002pt too wide) in paragraph at lines 97--99 \/cmr/m/n/10 { [] @@ -12316,8 +11847,8 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.98 K - inetic energies of the ions can be easily deduced from experimental p... +l.100 K + inetic energies of the ions can be easily deduced from experimental ... You're in trouble here. Try typing to proceed. If that doesn't work, type X to quit. @@ -12773,7 +12304,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.98 ...ribution of the ions. \cite{Chirot2006new} +l.100 ...ibution of the ions. \cite{Chirot2006new} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -12782,16 +12313,16 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Chirot2006new' on page undefined on input line 98. +LaTeX Warning: Citation `Chirot2006new' on page undefined on input line 100. Missing character: There is no ] in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 98--99 +Overfull \hbox (20.0pt too wide) in paragraph at lines 100--101 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 98--99 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 100--101 [] [] @@ -12802,7 +12333,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.100 T +l.102 T he simplified experiment setup is shown in Figure \ref{exp-setup}. You're in trouble here. Try typing to proceed. If that doesn't work, type X to quit. @@ -12853,7 +12384,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...Reference `exp-setup' on page \thepage \space undefined\on@line . -l.100 ... setup is shown in Figure \ref{exp-setup} +l.102 ... setup is shown in Figure \ref{exp-setup} . The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -12862,7 +12393,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `exp-setup' on page undefined on input line 100. +LaTeX Warning: Reference `exp-setup' on page undefined on input line 102. Missing character: There is no . in font nullfont! Missing character: There is no C in font nullfont! @@ -13081,7 +12612,7 @@ Missing character: There is no M in font nullfont! Missing character: There is no S in font nullfont! Missing character: There is no . in font nullfont! ! Undefined control sequence. -l.103 \figuremacrob +l.105 \figuremacrob {exp-setup}{Schematic of the simplified experimental setup.} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -13141,17 +12672,17 @@ Missing character: There is no u in font nullfont! Missing character: There is no p in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 100--104 +Overfull \hbox (20.0pt too wide) in paragraph at lines 102--106 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 100--104 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 102--106 [] [] ! Undefined control sequence. -l.105 \section +l.107 \section {Computational Details} \label{Comput_meth} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -13166,7 +12697,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.105 \section{C +l.107 \section{C omputational Details} \label{Comput_meth} You're in trouble here. Try typing to proceed. If that doesn't work, type X to quit. @@ -13192,12 +12723,12 @@ Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no s in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 105--106 +Overfull \hbox (20.0pt too wide) in paragraph at lines 107--108 [] [] ! Undefined control sequence. -l.107 \subsection +l.109 \subsection {SCC-DFTB Potential} \label{DFTBpotential} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -13212,7 +12743,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.107 \subsection{S +l.109 \subsection{S CC-DFTB Potential} \label{DFTBpotential} You're in trouble here. Try typing to proceed. If that doesn't work, type X to quit. @@ -13235,7 +12766,7 @@ Missing character: There is no i in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 107--108 +Overfull \hbox (20.0pt too wide) in paragraph at lines 109--110 [] [] @@ -13246,7 +12777,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.109 F +l.111 F or the work in this chapter, the SCC-DFTB in combination with the mio... You're in trouble here. Try typing to proceed. @@ -13365,7 +12896,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.109 ...Frenzel2004, Elstner2014, Spiegelman2020} +l.111 ...Frenzel2004, Elstner2014, Spiegelman2020} The SCC-DFTB potential f... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -13374,14 +12905,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Elstner1998' on page undefined on input line 109. +LaTeX Warning: Citation `Elstner1998' on page undefined on input line 111. Missing character: There is no , in font nullfont! \citation{Porezag1995} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.109 ...Frenzel2004, Elstner2014, Spiegelman2020} +l.111 ...Frenzel2004, Elstner2014, Spiegelman2020} The SCC-DFTB potential f... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -13390,14 +12921,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Porezag1995' on page undefined on input line 109. +LaTeX Warning: Citation `Porezag1995' on page undefined on input line 111. Missing character: There is no , in font nullfont! \citation{Seifert1996} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.109 ...Frenzel2004, Elstner2014, Spiegelman2020} +l.111 ...Frenzel2004, Elstner2014, Spiegelman2020} The SCC-DFTB potential f... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -13406,14 +12937,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Seifert1996' on page undefined on input line 109. +LaTeX Warning: Citation `Seifert1996' on page undefined on input line 111. Missing character: There is no , in font nullfont! \citation{Frenzel2004} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.109 ...Frenzel2004, Elstner2014, Spiegelman2020} +l.111 ...Frenzel2004, Elstner2014, Spiegelman2020} The SCC-DFTB potential f... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -13422,14 +12953,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Frenzel2004' on page undefined on input line 109. +LaTeX Warning: Citation `Frenzel2004' on page undefined on input line 111. Missing character: There is no , in font nullfont! \citation{Elstner2014} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.109 ...Frenzel2004, Elstner2014, Spiegelman2020} +l.111 ...Frenzel2004, Elstner2014, Spiegelman2020} The SCC-DFTB potential f... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -13438,14 +12969,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Elstner2014' on page undefined on input line 109. +LaTeX Warning: Citation `Elstner2014' on page undefined on input line 111. Missing character: There is no , in font nullfont! \citation{Spiegelman2020} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.109 ...Frenzel2004, Elstner2014, Spiegelman2020} +l.111 ...Frenzel2004, Elstner2014, Spiegelman2020} The SCC-DFTB potential f... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -13454,7 +12985,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Spiegelman2020' on page undefined on input line 109. +LaTeX Warning: Citation `Spiegelman2020' on page undefined on input line 111. Missing character: There is no ] in font nullfont! Missing character: There is no T in font nullfont! @@ -13528,7 +13059,7 @@ Missing character: There is no n in font nullfont! ! Undefined control sequence. ...ec:structure-methods' on page \thepage \space undefined\on@line . -l.109 ...wn in section \ref{sec:structure-methods} +l.111 ...wn in section \ref{sec:structure-methods} . The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -13538,46 +13069,46 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `sec:structure-methods' on page undefined on input li -ne 109. +ne 111. Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 109--110 +Overfull \hbox (20.0pt too wide) in paragraph at lines 111--112 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 109--110 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 111--112 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 109--110 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 111--112 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 109--110 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 111--112 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 109--110 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 111--112 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 109--110 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 111--112 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 109--110 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 111--112 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 109--110 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 111--112 [] [] @@ -13588,7 +13119,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.111 D +l.113 D FTB is an efficient tool to perform MD simulations, in particular add... You're in trouble here. Try typing to proceed. @@ -13726,7 +13257,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.111 ...Korchagina2017, Rapacioli2018, Simon2018} +l.113 ...Korchagina2017, Rapacioli2018, Simon2018} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -13735,14 +13266,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Simon2017' on page undefined on input line 111. +LaTeX Warning: Citation `Simon2017' on page undefined on input line 113. Missing character: There is no , in font nullfont! \citation{Korchagina2017} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.111 ...Korchagina2017, Rapacioli2018, Simon2018} +l.113 ...Korchagina2017, Rapacioli2018, Simon2018} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -13751,14 +13282,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Korchagina2017' on page undefined on input line 111. +LaTeX Warning: Citation `Korchagina2017' on page undefined on input line 113. Missing character: There is no , in font nullfont! \citation{Rapacioli2018} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.111 ...Korchagina2017, Rapacioli2018, Simon2018} +l.113 ...Korchagina2017, Rapacioli2018, Simon2018} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -13767,14 +13298,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Rapacioli2018' on page undefined on input line 111. +LaTeX Warning: Citation `Rapacioli2018' on page undefined on input line 113. Missing character: There is no , in font nullfont! \citation{Simon2018} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.111 ...Korchagina2017, Rapacioli2018, Simon2018} +l.113 ...Korchagina2017, Rapacioli2018, Simon2018} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -13783,7 +13314,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Simon2018' on page undefined on input line 111. +LaTeX Warning: Citation `Simon2018' on page undefined on input line 113. Missing character: There is no ] in font nullfont! Missing character: There is no T in font nullfont! @@ -13863,7 +13394,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.112 ...ed with a QM/MM scheme \cite{Warshel1976} +l.114 ...ed with a QM/MM scheme \cite{Warshel1976} whose details can be foun... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -13872,7 +13403,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Warshel1976' on page undefined on input line 112. +LaTeX Warning: Citation `Warshel1976' on page undefined on input line 114. Missing character: There is no ] in font nullfont! Missing character: There is no w in font nullfont! @@ -13920,7 +13451,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.112 ... original paper\cite{Cui2001, Iftner2014} +l.114 ... original paper\cite{Cui2001, Iftner2014} . The projectile argon is ... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -13929,14 +13460,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Cui2001' on page undefined on input line 112. +LaTeX Warning: Citation `Cui2001' on page undefined on input line 114. Missing character: There is no , in font nullfont! \citation{Iftner2014} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.112 ... original paper\cite{Cui2001, Iftner2014} +l.114 ... original paper\cite{Cui2001, Iftner2014} . The projectile argon is ... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -13945,7 +13476,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Iftner2014' on page undefined on input line 112. +LaTeX Warning: Citation `Iftner2014' on page undefined on input line 114. Missing character: There is no ] in font nullfont! Missing character: There is no . in font nullfont! @@ -14344,7 +13875,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.112 ...self-consistent procedure.\cite{Kukk2015} +l.114 ...self-consistent procedure.\cite{Kukk2015} The Fermi distribution al... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -14353,7 +13884,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Kukk2015' on page undefined on input line 112. +LaTeX Warning: Citation `Kukk2015' on page undefined on input line 114. Missing character: There is no ] in font nullfont! Missing character: There is no T in font nullfont! @@ -14454,7 +13985,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.112 ...e case of level crossing. \cite{Kukk2015} +l.114 ...e case of level crossing. \cite{Kukk2015} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -14463,7 +13994,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Kukk2015' on page undefined on input line 112. +LaTeX Warning: Citation `Kukk2015' on page undefined on input line 114. Missing character: There is no ] in font nullfont! Missing character: There is no I in font nullfont! @@ -14753,7 +14284,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.113 ...al computed mass spectra \cite{Simon2017} +l.115 ...al computed mass spectra \cite{Simon2017} . I also mention that the ... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -14762,7 +14293,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Simon2017' on page undefined on input line 113. +LaTeX Warning: Citation `Simon2017' on page undefined on input line 115. Missing character: There is no ] in font nullfont! Missing character: There is no . in font nullfont! @@ -15443,7 +14974,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.113 ...imon2017, Simon2018, Rapacioli2018atomic} +l.115 ...imon2017, Simon2018, Rapacioli2018atomic} . The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -15452,14 +14983,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Simon2017' on page undefined on input line 113. +LaTeX Warning: Citation `Simon2017' on page undefined on input line 115. Missing character: There is no , in font nullfont! \citation{Simon2018} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.113 ...imon2017, Simon2018, Rapacioli2018atomic} +l.115 ...imon2017, Simon2018, Rapacioli2018atomic} . The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -15468,14 +14999,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Simon2018' on page undefined on input line 113. +LaTeX Warning: Citation `Simon2018' on page undefined on input line 115. Missing character: There is no , in font nullfont! \citation{Rapacioli2018atomic} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.113 ...imon2017, Simon2018, Rapacioli2018atomic} +l.115 ...imon2017, Simon2018, Rapacioli2018atomic} . The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -15485,87 +15016,87 @@ and I'll forget about whatever was undefined. LaTeX Warning: Citation `Rapacioli2018atomic' on page undefined on input line -113. +115. Missing character: There is no ] in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 111--114 +Overfull \hbox (20.0pt too wide) in paragraph at lines 113--116 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 111--114 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 113--116 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 111--114 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 113--116 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 111--114 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 113--116 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 111--114 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 113--116 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 111--114 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 113--116 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 111--114 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 113--116 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 111--114 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 113--116 [] [] -Overfull \hbox (6.63892pt too wide) in paragraph at lines 111--114 +Overfull \hbox (6.63892pt too wide) in paragraph at lines 113--116 []$ [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 111--114 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 113--116 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 111--114 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 113--116 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 111--114 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 113--116 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 111--114 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 113--116 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 111--114 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 113--116 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 111--114 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 113--116 [] [] ! Undefined control sequence. -l.115 \subsection +l.117 \subsection {Collision Trajectories} \label{makingtrajectories} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -15580,7 +15111,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.115 \subsection{C +l.117 \subsection{C ollision Trajectories} \label{makingtrajectories} You're in trouble here. Try typing to proceed. If that doesn't work, type X to quit. @@ -15607,7 +15138,7 @@ Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 115--116 +Overfull \hbox (20.0pt too wide) in paragraph at lines 117--118 [] [] @@ -15618,7 +15149,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.117 T +l.119 T he preparation for the collisional trajectories for the collision of ... You're in trouble here. Try typing to proceed. @@ -15795,7 +15326,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...Reference `howinputs' on page \thepage \space undefined\on@line . -l.117 ...ith Ar is shown in Figure \ref{howinputs} +l.119 ...ith Ar is shown in Figure \ref{howinputs} . Starting from the optimi... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -15804,7 +15335,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `howinputs' on page undefined on input line 117. +LaTeX Warning: Reference `howinputs' on page undefined on input line 119. Missing character: There is no . in font nullfont! Missing character: There is no S in font nullfont! @@ -15846,7 +15377,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.117 ...mized Py$_2^+$ geometry \cite{Dontot2019} +l.119 ...mized Py$_2^+$ geometry \cite{Dontot2019} , a preliminary thermaliza... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -15855,7 +15386,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Dontot2019' on page undefined on input line 117. +LaTeX Warning: Citation `Dontot2019' on page undefined on input line 119. Missing character: There is no ] in font nullfont! Missing character: There is no , in font nullfont! @@ -15944,7 +15475,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.117 ...in thermostat \cite{Nose1984, Hoover1985} +l.119 ...in thermostat \cite{Nose1984, Hoover1985} ) is performed. Then, the ... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -15953,14 +15484,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Nose1984' on page undefined on input line 117. +LaTeX Warning: Citation `Nose1984' on page undefined on input line 119. Missing character: There is no , in font nullfont! \citation{Hoover1985} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.117 ...in thermostat \cite{Nose1984, Hoover1985} +l.119 ...in thermostat \cite{Nose1984, Hoover1985} ) is performed. Then, the ... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -15969,7 +15500,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Hoover1985' on page undefined on input line 117. +LaTeX Warning: Citation `Hoover1985' on page undefined on input line 119. Missing character: There is no ] in font nullfont! Missing character: There is no ) in font nullfont! @@ -16804,8 +16335,7 @@ Missing character: There is no g in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no , in font nullfont! -Missing character: There is no w in font nullfont! -Missing character: There is no e in font nullfont! +Missing character: There is no I in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no v in font nullfont! @@ -16951,7 +16481,7 @@ Missing character: There is no n in font nullfont! ! Undefined control sequence. ...ence `sec:MDanalysis' on page \thepage \space undefined\on@line . -l.121 ... be shown in section \ref{sec:MDanalysis} +l.123 ... be shown in section \ref{sec:MDanalysis} . The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -16960,123 +16490,236 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `sec:MDanalysis' on page undefined on input line 121. +LaTeX Warning: Reference `sec:MDanalysis' on page undefined on input line 123. Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 117--122 +Overfull \hbox (20.0pt too wide) in paragraph at lines 119--124 [] [] -Overfull \hbox (6.63892pt too wide) in paragraph at lines 117--122 +Overfull \hbox (6.63892pt too wide) in paragraph at lines 119--124 []$ [] -Overfull \hbox (6.63892pt too wide) in paragraph at lines 117--122 +Overfull \hbox (6.63892pt too wide) in paragraph at lines 119--124 []$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 117--122 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 119--124 [] [] -Overfull \hbox (6.63892pt too wide) in paragraph at lines 117--122 +Overfull \hbox (6.63892pt too wide) in paragraph at lines 119--124 []$ [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 117--122 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 119--124 [] [] -Overfull \hbox (4.44444pt too wide) in paragraph at lines 117--122 +Overfull \hbox (4.44444pt too wide) in paragraph at lines 119--124 \/cmr/m/n/10 ^^Se [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 117--122 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 119--124 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 117--122 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 119--124 [] [] -Overfull \hbox (6.63892pt too wide) in paragraph at lines 117--122 +Overfull \hbox (6.63892pt too wide) in paragraph at lines 119--124 []$ [] -Overfull \hbox (4.29166pt too wide) in paragraph at lines 117--122 +Overfull \hbox (4.29166pt too wide) in paragraph at lines 119--124 \OML/cmm/m/it/10 b$ [] -Overfull \hbox (7.50002pt too wide) in paragraph at lines 117--122 +Overfull \hbox (7.50002pt too wide) in paragraph at lines 119--124 []\/cmr/m/n/10 A [] -Overfull \hbox (4.29166pt too wide) in paragraph at lines 117--122 +Overfull \hbox (4.29166pt too wide) in paragraph at lines 119--124 \OML/cmm/m/it/10 b$ [] -Overfull \hbox (17.97237pt too wide) in paragraph at lines 117--122 +Overfull \hbox (17.97237pt too wide) in paragraph at lines 119--124 \OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (4.29166pt too wide) in paragraph at lines 117--122 +Overfull \hbox (4.29166pt too wide) in paragraph at lines 119--124 \OML/cmm/m/it/10 b$ [] -Overfull \hbox (7.50002pt too wide) in paragraph at lines 117--122 +Overfull \hbox (7.50002pt too wide) in paragraph at lines 119--124 []\/cmr/m/n/10 A [] -Overfull \hbox (7.50002pt too wide) in paragraph at lines 117--122 +Overfull \hbox (7.50002pt too wide) in paragraph at lines 119--124 []\/cmr/m/n/10 A [] -Overfull \hbox (6.63892pt too wide) in paragraph at lines 117--122 +Overfull \hbox (6.63892pt too wide) in paragraph at lines 119--124 []$ [] -Overfull \hbox (6.63892pt too wide) in paragraph at lines 117--122 +Overfull \hbox (6.63892pt too wide) in paragraph at lines 119--124 []$ [] -Overfull \hbox (6.63892pt too wide) in paragraph at lines 117--122 +Overfull \hbox (6.63892pt too wide) in paragraph at lines 119--124 []$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 117--122 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 119--124 [] [] +! LaTeX Error: The font size command \normalsize is not defined: + there is probably something wrong with the class file. + +See the LaTeX manual or LaTeX Companion for explanation. +Type H for immediate help. + ... + +l.124 + +Your command was ignored. +Type I to replace it with another command, +or to continue without it. + +[1 +! Undefined control sequence. + \newlabel{chap:collision}{{}{\thepage + }} +l.124 + +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + +\newlabel{chap:collision}{{}{}} +{/usr/local/texlive/2019/texmf-var/fonts/map/pdftex/updmap/pdftex.map} +! Undefined control sequence. + \newlabel{exp_cid}{{}{\thepage + }} +l.124 + +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + +\newlabel{exp_cid}{{}{}} +! Undefined control sequence. + \newlabel{principleTCID}{{}{\thepage + }} +l.124 + +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + +\newlabel{principleTCID}{{}{}} +! Undefined control sequence. + \newlabel{CIDcross}{{1}{\thepage + }} +l.124 + +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + +\newlabel{CIDcross}{{1}{}} +! Undefined control sequence. + \newlabel{EXPsetup}{{}{\thepage + }} +l.124 + +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + +\newlabel{EXPsetup}{{}{}} +! Undefined control sequence. + \newlabel{Comput_meth}{{}{\thepage + }} +l.124 + +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + +\newlabel{Comput_meth}{{}{}} +! Undefined control sequence. + \newlabel{DFTBpotential}{{}{\thepage + }} +l.124 + +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + +\newlabel{DFTBpotential}{{}{}} +! Undefined control sequence. + \newlabel{makingtrajectories}{{}{\thepage + }} +l.124 + +The control sequence at the end of the top line +of your error message was never \def'ed. If you have +misspelled it (e.g., `\hobx'), type `I' and the correct +spelling (e.g., `I\hbox'). Otherwise just continue, +and I'll forget about whatever was undefined. + +\newlabel{makingtrajectories}{{}{}} +] + ! LaTeX Error: Missing \begin{document}. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.123 I +l.125 I t should be noted that the quaternion was used for rotation process i... You're in trouble here. Try typing to proceed. @@ -17587,7 +17230,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.129 \begin{align} +l.131 \begin{align} Your command was ignored. Type I to replace it with another command, @@ -17597,7 +17240,7 @@ Missing character: There is no q in font nullfont! ! Missing $ inserted. $ -l.130 q_ +l.132 q_ 0^2+ q_1^2+ q_2^2+ q_3^2=1 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. @@ -17609,7 +17252,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.132 \end{align} +l.134 \end{align} Your command was ignored. Type I to replace it with another command, @@ -17618,7 +17261,7 @@ or to continue without it. ! Missing $ inserted. $ -l.132 \end{align} +l.134 \end{align} I've inserted something that you may have forgotten. (See the above.) @@ -17627,7 +17270,7 @@ really didn't forget anything, try typing `2' now; then my insertion and my current dilemma will both disappear. ! Undefined control sequence. -l.133 \figuremacrob +l.135 \figuremacrob {howinputs}{Schematic of the generation of the initial in... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -17688,200 +17331,87 @@ Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 123--134 +Overfull \hbox (20.0pt too wide) in paragraph at lines 125--136 [] [] -Overfull \hbox (18.78017pt too wide) in paragraph at lines 123--134 +Overfull \hbox (18.78017pt too wide) in paragraph at lines 125--136 \/cmr/m/n/10 3\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^@ [] -Overfull \hbox (5.00002pt too wide) in paragraph at lines 123--134 +Overfull \hbox (5.00002pt too wide) in paragraph at lines 125--136 \/cmr/m/n/10 6$ [] -Overfull \hbox (21.90279pt too wide) in paragraph at lines 123--134 +Overfull \hbox (21.90279pt too wide) in paragraph at lines 125--136 \/cmr/m/n/10 6\OML/cmm/m/it/10 N \OMS/cmsy/m/n/10 ^^@ [] -Overfull \hbox (5.00002pt too wide) in paragraph at lines 123--134 +Overfull \hbox (5.00002pt too wide) in paragraph at lines 125--136 \/cmr/m/n/10 6$ [] -Overfull \hbox (6.00235pt too wide) in paragraph at lines 123--134 +Overfull \hbox (6.00235pt too wide) in paragraph at lines 125--136 \OML/cmm/m/it/10 n$ [] -Overfull \hbox (9.12497pt too wide) in paragraph at lines 123--134 +Overfull \hbox (9.12497pt too wide) in paragraph at lines 125--136 \OML/cmm/m/it/10 N$ [] -Overfull \hbox (6.37216pt too wide) in paragraph at lines 123--134 +Overfull \hbox (6.37216pt too wide) in paragraph at lines 125--136 []$ [] -Overfull \hbox (49.13426pt too wide) in paragraph at lines 123--134 +Overfull \hbox (49.13426pt too wide) in paragraph at lines 125--136 \OML/cmm/m/it/10 q[]; q[]; q[]; q[]$ [] -Overfull \hbox (26.6921pt too wide) in paragraph at lines 123--134 +Overfull \hbox (26.6921pt too wide) in paragraph at lines 125--136 \OML/cmm/m/it/10 ^^R; ^^^; $ [] -Overfull \hbox (5.32216pt too wide) in paragraph at lines 123--134 +Overfull \hbox (5.32216pt too wide) in paragraph at lines 125--136 \OT1/cmr/bx/it/10 q [] -Overfull \hbox (12.26393pt too wide) in paragraph at lines 123--134 +Overfull \hbox (12.26393pt too wide) in paragraph at lines 125--136 [] \/cmr/m/n/10 + [] -Overfull \hbox (17.08684pt too wide) in paragraph at lines 123--134 +Overfull \hbox (17.08684pt too wide) in paragraph at lines 125--136 \OML/cmm/m/it/10 q[] \/cmr/m/n/10 + [] -Overfull \hbox (17.08684pt too wide) in paragraph at lines 123--134 +Overfull \hbox (17.08684pt too wide) in paragraph at lines 125--136 \OML/cmm/m/it/10 q[] \/cmr/m/n/10 + [] -Overfull \hbox (19.86455pt too wide) in paragraph at lines 123--134 +Overfull \hbox (19.86455pt too wide) in paragraph at lines 125--136 \OML/cmm/m/it/10 q[] \/cmr/m/n/10 = [] -Overfull \hbox (5.00002pt too wide) in paragraph at lines 123--134 +Overfull \hbox (5.00002pt too wide) in paragraph at lines 125--136 \/cmr/m/n/10 1[]$ [] - -! LaTeX Error: The font size command \normalsize is not defined: - there is probably something wrong with the class file. - -See the LaTeX manual or LaTeX Companion for explanation. -Type H for immediate help. - ... - -l.134 - -Your command was ignored. -Type I to replace it with another command, -or to continue without it. - -[1 ! Undefined control sequence. - \newlabel{chap:collision}{{}{\thepage - }} -l.134 - -The control sequence at the end of the top line -of your error message was never \def'ed. If you have -misspelled it (e.g., `\hobx'), type `I' and the correct -spelling (e.g., `I\hbox'). Otherwise just continue, -and I'll forget about whatever was undefined. - -\newlabel{chap:collision}{{}{}} -{/usr/local/texlive/2018/texmf-var/fonts/map/pdftex/updmap/pdftex.map} -! Undefined control sequence. - \newlabel{exp_cid}{{}{\thepage - }} -l.134 - -The control sequence at the end of the top line -of your error message was never \def'ed. If you have -misspelled it (e.g., `\hobx'), type `I' and the correct -spelling (e.g., `I\hbox'). Otherwise just continue, -and I'll forget about whatever was undefined. - -\newlabel{exp_cid}{{}{}} -! Undefined control sequence. - \newlabel{principleTCID}{{}{\thepage - }} -l.134 - -The control sequence at the end of the top line -of your error message was never \def'ed. If you have -misspelled it (e.g., `\hobx'), type `I' and the correct -spelling (e.g., `I\hbox'). Otherwise just continue, -and I'll forget about whatever was undefined. - -\newlabel{principleTCID}{{}{}} -! Undefined control sequence. - \newlabel{CIDcross}{{1}{\thepage - }} -l.134 - -The control sequence at the end of the top line -of your error message was never \def'ed. If you have -misspelled it (e.g., `\hobx'), type `I' and the correct -spelling (e.g., `I\hbox'). Otherwise just continue, -and I'll forget about whatever was undefined. - -\newlabel{CIDcross}{{1}{}} -! Undefined control sequence. - \newlabel{EXPsetup}{{}{\thepage - }} -l.134 - -The control sequence at the end of the top line -of your error message was never \def'ed. If you have -misspelled it (e.g., `\hobx'), type `I' and the correct -spelling (e.g., `I\hbox'). Otherwise just continue, -and I'll forget about whatever was undefined. - -\newlabel{EXPsetup}{{}{}} -! Undefined control sequence. - \newlabel{Comput_meth}{{}{\thepage - }} -l.134 - -The control sequence at the end of the top line -of your error message was never \def'ed. If you have -misspelled it (e.g., `\hobx'), type `I' and the correct -spelling (e.g., `I\hbox'). Otherwise just continue, -and I'll forget about whatever was undefined. - -\newlabel{Comput_meth}{{}{}} -! Undefined control sequence. - \newlabel{DFTBpotential}{{}{\thepage - }} -l.134 - -The control sequence at the end of the top line -of your error message was never \def'ed. If you have -misspelled it (e.g., `\hobx'), type `I' and the correct -spelling (e.g., `I\hbox'). Otherwise just continue, -and I'll forget about whatever was undefined. - -\newlabel{DFTBpotential}{{}{}} -! Undefined control sequence. - \newlabel{makingtrajectories}{{}{\thepage - }} -l.134 - -The control sequence at the end of the top line -of your error message was never \def'ed. If you have -misspelled it (e.g., `\hobx'), type `I' and the correct -spelling (e.g., `I\hbox'). Otherwise just continue, -and I'll forget about whatever was undefined. - -\newlabel{makingtrajectories}{{}{}} -] -! Undefined control sequence. -l.136 \subsection +l.138 \subsection {Trajectory Analysis} \label{trajecanylysis} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -17896,7 +17426,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.136 \subsection{T +l.138 \subsection{T rajectory Analysis} \label{trajecanylysis} You're in trouble here. Try typing to proceed. If that doesn't work, type X to quit. @@ -17920,7 +17450,7 @@ Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 136--137 +Overfull \hbox (20.0pt too wide) in paragraph at lines 138--139 [] [] @@ -17931,7 +17461,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.138 D +l.140 D uring the results collection, the final snapshot was extracted for e... You're in trouble here. Try typing to proceed. @@ -18858,82 +18388,82 @@ Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 138--141 +Overfull \hbox (20.0pt too wide) in paragraph at lines 140--143 [] [] -Overfull \hbox (6.63892pt too wide) in paragraph at lines 138--141 +Overfull \hbox (6.63892pt too wide) in paragraph at lines 140--143 []$ [] -Overfull \hbox (7.50002pt too wide) in paragraph at lines 138--141 +Overfull \hbox (7.50002pt too wide) in paragraph at lines 140--143 []\/cmr/m/n/10 A [] -Overfull \hbox (6.63892pt too wide) in paragraph at lines 138--141 +Overfull \hbox (6.63892pt too wide) in paragraph at lines 140--143 []$ [] -Overfull \hbox (7.50002pt too wide) in paragraph at lines 138--141 +Overfull \hbox (7.50002pt too wide) in paragraph at lines 140--143 []\/cmr/m/n/10 A [] -Overfull \hbox (5.52084pt too wide) in paragraph at lines 138--141 +Overfull \hbox (5.52084pt too wide) in paragraph at lines 140--143 \OML/cmm/m/it/10 k$ [] -Overfull \hbox (3.18057pt too wide) in paragraph at lines 138--141 +Overfull \hbox (3.18057pt too wide) in paragraph at lines 140--143 \OML/cmm/m/it/10 l$ [] -Overfull \hbox (8.78014pt too wide) in paragraph at lines 138--141 +Overfull \hbox (8.78014pt too wide) in paragraph at lines 140--143 \OML/cmm/m/it/10 m$ [] -Overfull \hbox (13.73608pt too wide) in paragraph at lines 138--141 +Overfull \hbox (13.73608pt too wide) in paragraph at lines 140--143 \OML/cmm/m/it/10 l \/cmr/m/n/10 = [] -Overfull \hbox (5.00002pt too wide) in paragraph at lines 138--141 +Overfull \hbox (5.00002pt too wide) in paragraph at lines 140--143 \/cmr/m/n/10 0$ [] -Overfull \hbox (16.07635pt too wide) in paragraph at lines 138--141 +Overfull \hbox (16.07635pt too wide) in paragraph at lines 140--143 \OML/cmm/m/it/10 k \/cmr/m/n/10 = [] -Overfull \hbox (21.55795pt too wide) in paragraph at lines 138--141 +Overfull \hbox (21.55795pt too wide) in paragraph at lines 140--143 \/cmr/m/n/10 2\OML/cmm/m/it/10 m \/cmr/m/n/10 + [] -Overfull \hbox (5.00002pt too wide) in paragraph at lines 138--141 +Overfull \hbox (5.00002pt too wide) in paragraph at lines 140--143 \/cmr/m/n/10 1$ [] -Overfull \hbox (5.52084pt too wide) in paragraph at lines 138--141 +Overfull \hbox (5.52084pt too wide) in paragraph at lines 140--143 \OML/cmm/m/it/10 k$ [] -Overfull \hbox (3.18057pt too wide) in paragraph at lines 138--141 +Overfull \hbox (3.18057pt too wide) in paragraph at lines 140--143 \OML/cmm/m/it/10 l$ [] -Overfull \hbox (8.78014pt too wide) in paragraph at lines 138--141 +Overfull \hbox (8.78014pt too wide) in paragraph at lines 140--143 \OML/cmm/m/it/10 m$ [] @@ -18944,7 +18474,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.142 T +l.144 T he opacity $P(b,E_{col})$, {\textit i.e.} the dissociation probabilit... You're in trouble here. Try typing to proceed. @@ -19176,22 +18706,22 @@ Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no : in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 142--144 +Overfull \hbox (20.0pt too wide) in paragraph at lines 144--146 [] [] -Overfull \hbox (42.29527pt too wide) in paragraph at lines 142--144 +Overfull \hbox (42.29527pt too wide) in paragraph at lines 144--146 \OML/cmm/m/it/10 P\/cmr/m/n/10 (\OML/cmm/m/it/10 b; E[]\/cmr/m/n/10 )$ [] -Overfull \hbox (3.06665pt too wide) in paragraph at lines 142--144 +Overfull \hbox (3.06665pt too wide) in paragraph at lines 144--146 \OT1/cmr/m/it/10 i [] -Overfull \hbox (245.07751pt too wide) in alignment at lines 144--148 +Overfull \hbox (245.07751pt too wide) in alignment at lines 146--150 [][][] [] [] @@ -19437,22 +18967,22 @@ Missing character: There is no r in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (26.8192pt too wide) in paragraph at lines 148--150 +Overfull \hbox (26.8192pt too wide) in paragraph at lines 150--152 $\OML/cmm/m/it/10 ^^Yb[]$ [] -Overfull \hbox (12.98267pt too wide) in paragraph at lines 148--150 +Overfull \hbox (12.98267pt too wide) in paragraph at lines 150--152 \OMS/cmsy/m/n/10 ^^@\OML/cmm/m/it/10 d$ [] -Overfull \hbox (18.70724pt too wide) in paragraph at lines 148--150 +Overfull \hbox (18.70724pt too wide) in paragraph at lines 150--152 \OMS/cmsy/m/n/10 ^^@\OML/cmm/m/it/10 ud$ [] ! Undefined control sequence. -l.151 \section +l.153 \section {\label{sec:collisionwUH}Dynamical Simulation of Collision-Ind... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -19467,7 +18997,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.151 \section{\label{sec:collisionwUH}D +l.153 \section{\label{sec:collisionwUH}D ynamical Simulation of Collision-Ind... You're in trouble here. Try typing to proceed. @@ -19555,12 +19085,12 @@ Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 151--152 +Overfull \hbox (20.0pt too wide) in paragraph at lines 153--154 [] [] ! Undefined control sequence. -l.153 \subsection +l.155 \subsection {Introduction} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -19575,7 +19105,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.153 \subsection{I +l.155 \subsection{I ntroduction} You're in trouble here. Try typing to proceed. If that doesn't work, type X to quit. @@ -19593,7 +19123,7 @@ Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 153--154 +Overfull \hbox (20.0pt too wide) in paragraph at lines 155--156 [] [] @@ -19604,8 +19134,8 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.155 M - otivated by the recent CID experiments conducted by Braud \textit{et ... +l.157 M + otivated by the recent CID experiments conducted by I. Braud \textit... You're in trouble here. Try typing to proceed. If that doesn't work, type X to quit. @@ -19655,6 +19185,8 @@ Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no y in font nullfont! +Missing character: There is no I in font nullfont! +Missing character: There is no . in font nullfont! Missing character: There is no B in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! @@ -19799,7 +19331,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.155 ...llision energy of 7.2~eV,\cite{Braud2019} +l.157 ...llision energy of 7.2~eV,\cite{Braud2019} the dynamical simulations... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -19808,7 +19340,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Braud2019' on page undefined on input line 155. +LaTeX Warning: Citation `Braud2019' on page undefined on input line 157. Missing character: There is no ] in font nullfont! Missing character: There is no t in font nullfont! @@ -20517,7 +20049,6 @@ Missing character: There is no % in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! -Missing character: There is no n in font nullfont! Missing character: There is no = in font nullfont! Missing character: There is no 4 in font nullfont! Missing character: There is no a in font nullfont! @@ -20683,7 +20214,7 @@ Missing character: There is no n in font nullfont! ! Undefined control sequence. ...ference `structureUH' on page \thepage \space undefined\on@line . -l.164 ...) clusters (see section \ref{structureUH} +l.166 ...) clusters (see section \ref{structureUH} ), which The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -20692,7 +20223,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `structureUH' on page undefined on input line 164. +LaTeX Warning: Reference `structureUH' on page undefined on input line 166. Missing character: There is no ) in font nullfont! Missing character: There is no , in font nullfont! @@ -21259,72 +20790,77 @@ Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no ? in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 155--172 +Overfull \hbox (20.0pt too wide) in paragraph at lines 157--174 [] [] -Overfull \hbox (7.92215pt too wide) in paragraph at lines 155--172 +Overfull \hbox (7.92215pt too wide) in paragraph at lines 157--174 \OT1/cmr/m/it/10 et [] -Overfull \hbox (10.73328pt too wide) in paragraph at lines 155--172 +Overfull \hbox (10.73328pt too wide) in paragraph at lines 157--174 \OT1/cmr/m/it/10 al. [] -Overfull \hbox (29.83345pt too wide) in paragraph at lines 155--172 +Overfull \hbox (29.83345pt too wide) in paragraph at lines 157--174 []$$[]$$[]$ [] -Overfull \hbox (4.48613pt too wide) in paragraph at lines 155--172 +Overfull \hbox (4.48613pt too wide) in paragraph at lines 157--174 []$ [] -Overfull \hbox (4.48613pt too wide) in paragraph at lines 155--172 +Overfull \hbox (4.48613pt too wide) in paragraph at lines 157--174 []$ [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 155--172 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 157--174 [] [] -Overfull \hbox (57.62408pt too wide) in paragraph at lines 155--172 +Overfull \hbox (46.54184pt too wide) in paragraph at lines 157--174 []$$[]$$[]$ [] -Overfull \hbox (40.9157pt too wide) in paragraph at lines 155--172 +Overfull \hbox (29.83345pt too wide) in paragraph at lines 157--174 []$$[]$$[]$ [] -Overfull \hbox (6.00235pt too wide) in paragraph at lines 155--172 +Overfull \hbox (6.00235pt too wide) in paragraph at lines 157--174 \OML/cmm/m/it/10 n$ [] -Overfull \hbox (6.00235pt too wide) in paragraph at lines 155--172 +Overfull \hbox (6.00235pt too wide) in paragraph at lines 157--174 \OML/cmm/m/it/10 n$ [] -Overfull \hbox (16.56837pt too wide) in paragraph at lines 155--172 +Overfull \hbox (6.00235pt too wide) in paragraph at lines 157--174 +\OML/cmm/m/it/10 n$ + [] + + +Overfull \hbox (16.56837pt too wide) in paragraph at lines 157--174 []$$[]$$[]$ [] -Overfull \hbox (6.00235pt too wide) in paragraph at lines 155--172 +Overfull \hbox (6.00235pt too wide) in paragraph at lines 157--174 \OML/cmm/m/it/10 n$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 155--172 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 157--174 [] [] @@ -21335,7 +20871,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.173 T +l.175 T o answer these questions, this simulations present a complete MD stud... You're in trouble here. Try typing to proceed. @@ -21481,7 +21017,7 @@ Missing character: There is no n in font nullfont! ! Undefined control sequence. ...eference `resul_disc' on page \thepage \space undefined\on@line . -l.173 ...h an argon atom. Section~\ref{resul_disc} +l.175 ...h an argon atom. Section~\ref{resul_disc} discusses the statistical... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -21490,7 +21026,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `resul_disc' on page undefined on input line 173. +LaTeX Warning: Reference `resul_disc' on page undefined on input line 175. Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! @@ -21856,7 +21392,7 @@ Missing character: There is no n in font nullfont! ! Undefined control sequence. ...ng: Reference `Concl' on page \thepage \space undefined\on@line . -l.174 ...mes are summarized in section~\ref{Concl} +l.176 ...mes are summarized in section~\ref{Concl} . The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -21865,36 +21401,36 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `Concl' on page undefined on input line 174. +LaTeX Warning: Reference `Concl' on page undefined on input line 176. Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 173--175 +Overfull \hbox (20.0pt too wide) in paragraph at lines 175--177 [] [] -Overfull \hbox (57.62408pt too wide) in paragraph at lines 173--175 +Overfull \hbox (46.54184pt too wide) in paragraph at lines 175--177 []$$[]$$[]$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 173--175 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 175--177 [] [] -Overfull \hbox (6.00235pt too wide) in paragraph at lines 173--175 +Overfull \hbox (6.00235pt too wide) in paragraph at lines 175--177 \OML/cmm/m/it/10 n$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 173--175 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 175--177 [] [] ! Undefined control sequence. -l.177 \subsection +l.179 \subsection {Results and Discussion} \label{resul_disc} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -21909,7 +21445,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.177 \subsection{R +l.179 \subsection{R esults and Discussion} \label{resul_disc} You're in trouble here. Try typing to proceed. If that doesn't work, type X to quit. @@ -21935,12 +21471,12 @@ Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 177--178 +Overfull \hbox (20.0pt too wide) in paragraph at lines 179--180 [] [] ! Undefined control sequence. -l.180 \subsubsection +l.182 \subsubsection {Statistical Convergence} \label{convergence} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -21955,7 +21491,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.180 \subsubsection{S +l.182 \subsubsection{S tatistical Convergence} \label{convergence} You're in trouble here. Try typing to proceed. If that doesn't work, type X to quit. @@ -21983,7 +21519,7 @@ Missing character: There is no n in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no e in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 180--181 +Overfull \hbox (20.0pt too wide) in paragraph at lines 182--183 [] [] @@ -21994,7 +21530,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.182 I +l.184 I n order to ensure that the statistical convergence is reached in the ... You're in trouble here. Try typing to proceed. @@ -22234,7 +21770,7 @@ Missing character: There is no n in font nullfont! ! Undefined control sequence. ... `makingtrajectories' on page \thepage \space undefined\on@line . -l.183 ...ribed in section \ref{makingtrajectories} +l.185 ...ribed in section \ref{makingtrajectories} . The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -22244,7 +21780,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `makingtrajectories' on page undefined on input line -183. +185. Missing character: There is no . in font nullfont! Missing character: There is no A in font nullfont! @@ -22288,7 +21824,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...Reference `3b-sphere' on page \thepage \space undefined\on@line . -l.184 ...res a, b and c in Figure ~\ref{3b-sphere} +l.186 ...res a, b and c in Figure ~\ref{3b-sphere} represent 200, 400 and 60... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -22297,7 +21833,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `3b-sphere' on page undefined on input line 184. +LaTeX Warning: Reference `3b-sphere' on page undefined on input line 186. Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! @@ -22653,7 +22189,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...Reference `3b-sphere' on page \thepage \space undefined\on@line . -l.184 ...ated. Picture d in Figure~\ref{3b-sphere} +l.186 ...ated. Picture d in Figure~\ref{3b-sphere} presents 200 random argon... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -22662,7 +22198,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `3b-sphere' on page undefined on input line 184. +LaTeX Warning: Reference `3b-sphere' on page undefined on input line 186. Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! @@ -22802,7 +22338,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...eference `12f-sphere' on page \thepage \space undefined\on@line . -l.184 ... are displayed in Figure \ref{12f-sphere} +l.186 ... are displayed in Figure \ref{12f-sphere} . These Figures demonstrat... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -22811,7 +22347,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `12f-sphere' on page undefined on input line 184. +LaTeX Warning: Reference `12f-sphere' on page undefined on input line 186. Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! @@ -22956,52 +22492,52 @@ Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 182--185 +Overfull \hbox (20.0pt too wide) in paragraph at lines 184--187 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 182--185 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 184--187 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 182--185 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 184--187 [] [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 182--185 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 184--187 []$$[]$$[]$ [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 182--185 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 184--187 []$$[]$$[]$ [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 182--185 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 184--187 []$$[]$$[]$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 182--185 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 184--187 [] [] -Overfull \hbox (19.5973pt too wide) in paragraph at lines 182--185 +Overfull \hbox (19.5973pt too wide) in paragraph at lines 184--187 []$$[]$$[]$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 182--185 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 184--187 [] [] ! Undefined control sequence. -l.186 \figuremacro +l.188 \figuremacro {3b-sphere}{Schematic representation of random argon orien... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -23016,7 +22552,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.186 \figuremacro{3 +l.188 \figuremacro{3 b-sphere}{Schematic representation of random argon orien... You're in trouble here. Try typing to proceed. @@ -23299,17 +22835,17 @@ Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 186--187 +Overfull \hbox (20.0pt too wide) in paragraph at lines 188--189 [] [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 186--187 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 188--189 []$$[]$$[]$ [] ! Undefined control sequence. -l.188 \figuremacro +l.190 \figuremacro {12f-sphere}{Schematic representation of random argon orie... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -23324,7 +22860,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.188 \figuremacro{1 +l.190 \figuremacro{1 2f-sphere}{Schematic representation of random argon orie... You're in trouble here. Try typing to proceed. @@ -23613,12 +23149,12 @@ Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 188--189 +Overfull \hbox (20.0pt too wide) in paragraph at lines 190--191 [] [] -Overfull \hbox (19.5973pt too wide) in paragraph at lines 188--189 +Overfull \hbox (19.5973pt too wide) in paragraph at lines 190--191 []$$[]$$[]$ [] @@ -23629,7 +23165,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.190 I +l.192 I n addition, to confirm that statistical convergence is reached for th... You're in trouble here. Try typing to proceed. @@ -23728,7 +23264,7 @@ Missing character: There is no s in font nullfont! ! Undefined control sequence. ...ing: Reference `time' on page \thepage \space undefined\on@line . -l.190 ...operties discussed in sections \ref{time} +l.192 ...operties discussed in sections \ref{time} , \ref{small}, \ref{large}... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -23737,13 +23273,13 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `time' on page undefined on input line 190. +LaTeX Warning: Reference `time' on page undefined on input line 192. Missing character: There is no , in font nullfont! ! Undefined control sequence. ...ng: Reference `small' on page \thepage \space undefined\on@line . -l.190 ...ussed in sections \ref{time}, \ref{small} +l.192 ...ussed in sections \ref{time}, \ref{small} , \ref{large}, and \ref{ma... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -23752,13 +23288,13 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `small' on page undefined on input line 190. +LaTeX Warning: Reference `small' on page undefined on input line 192. Missing character: There is no , in font nullfont! ! Undefined control sequence. ...ng: Reference `large' on page \thepage \space undefined\on@line . -l.190 ...ions \ref{time}, \ref{small}, \ref{large} +l.192 ...ions \ref{time}, \ref{small}, \ref{large} , and \ref{mass-spectra}, ... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -23767,7 +23303,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `large' on page undefined on input line 190. +LaTeX Warning: Reference `large' on page undefined on input line 192. Missing character: There is no , in font nullfont! Missing character: There is no a in font nullfont! @@ -23776,7 +23312,7 @@ Missing character: There is no d in font nullfont! ! Undefined control sequence. ...erence `mass-spectra' on page \thepage \space undefined\on@line . -l.190 ...all}, \ref{large}, and \ref{mass-spectra} +l.192 ...all}, \ref{large}, and \ref{mass-spectra} , Tables~\ref{tab:converge... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -23785,7 +23321,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `mass-spectra' on page undefined on input line 190. +LaTeX Warning: Reference `mass-spectra' on page undefined on input line 192. Missing character: There is no , in font nullfont! Missing character: There is no T in font nullfont! @@ -23797,7 +23333,7 @@ Missing character: There is no s in font nullfont! ! Undefined control sequence. ... `tab:converge-1w-5w' on page \thepage \space undefined\on@line . -l.190 ...spectra}, Tables~\ref{tab:converge-1w-5w} +l.192 ...spectra}, Tables~\ref{tab:converge-1w-5w} and \ref{tab:converge-6w-... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -23807,7 +23343,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `tab:converge-1w-5w' on page undefined on input line -190. +192. Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! @@ -23815,7 +23351,7 @@ Missing character: There is no d in font nullfont! ! Undefined control sequence. ...`tab:converge-6w-12w' on page \thepage \space undefined\on@line . -l.190 ...erge-1w-5w} and \ref{tab:converge-6w-12w} +l.192 ...erge-1w-5w} and \ref{tab:converge-6w-12w} present the $P_{NUL}$ inv... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -23825,7 +23361,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `tab:converge-6w-12w' on page undefined on input line - 190. + 192. Missing character: There is no p in font nullfont! Missing character: There is no r in font nullfont! @@ -23871,7 +23407,7 @@ Missing character: There is no a in font nullfont! ! Undefined control sequence. ...ing: Reference `PNUL' on page \thepage \space undefined\on@line . -l.190 ...ved from the following formula \ref{PNUL} +l.192 ...ved from the following formula \ref{PNUL} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -23880,55 +23416,55 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `PNUL' on page undefined on input line 190. +LaTeX Warning: Reference `PNUL' on page undefined on input line 192. -Overfull \hbox (20.0pt too wide) in paragraph at lines 190--191 +Overfull \hbox (20.0pt too wide) in paragraph at lines 192--193 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 190--191 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 192--193 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 190--191 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 192--193 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 190--191 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 192--193 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 190--191 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 192--193 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 190--191 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 192--193 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 190--191 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 192--193 [] [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 190--191 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 192--193 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 190--191 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 192--193 [] [] -Overfull \hbox (300.60359pt too wide) in alignment at lines 191--197 +Overfull \hbox (300.60359pt too wide) in alignment at lines 193--199 [][][] [] [] @@ -24120,17 +23656,17 @@ Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (23.31656pt too wide) in paragraph at lines 197--199 +Overfull \hbox (23.31656pt too wide) in paragraph at lines 199--201 $\OML/cmm/m/it/10 ^^[[]$ [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 197--199 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 199--201 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (57.62408pt too wide) in paragraph at lines 197--199 +Overfull \hbox (46.54184pt too wide) in paragraph at lines 199--201 []$$[]$$[]$ [] @@ -24141,7 +23677,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.200 W +l.202 W hatever the considered isomer, the three $P_{NUL}$ and $\sigma_{frag}... You're in trouble here. Try typing to proceed. @@ -24660,22 +24196,22 @@ Missing character: There is no z in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 200--202 +Overfull \hbox (20.0pt too wide) in paragraph at lines 202--204 [] [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 200--202 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 202--204 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (23.31656pt too wide) in paragraph at lines 200--202 +Overfull \hbox (23.31656pt too wide) in paragraph at lines 202--204 \OML/cmm/m/it/10 ^^[[]$ [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 200--202 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 202--204 \OML/cmm/m/it/10 P[]$ [] @@ -24686,7 +24222,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.211 \begin{table} +l.213 \begin{table} Your command was ignored. Type I to replace it with another command, @@ -24699,13 +24235,13 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.212 \begin{center} +l.214 \begin{center} You're in trouble here. Try typing to proceed. If that doesn't work, type X to quit. -Overfull \hbox (20.0pt too wide) in paragraph at lines 212--212 +Overfull \hbox (20.0pt too wide) in paragraph at lines 214--214 [] [] @@ -24716,7 +24252,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.213 \caption +l.215 \caption {The proportions of $P_{NUL}$ and $\sigma_{frag}$ of firs... You're in trouble here. Try typing to proceed. @@ -24871,7 +24407,7 @@ Missing character: There is no . in font nullfont! ! Undefined control sequence. \boldm -l.217 ...f{Simu} & \textbf{\boldm{$P_{NUL}$} (\%)} +l.219 ...f{Simu} & \textbf{\boldm{$P_{NUL}$} (\%)} & \textbf{\boldm{$\sigma_... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -24882,7 +24418,7 @@ and I'll forget about whatever was undefined. ! Undefined control sequence. \boldm -l.217 ...\textbf{\boldm{$\sigma_{frag}$ (Å$^2$)}} +l.219 ...\textbf{\boldm{$\sigma_{frag}$ (Å$^2$)}} \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -24893,7 +24429,7 @@ and I'll forget about whatever was undefined. ! Undefined control sequence. \rowcolor -l.219 \rowcolor +l.221 \rowcolor {lightgray} \bf{1a} & 200 & 0.1 & 28.4 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -24911,7 +24447,7 @@ Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! ! Undefined control sequence. -l.219 \rowcolor{lightgray} \bf +l.221 \rowcolor{lightgray} \bf {1a} & 200 & 0.1 & 28.4 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -24934,7 +24470,7 @@ Missing character: There is no 4 in font nullfont! ! Undefined control sequence. \rowcolor -l.220 \rowcolor +l.222 \rowcolor {lightgray} \bf{1a} & 400 & 0.1 & 28.3 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -24952,7 +24488,7 @@ Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! ! Undefined control sequence. -l.220 \rowcolor{lightgray} \bf +l.222 \rowcolor{lightgray} \bf {1a} & 400 & 0.1 & 28.3 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -24975,7 +24511,7 @@ Missing character: There is no 3 in font nullfont! ! Undefined control sequence. \rowcolor -l.221 \rowcolor +l.223 \rowcolor {lightgray} \bf{1a} & 600 & 0.2 & 28.9 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -24993,7 +24529,7 @@ Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! ! Undefined control sequence. -l.221 \rowcolor{lightgray} \bf +l.223 \rowcolor{lightgray} \bf {1a} & 600 & 0.2 & 28.9 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -25052,7 +24588,7 @@ Missing character: There is no 9 in font nullfont! ! Undefined control sequence. \rowcolor -l.225 \rowcolor +l.227 \rowcolor {lightgray} 2a & 200 & 0.0 & 35.9 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -25084,7 +24620,7 @@ Missing character: There is no 9 in font nullfont! ! Undefined control sequence. \rowcolor -l.226 \rowcolor +l.228 \rowcolor {lightgray} 2a & 400 & 0.0 & 36.5 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -25116,7 +24652,7 @@ Missing character: There is no 5 in font nullfont! ! Undefined control sequence. \rowcolor -l.227 \rowcolor +l.229 \rowcolor {lightgray} 2a & 600 & 0.0 & 36.3 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -25148,7 +24684,7 @@ Missing character: There is no 3 in font nullfont! ! Undefined control sequence. \bf -l.228 \bf +l.230 \bf {2b} & 200 & 0.0 & 34.7 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -25171,7 +24707,7 @@ Missing character: There is no 7 in font nullfont! ! Undefined control sequence. \bf -l.229 \bf +l.231 \bf {2b} & 400 & 0.1 & 34.8 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -25194,7 +24730,7 @@ Missing character: There is no 8 in font nullfont! ! Undefined control sequence. \bf -l.230 \bf +l.232 \bf {2b} & 600 & 0.1 & 34.9 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -25217,7 +24753,7 @@ Missing character: There is no 9 in font nullfont! ! Undefined control sequence. \rowcolor -l.231 \rowcolor +l.233 \rowcolor {lightgray} 3a & 200 & 5.4 & 37.4 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -25249,7 +24785,7 @@ Missing character: There is no 4 in font nullfont! ! Undefined control sequence. \rowcolor -l.232 \rowcolor +l.234 \rowcolor {lightgray} 3a & 400 & 5.2 & 36.2 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -25281,7 +24817,7 @@ Missing character: There is no 2 in font nullfont! ! Undefined control sequence. \rowcolor -l.233 \rowcolor +l.235 \rowcolor {lightgray} 3a & 600 & 5.7 & 36.3 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -25313,7 +24849,7 @@ Missing character: There is no 3 in font nullfont! ! Undefined control sequence. \bf -l.234 \bf +l.236 \bf {3b} & 200 & 0.0 & 41.2 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -25336,7 +24872,7 @@ Missing character: There is no 2 in font nullfont! ! Undefined control sequence. \bf -l.235 \bf +l.237 \bf {3b} & 400 & 0.0 & 41.5 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -25359,7 +24895,7 @@ Missing character: There is no 5 in font nullfont! ! Undefined control sequence. \bf -l.236 \bf +l.238 \bf {3b} & 600 & 0.0 & 41.9 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -25382,7 +24918,7 @@ Missing character: There is no 9 in font nullfont! ! Undefined control sequence. \rowcolor -l.237 \rowcolor +l.239 \rowcolor {lightgray} 4a & 200 & 26.9 & 40.1 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -25415,7 +24951,7 @@ Missing character: There is no 1 in font nullfont! ! Undefined control sequence. \rowcolor -l.238 \rowcolor +l.240 \rowcolor {lightgray} 4a & 400 & 28.2 & 40.3 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -25448,7 +24984,7 @@ Missing character: There is no 3 in font nullfont! ! Undefined control sequence. \rowcolor -l.239 \rowcolor +l.241 \rowcolor {lightgray} 4a & 600 & 29.4 & 40.1 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -25481,7 +25017,7 @@ Missing character: There is no 1 in font nullfont! ! Undefined control sequence. \bf -l.240 \bf +l.242 \bf {4b} & 200 & 2.7 & 45.3 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -25504,7 +25040,7 @@ Missing character: There is no 3 in font nullfont! ! Undefined control sequence. \bf -l.241 \bf +l.243 \bf {4b} & 400 & 2.6 & 45.6 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -25527,7 +25063,7 @@ Missing character: There is no 6 in font nullfont! ! Undefined control sequence. \bf -l.242 \bf +l.244 \bf {4b} & 600 & 2.6 & 45.2 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -25550,7 +25086,7 @@ Missing character: There is no 2 in font nullfont! ! Undefined control sequence. \rowcolor -l.243 \rowcolor +l.245 \rowcolor {lightgray} 5a & 200 & 37.2 & 45.7 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -25583,7 +25119,7 @@ Missing character: There is no 7 in font nullfont! ! Undefined control sequence. \rowcolor -l.244 \rowcolor +l.246 \rowcolor {lightgray} 5a & 400 & 37.8 & 46.1 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -25616,7 +25152,7 @@ Missing character: There is no 1 in font nullfont! ! Undefined control sequence. \rowcolor -l.245 \rowcolor +l.247 \rowcolor {lightgray} 5a & 600 & 38.2 & 46.6 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -25649,7 +25185,7 @@ Missing character: There is no 6 in font nullfont! ! Undefined control sequence. \bf -l.246 \bf +l.248 \bf {5d} & 200 & 0.1 & 47.3 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -25672,7 +25208,7 @@ Missing character: There is no 3 in font nullfont! ! Undefined control sequence. \bf -l.247 \bf +l.249 \bf {5d} & 400 & 0.1 & 47.3 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -25695,7 +25231,7 @@ Missing character: There is no 3 in font nullfont! ! Undefined control sequence. \bf -l.248 \bf +l.250 \bf {5d} & 600 & 0.1 & 47.5 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -25716,27 +25252,27 @@ Missing character: There is no 7 in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no 5 in font nullfont! -Overfull \hbox (25.68921pt too wide) in paragraph at lines 213--251 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 215--253 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (23.31656pt too wide) in paragraph at lines 213--251 +Overfull \hbox (23.31656pt too wide) in paragraph at lines 215--253 \OML/cmm/m/it/10 ^^[[]$ [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 213--251 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 215--253 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (25.84732pt too wide) in paragraph at lines 213--251 +Overfull \hbox (25.84732pt too wide) in paragraph at lines 215--253 []$$[]$$[]$ [] -Overfull \hbox (159.46495pt too wide) in paragraph at lines 213--251 +Overfull \hbox (159.46495pt too wide) in paragraph at lines 215--253 [] [] @@ -25747,7 +25283,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.252 \end{table} +l.254 \end{table} Your command was ignored. Type I to replace it with another command, @@ -25760,14 +25296,14 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.255 \begin{table} +l.257 \begin{table} Your command was ignored. Type I to replace it with another command, or to continue without it. -Overfull \hbox (20.0pt too wide) in paragraph at lines 256--256 +Overfull \hbox (20.0pt too wide) in paragraph at lines 258--258 [] [] @@ -25778,7 +25314,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.257 \caption +l.259 \caption {The proportions of $P_{NUL}$ and $\sigma_{frag}$ of firs... You're in trouble here. Try typing to proceed. @@ -25933,7 +25469,7 @@ Missing character: There is no . in font nullfont! ! Undefined control sequence. \boldm -l.261 ...f{Simu} & \textbf{\boldm{$P_{NUL}$} (\%)} +l.263 ...f{Simu} & \textbf{\boldm{$P_{NUL}$} (\%)} & \textbf{\boldm{$\sigma_... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -25944,7 +25480,7 @@ and I'll forget about whatever was undefined. ! Undefined control sequence. \boldm -l.261 ...\textbf{\boldm{$\sigma_{frag}$ (Å$^2$)}} +l.263 ...\textbf{\boldm{$\sigma_{frag}$ (Å$^2$)}} \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -25955,7 +25491,7 @@ and I'll forget about whatever was undefined. ! Undefined control sequence. \rowcolor -l.263 \rowcolor +l.265 \rowcolor {lightgray} 6a & 200 & 38.0 & 46.6 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -25988,7 +25524,7 @@ Missing character: There is no 6 in font nullfont! ! Undefined control sequence. \rowcolor -l.264 \rowcolor +l.266 \rowcolor {lightgray} 6a & 400 & 38.0 & 45.6 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -26021,7 +25557,7 @@ Missing character: There is no 6 in font nullfont! ! Undefined control sequence. \rowcolor -l.265 \rowcolor +l.267 \rowcolor {lightgray} 6a & 600 & 39.3 & 45.8 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -26054,7 +25590,7 @@ Missing character: There is no 8 in font nullfont! ! Undefined control sequence. \bf -l.266 \bf +l.268 \bf {6f} & 200 & 18.9 & 54.2 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -26078,7 +25614,7 @@ Missing character: There is no 2 in font nullfont! ! Undefined control sequence. \bf -l.267 \bf +l.269 \bf {6f} & 400 & 19.0 & 55.2 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -26102,7 +25638,7 @@ Missing character: There is no 2 in font nullfont! ! Undefined control sequence. \bf -l.268 \bf +l.270 \bf {6f} & 600 & 18.5 & 55.0 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -26126,7 +25662,7 @@ Missing character: There is no 0 in font nullfont! ! Undefined control sequence. \rowcolor -l.269 \rowcolor +l.271 \rowcolor {lightgray} 7a & 200 & 29.5 & 54.8 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -26159,7 +25695,7 @@ Missing character: There is no 8 in font nullfont! ! Undefined control sequence. \rowcolor -l.270 \rowcolor +l.272 \rowcolor {lightgray} 7a & 400 & 31.3 & 53.4 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -26192,7 +25728,7 @@ Missing character: There is no 4 in font nullfont! ! Undefined control sequence. \rowcolor -l.271 \rowcolor +l.273 \rowcolor {lightgray} 7a & 600 & 31.3 & 53.4 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -26225,7 +25761,7 @@ Missing character: There is no 4 in font nullfont! ! Undefined control sequence. \bf -l.272 \bf +l.274 \bf {7d} & 200 & 22.6 & 55.3 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -26249,7 +25785,7 @@ Missing character: There is no 3 in font nullfont! ! Undefined control sequence. \bf -l.273 \bf +l.275 \bf {7d} & 400 & 22.9 & 54.3 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -26273,7 +25809,7 @@ Missing character: There is no 3 in font nullfont! ! Undefined control sequence. \bf -l.274 \bf +l.276 \bf {7d} & 600 & 23.0 & 54.0 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -26297,7 +25833,7 @@ Missing character: There is no 0 in font nullfont! ! Undefined control sequence. \rowcolor -l.275 \rowcolor +l.277 \rowcolor {lightgray} 11a & 200 & 26.7 & 53.8 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -26331,7 +25867,7 @@ Missing character: There is no 8 in font nullfont! ! Undefined control sequence. \rowcolor -l.276 \rowcolor +l.278 \rowcolor {lightgray} 11a & 400 & 28.2 & 53.5 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -26365,7 +25901,7 @@ Missing character: There is no 5 in font nullfont! ! Undefined control sequence. \rowcolor -l.277 \rowcolor +l.279 \rowcolor {lightgray} 11a & 600 & 28.3 & 52.9 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -26399,7 +25935,7 @@ Missing character: There is no 9 in font nullfont! ! Undefined control sequence. \bf -l.278 \bf +l.280 \bf {11d} & 200 & 14.5 & 55.2 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -26424,7 +25960,7 @@ Missing character: There is no 2 in font nullfont! ! Undefined control sequence. \bf -l.279 \bf +l.281 \bf {11d} & 400 & 15.4 & 56.1 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -26449,7 +25985,7 @@ Missing character: There is no 1 in font nullfont! ! Undefined control sequence. \bf -l.280 \bf +l.282 \bf {11d} & 600 & 15.6 & 56.5 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -26474,7 +26010,7 @@ Missing character: There is no 5 in font nullfont! ! Undefined control sequence. \rowcolor -l.281 \rowcolor +l.283 \rowcolor {lightgray} 12a & 200 & 8.0 & 59.2 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -26507,7 +26043,7 @@ Missing character: There is no 2 in font nullfont! ! Undefined control sequence. \rowcolor -l.282 \rowcolor +l.284 \rowcolor {lightgray} 12a & 400 & 7.5 & 60.5 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -26540,7 +26076,7 @@ Missing character: There is no 5 in font nullfont! ! Undefined control sequence. \rowcolor -l.283 \rowcolor +l.285 \rowcolor {lightgray} 12a & 600 & 7.6 & 60.2 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -26573,7 +26109,7 @@ Missing character: There is no 2 in font nullfont! ! Undefined control sequence. \bf -l.284 \bf +l.286 \bf {12c} & 200 & 10.4 & 55.3 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -26598,7 +26134,7 @@ Missing character: There is no 3 in font nullfont! ! Undefined control sequence. \bf -l.285 \bf +l.287 \bf {12c} & 400 & 10.8 & 55.8 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -26623,7 +26159,7 @@ Missing character: There is no 8 in font nullfont! ! Undefined control sequence. \bf -l.286 \bf +l.288 \bf {12c} & 600 & 10.8 & 55.4 \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -26646,27 +26182,27 @@ Missing character: There is no 5 in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no 4 in font nullfont! -Overfull \hbox (25.68921pt too wide) in paragraph at lines 257--289 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 259--291 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (23.31656pt too wide) in paragraph at lines 257--289 +Overfull \hbox (23.31656pt too wide) in paragraph at lines 259--291 \OML/cmm/m/it/10 ^^[[]$ [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 257--289 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 259--291 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (42.66682pt too wide) in paragraph at lines 257--289 +Overfull \hbox (42.66682pt too wide) in paragraph at lines 259--291 []$$[]$$[]$ [] -Overfull \hbox (159.46495pt too wide) in paragraph at lines 257--289 +Overfull \hbox (159.46495pt too wide) in paragraph at lines 259--291 [] [] @@ -26677,14 +26213,14 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.290 \end{table} +l.292 \end{table} Your command was ignored. Type I to replace it with another command, or to continue without it. ! Undefined control sequence. -l.293 \subsection +l.295 \subsection {Time-Dependent Proportion of Fragments} \label{time} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -26728,7 +26264,7 @@ Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 293--294 +Overfull \hbox (20.0pt too wide) in paragraph at lines 295--296 [] [] @@ -26892,7 +26428,7 @@ Missing character: There is no s in font nullfont! ! Undefined control sequence. ...`proporEachFrag-1a2a' on page \thepage \space undefined\on@line . -l.295 ... size, Figures~\ref{proporEachFrag-1a2a} +l.297 ... size, Figures~\ref{proporEachFrag-1a2a} -\ref{proporEachFrag-7d12c... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -26902,13 +26438,13 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `proporEachFrag-1a2a' on page undefined on input line - 295. + 297. Missing character: There is no - in font nullfont! ! Undefined control sequence. ...rEachFrag-7d12c-zoom' on page \thepage \space undefined\on@line . -l.295 ...rag-1a2a}-\ref{proporEachFrag-7d12c-zoom} +l.297 ...rag-1a2a}-\ref{proporEachFrag-7d12c-zoom} display the time-dependen... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -26918,7 +26454,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `proporEachFrag-7d12c-zoom' on page undefined on inpu -t line 295. +t line 297. Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! @@ -27029,17 +26565,17 @@ Missing character: There is no U in font nullfont! Missing character: There is no H in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 295--296 +Overfull \hbox (20.0pt too wide) in paragraph at lines 297--298 [] [] -Overfull \hbox (21.7221pt too wide) in paragraph at lines 295--296 +Overfull \hbox (21.7221pt too wide) in paragraph at lines 297--298 [][] [] -Overfull \hbox (46.54184pt too wide) in paragraph at lines 295--296 +Overfull \hbox (46.54184pt too wide) in paragraph at lines 297--298 []$$[]$$[]$ [] @@ -27283,7 +26819,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...rEachFrag-7a12a-zoom' on page \thepage \space undefined\on@line . -l.298 ...in Figure \ref{proporEachFrag-7a12a-zoom} +l.300 ...in Figure \ref{proporEachFrag-7a12a-zoom} . This corresponds to the ... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -27293,7 +26829,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `proporEachFrag-7a12a-zoom' on page undefined on inpu -t line 298. +t line 300. Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! @@ -27387,7 +26923,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...rEachFrag-7a12a-zoom' on page \thepage \space undefined\on@line . -l.299 From Figure~\ref{proporEachFrag-7a12a-zoom} +l.301 From Figure~\ref{proporEachFrag-7a12a-zoom} , it is clear that for both... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -27397,7 +26933,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `proporEachFrag-7a12a-zoom' on page undefined on inpu -t line 299. +t line 301. Missing character: There is no , in font nullfont! Missing character: There is no i in font nullfont! @@ -28352,7 +27888,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...rEachFrag-7d12c-zoom' on page \thepage \space undefined\on@line . -l.302 ...in Figure \ref{proporEachFrag-7d12c-zoom} +l.304 ...in Figure \ref{proporEachFrag-7d12c-zoom} display similar behavior ... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -28362,7 +27898,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `proporEachFrag-7d12c-zoom' on page undefined on inpu -t line 302. +t line 304. Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! @@ -28428,7 +27964,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...rEachFrag-7a12a-zoom' on page \thepage \space undefined\on@line . -l.303 ...n, Figure~\ref{proporEachFrag-7a12a-zoom} +l.305 ...n, Figure~\ref{proporEachFrag-7a12a-zoom} suggests that clusters wi... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -28438,7 +27974,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `proporEachFrag-7a12a-zoom' on page undefined on inpu -t line 303. +t line 305. Missing character: There is no s in font nullfont! Missing character: There is no u in font nullfont! @@ -28536,6 +28072,8 @@ Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no y in font nullfont! +Missing character: There is no I in font nullfont! +Missing character: There is no . in font nullfont! Missing character: There is no B in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! @@ -28547,7 +28085,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.303 ...by Braud \textit{et al.}.\cite{Braud2019} +l.305 ...I. Braud \textit{et al.}.\cite{Braud2019} A similar conclusion can ... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -28556,7 +28094,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Braud2019' on page undefined on input line 303. +LaTeX Warning: Citation `Braud2019' on page undefined on input line 305. Missing character: There is no ] in font nullfont! Missing character: There is no A in font nullfont! @@ -28632,7 +28170,7 @@ Missing character: There is no s in font nullfont! ! Undefined control sequence. ...`proporEachFrag-1a2a' on page \thepage \space undefined\on@line . -l.303 ...rted by Figures \ref{proporEachFrag-1a2a} +l.305 ...rted by Figures \ref{proporEachFrag-1a2a} -\ref{proporEachFrag-5a6a-... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -28642,13 +28180,13 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `proporEachFrag-1a2a' on page undefined on input line - 303. + 305. Missing character: There is no - in font nullfont! ! Undefined control sequence. ...orEachFrag-5a6a-zoom' on page \thepage \space undefined\on@line . -l.303 ...Frag-1a2a}-\ref{proporEachFrag-5a6a-zoom} +l.305 ...Frag-1a2a}-\ref{proporEachFrag-5a6a-zoom} . In contrast, cluster wit... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -28658,7 +28196,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `proporEachFrag-5a6a-zoom' on page undefined on input - line 303. + line 305. Missing character: There is no . in font nullfont! Missing character: There is no I in font nullfont! @@ -28698,7 +28236,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...porEachFrag-11a-zoom' on page \thepage \space undefined\on@line . -l.303 ...(see Figure \ref{proporEachFrag-11a-zoom} +l.305 ...(see Figure \ref{proporEachFrag-11a-zoom} ) and 12 water molecules s... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -28708,7 +28246,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `proporEachFrag-11a-zoom' on page undefined on input -line 303. +line 305. Missing character: There is no ) in font nullfont! Missing character: There is no a in font nullfont! @@ -28934,97 +28472,97 @@ Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 297--304 +Overfull \hbox (20.0pt too wide) in paragraph at lines 299--306 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 297--304 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 299--306 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 297--304 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 299--306 [] [] -Overfull \hbox (4.48613pt too wide) in paragraph at lines 297--304 +Overfull \hbox (4.48613pt too wide) in paragraph at lines 299--306 []$ [] -Overfull \hbox (23.38898pt too wide) in paragraph at lines 297--304 +Overfull \hbox (23.38898pt too wide) in paragraph at lines 299--306 \OMS/cmsy/m/n/10 ^^X$ $[]$$[]$$[]$ [] -Overfull \hbox (19.5973pt too wide) in paragraph at lines 297--304 +Overfull \hbox (19.5973pt too wide) in paragraph at lines 299--306 []$$[]$$[]$ [] -Overfull \hbox (19.5973pt too wide) in paragraph at lines 297--304 +Overfull \hbox (19.5973pt too wide) in paragraph at lines 299--306 []$$[]$$[]$ [] -Overfull \hbox (19.5973pt too wide) in paragraph at lines 297--304 +Overfull \hbox (19.5973pt too wide) in paragraph at lines 299--306 []$$[]$$[]$ [] -Overfull \hbox (19.5973pt too wide) in paragraph at lines 297--304 +Overfull \hbox (19.5973pt too wide) in paragraph at lines 299--306 []$$[]$$[]$ [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 297--304 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 299--306 []$$[]$$[]$ [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 297--304 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 299--306 []$$[]$$[]$ [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 297--304 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 299--306 []$$[]$$[]$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 297--304 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 299--306 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 297--304 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 299--306 [] [] -Overfull \hbox (7.92215pt too wide) in paragraph at lines 297--304 +Overfull \hbox (7.92215pt too wide) in paragraph at lines 299--306 \OT1/cmr/m/it/10 et [] -Overfull \hbox (16.1638pt too wide) in paragraph at lines 297--304 +Overfull \hbox (16.1638pt too wide) in paragraph at lines 299--306 \OT1/cmr/m/it/10 al.[] [] -Overfull \hbox (21.7221pt too wide) in paragraph at lines 297--304 +Overfull \hbox (21.7221pt too wide) in paragraph at lines 299--306 [][] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 297--304 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 299--306 [] [] ! Undefined control sequence. -l.305 \figuremacrob +l.307 \figuremacrob {proporEachFrag-1a2a}{Time-dependent proportions of the m... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -29178,22 +28716,22 @@ Missing character: There is no t in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 305--306 +Overfull \hbox (20.0pt too wide) in paragraph at lines 307--308 [] [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 305--306 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 307--308 []$$[]$$[]$ [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 305--306 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 307--308 []$$[]$$[]$ [] ! Undefined control sequence. -l.307 \figuremacro +l.309 \figuremacro {proporEachFrag-3a4a-zoom}{Time-dependent proportions of t... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -29405,22 +28943,22 @@ Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 307--308 +Overfull \hbox (20.0pt too wide) in paragraph at lines 309--310 [] [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 307--308 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 309--310 []$$[]$$[]$ [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 307--308 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 309--310 []$$[]$$[]$ [] ! Undefined control sequence. -l.309 \figuremacro +l.311 \figuremacro {proporEachFrag-5a6a-zoom}{Time-dependent proportions of t... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -29632,22 +29170,22 @@ Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 309--310 +Overfull \hbox (20.0pt too wide) in paragraph at lines 311--312 [] [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 309--310 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 311--312 []$$[]$$[]$ [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 309--310 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 311--312 []$$[]$$[]$ [] ! Undefined control sequence. -l.311 \figuremacro +l.313 \figuremacro {proporEachFrag-11a-zoom}{Time-dependent proportions of th... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -29834,17 +29372,17 @@ Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 311--312 +Overfull \hbox (20.0pt too wide) in paragraph at lines 313--314 [] [] -Overfull \hbox (19.5973pt too wide) in paragraph at lines 311--312 +Overfull \hbox (19.5973pt too wide) in paragraph at lines 313--314 []$$[]$$[]$ [] ! Undefined control sequence. -l.313 \figuremacro +l.315 \figuremacro {proporEachFrag-7a12a-zoom}{Time-dependent proportions of ... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -30057,22 +29595,22 @@ Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 313--314 +Overfull \hbox (20.0pt too wide) in paragraph at lines 315--316 [] [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 313--314 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 315--316 []$$[]$$[]$ [] -Overfull \hbox (19.5973pt too wide) in paragraph at lines 313--314 +Overfull \hbox (19.5973pt too wide) in paragraph at lines 315--316 []$$[]$$[]$ [] ! Undefined control sequence. -l.315 \figuremacro +l.317 \figuremacro {proporEachFrag-7d12c-zoom}{Time-dependent proportions of ... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -30319,22 +29857,22 @@ Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 315--316 +Overfull \hbox (20.0pt too wide) in paragraph at lines 317--318 [] [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 315--316 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 317--318 []$$[]$$[]$ [] -Overfull \hbox (19.5973pt too wide) in paragraph at lines 315--316 +Overfull \hbox (19.5973pt too wide) in paragraph at lines 317--318 []$$[]$$[]$ [] ! Undefined control sequence. -l.318 \subsection +l.320 \subsection {Proportion of Neutral Uracil Loss and Total Fragmentation ... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -30422,7 +29960,7 @@ Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 318--319 +Overfull \hbox (20.0pt too wide) in paragraph at lines 320--321 [] [] @@ -30569,7 +30107,7 @@ Missing character: There is no n in font nullfont! ! Undefined control sequence. ...ference `convergence' on page \thepage \space undefined\on@line . -l.320 ...L}$) defined in section \ref{convergence} +l.322 ...L}$) defined in section \ref{convergence} and total fragmentation The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -30578,7 +30116,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `convergence' on page undefined on input line 320. +LaTeX Warning: Reference `convergence' on page undefined on input line 322. Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! @@ -30635,7 +30173,7 @@ Missing character: There is no n in font nullfont! ! Undefined control sequence. ...ence `trajecanylysis' on page \thepage \space undefined\on@line . -l.321 ...) defined in section~\ref{trajecanylysis} +l.323 ...) defined in section~\ref{trajecanylysis} . These two properties are... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -30644,7 +30182,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `trajecanylysis' on page undefined on input line 321. +LaTeX Warning: Reference `trajecanylysis' on page undefined on input line 323. Missing character: There is no . in font nullfont! @@ -31533,8 +31071,8 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ... Reference `tab:full' on page \thepage \space undefined\on@line . -l.322 ...data are gathered in Table~\ref{tab:full} - and we first discuss the ... +l.324 ...data are gathered in Table~\ref{tab:full} + and will first discuss th... The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct @@ -31542,13 +31080,15 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `tab:full' on page undefined on input line 322. +LaTeX Warning: Reference `tab:full' on page undefined on input line 324. Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no w in font nullfont! -Missing character: There is no e in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no l in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no r in font nullfont! @@ -31597,47 +31137,47 @@ Missing character: There is no U in font nullfont! Missing character: There is no H in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 320--323 +Overfull \hbox (20.0pt too wide) in paragraph at lines 322--325 [] [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 320--323 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 322--325 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 320--323 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 322--325 [] [] -Overfull \hbox (23.31656pt too wide) in paragraph at lines 320--323 +Overfull \hbox (23.31656pt too wide) in paragraph at lines 322--325 \OML/cmm/m/it/10 ^^[[]$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 320--323 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 322--325 [] [] -Overfull \hbox (19.28604pt too wide) in paragraph at lines 320--323 +Overfull \hbox (19.28604pt too wide) in paragraph at lines 322--325 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (20.54877pt too wide) in paragraph at lines 320--323 +Overfull \hbox (20.54877pt too wide) in paragraph at lines 322--325 \OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 320--323 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 322--325 [] [] -Overfull \hbox (25.84732pt too wide) in paragraph at lines 320--323 +Overfull \hbox (25.84732pt too wide) in paragraph at lines 322--325 []$$[]$$[]$ [] @@ -31648,14 +31188,14 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.324 \begin{table*} +l.326 \begin{table*} Your command was ignored. Type I to replace it with another command, or to continue without it. -Overfull \hbox (20.0pt too wide) in paragraph at lines 325--325 +Overfull \hbox (20.0pt too wide) in paragraph at lines 327--327 [] [] @@ -31666,7 +31206,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.326 \caption +l.328 \caption {Relative energy $E_{rel.}$ (in kcal.mol$^{-1}$) at the MP2/De... You're in trouble here. Try typing to proceed. @@ -32029,7 +31569,7 @@ Missing character: There is no P in font nullfont! ! Undefined control sequence. \rowcolor -l.334 \rowcolor +l.336 \rowcolor {lightgray} \bf{1a} & 0.0 & U-H & 100 & 0.2 & & 28.9 & \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -32047,7 +31587,7 @@ Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! ! Undefined control sequence. -l.334 \rowcolor{lightgray} \bf +l.336 \rowcolor{lightgray} \bf {1a} & 0.0 & U-H & 100 & 0.2 & & 28.9 & \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -32076,7 +31616,7 @@ Missing character: There is no 9 in font nullfont! ! Undefined control sequence. \rowcolor -l.335 \rowcolor +l.337 \rowcolor {lightgray} 1b & 0.7 & U-H & 100 & 0.1 &\multirow{-2}*{0.9}... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -32108,7 +31648,7 @@ Missing character: There is no 0 in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no 1 in font nullfont! ! Undefined control sequence. -l.335 ...} 1b & 0.7 & U-H & 100 & 0.1 &\multirow +l.337 ...} 1b & 0.7 & U-H & 100 & 0.1 &\multirow {-2}*{0.9} & 25.9 & \multi... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -32127,7 +31667,7 @@ Missing character: There is no 5 in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no 9 in font nullfont! ! Undefined control sequence. -l.335 ...1 &\multirow{-2}*{0.9} & 25.9 & \multirow +l.337 ...1 &\multirow{-2}*{0.9} & 25.9 & \multirow {-2}*{12.3} \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -32163,7 +31703,7 @@ Missing character: There is no 3 in font nullfont! ! Undefined control sequence. \bf -l.337 \bf +l.339 \bf {2b} & 0.2 &U-H & 100 & 0.1 &\multirow{-2}*{0.4} &34.9 & \multir... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -32186,7 +31726,7 @@ Missing character: There is no 0 in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no 1 in font nullfont! ! Undefined control sequence. -l.337 \bf{2b} & 0.2 &U-H & 100 & 0.1 &\multirow +l.339 \bf{2b} & 0.2 &U-H & 100 & 0.1 &\multirow {-2}*{0.4} &34.9 & \multir... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -32205,7 +31745,7 @@ Missing character: There is no 4 in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no 9 in font nullfont! ! Undefined control sequence. -l.337 ....1 &\multirow{-2}*{0.4} &34.9 & \multirow +l.339 ....1 &\multirow{-2}*{0.4} &34.9 & \multirow {-2}*{22.8}\\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -32223,7 +31763,7 @@ Missing character: There is no 8 in font nullfont! ! Undefined control sequence. \rowcolor -l.338 \rowcolor +l.340 \rowcolor {lightgray} 3a & 0.0 & U-H & 100 & 5.7 & & 36.3 & \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -32261,7 +31801,7 @@ Missing character: There is no 3 in font nullfont! ! Undefined control sequence. \rowcolor -l.339 \rowcolor +l.341 \rowcolor {lightgray} \bf{3b} & 0.3 & U-H & 100 & 0.0 &\multirow{-2}*... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -32279,7 +31819,7 @@ Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! ! Undefined control sequence. -l.339 \rowcolor{lightgray} \bf +l.341 \rowcolor{lightgray} \bf {3b} & 0.3 & U-H & 100 & 0.0 &\multirow{-2}*... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -32302,7 +31842,7 @@ Missing character: There is no 0 in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no 0 in font nullfont! ! Undefined control sequence. -l.339 ...bf{3b} & 0.3 & U-H & 100 & 0.0 &\multirow +l.341 ...bf{3b} & 0.3 & U-H & 100 & 0.0 &\multirow {-2}*{1.7} & 41.9 & \multi... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -32321,7 +31861,7 @@ Missing character: There is no 1 in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no 9 in font nullfont! ! Undefined control sequence. -l.339 ...0 &\multirow{-2}*{1.7} & 41.9 & \multirow +l.341 ...0 &\multirow{-2}*{1.7} & 41.9 & \multirow {-2}*{31.2} \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -32361,7 +31901,7 @@ Missing character: There is no 1 in font nullfont! ! Undefined control sequence. \bf -l.341 \bf +l.343 \bf {4b} & 0.9 &U-H & 99.7 & 2.6 &\multirow{-2}*{2.8} &45.2 & \multi... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -32385,7 +31925,7 @@ Missing character: There is no 2 in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no 6 in font nullfont! ! Undefined control sequence. -l.341 ...bf{4b} & 0.9 &U-H & 99.7 & 2.6 &\multirow +l.343 ...bf{4b} & 0.9 &U-H & 99.7 & 2.6 &\multirow {-2}*{2.8} &45.2 & \multir... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -32404,7 +31944,7 @@ Missing character: There is no 5 in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no 2 in font nullfont! ! Undefined control sequence. -l.341 ....6 &\multirow{-2}*{2.8} &45.2 & \multirow +l.343 ....6 &\multirow{-2}*{2.8} &45.2 & \multirow {-2}*{43.4}\\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -32422,7 +31962,7 @@ Missing character: There is no 4 in font nullfont! ! Undefined control sequence. \rowcolor -l.342 \rowcolor +l.344 \rowcolor {lightgray} 5a & 0.0 &W-H & 78.5 & 46.6 && 38.2 & \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -32462,7 +32002,7 @@ Missing character: There is no 2 in font nullfont! ! Undefined control sequence. \rowcolor -l.343 \rowcolor +l.345 \rowcolor {lightgray} 5b & 0.3 &W-H-U & 89.0 & 28.5 && 38.7 & \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -32504,7 +32044,7 @@ Missing character: There is no 7 in font nullfont! ! Undefined control sequence. \rowcolor -l.344 \rowcolor +l.346 \rowcolor {lightgray} 5c & 2.0 &W-H-U & 87.8 & 27.1 && 44.6 & \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -32546,7 +32086,7 @@ Missing character: There is no 6 in font nullfont! ! Undefined control sequence. \rowcolor -l.345 \rowcolor +l.347 \rowcolor {lightgray} \bf{5d} & 2.4 &U-H & 100 & 0.1 &\multirow{-4}*{... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -32564,7 +32104,7 @@ Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! ! Undefined control sequence. -l.345 \rowcolor{lightgray} \bf +l.347 \rowcolor{lightgray} \bf {5d} & 2.4 &U-H & 100 & 0.1 &\multirow{-4}*{... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -32587,7 +32127,7 @@ Missing character: There is no 0 in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no 1 in font nullfont! ! Undefined control sequence. -l.345 ...\bf{5d} & 2.4 &U-H & 100 & 0.1 &\multirow +l.347 ...\bf{5d} & 2.4 &U-H & 100 & 0.1 &\multirow {-4}*{7.5}& 47.5 & \multir... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -32606,7 +32146,7 @@ Missing character: There is no 7 in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no 5 in font nullfont! ! Undefined control sequence. -l.345 ....1 &\multirow{-4}*{7.5}& 47.5 & \multirow +l.347 ....1 &\multirow{-4}*{7.5}& 47.5 & \multirow {-4}*{48.0}\\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -32724,7 +32264,7 @@ Missing character: There is no 5 in font nullfont! ! Undefined control sequence. \bf -l.351 \bf +l.353 \bf {6f} & 2.7 &W-H-U & 76.2 & 18.5 &\multirow{-6}*{18.0}& 55.0 & \... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -32751,7 +32291,7 @@ Missing character: There is no 8 in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no 5 in font nullfont! ! Undefined control sequence. -l.351 ...6f} & 2.7 &W-H-U & 76.2 & 18.5 &\multirow +l.353 ...6f} & 2.7 &W-H-U & 76.2 & 18.5 &\multirow {-6}*{18.0}& 55.0 & \mult... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -32771,7 +32311,7 @@ Missing character: There is no 5 in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no 0 in font nullfont! ! Undefined control sequence. -l.351 ... &\multirow{-6}*{18.0}& 55.0 & \multirow +l.353 ... &\multirow{-6}*{18.0}& 55.0 & \multirow {-6}*{54.3} \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -32789,7 +32329,7 @@ Missing character: There is no 3 in font nullfont! ! Undefined control sequence. \rowcolor -l.352 \rowcolor +l.354 \rowcolor {lightgray} 7a & 0.0 &W-H & 28.2 & 31.3 && 53.4 & \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -32829,7 +32369,7 @@ Missing character: There is no 4 in font nullfont! ! Undefined control sequence. \rowcolor -l.353 \rowcolor +l.355 \rowcolor {lightgray} 7b & 0.3 & W-H-U & 52.4 & 21.4 && 51.7 &\\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -32871,7 +32411,7 @@ Missing character: There is no 7 in font nullfont! ! Undefined control sequence. \rowcolor -l.354 \rowcolor +l.356 \rowcolor {lightgray} 7c & 0.3 & W-H & 41.3 & 31.1 && 49.5 &\\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -32911,7 +32451,7 @@ Missing character: There is no 5 in font nullfont! ! Undefined control sequence. \rowcolor -l.355 \rowcolor +l.357 \rowcolor {lightgray} \bf{7d} & 0.8 & W-H-U & 40.9 & 23.0 &\multirow{... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -32929,7 +32469,7 @@ Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! ! Undefined control sequence. -l.355 \rowcolor{lightgray} \bf +l.357 \rowcolor{lightgray} \bf {7d} & 0.8 & W-H-U & 40.9 & 23.0 &\multirow{... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -32956,7 +32496,7 @@ Missing character: There is no 3 in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no 0 in font nullfont! ! Undefined control sequence. -l.355 ...d} & 0.8 & W-H-U & 40.9 & 23.0 &\multirow +l.357 ...d} & 0.8 & W-H-U & 40.9 & 23.0 &\multirow {-4}*{25.0}& 54.0 & \mult... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -32976,7 +32516,7 @@ Missing character: There is no 4 in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no 0 in font nullfont! ! Undefined control sequence. -l.355 ... &\multirow{-4}*{25.0}& 54.0 & \multirow +l.357 ... &\multirow{-4}*{25.0}& 54.0 & \multirow {-4}*{59.7} \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -33054,7 +32594,7 @@ Missing character: There is no 2 in font nullfont! ! Undefined control sequence. \bf -l.359 \bf +l.361 \bf {11d}& 1.9 &W-H & 6.8 & 15.6 &\multirow{-4}*{11.8} & 56.5 & \mu... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -33079,7 +32619,7 @@ Missing character: There is no 5 in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no 6 in font nullfont! ! Undefined control sequence. -l.359 ...f{11d}& 1.9 &W-H & 6.8 & 15.6 &\multirow +l.361 ...f{11d}& 1.9 &W-H & 6.8 & 15.6 &\multirow {-4}*{11.8} & 56.5 & \mult... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -33099,7 +32639,7 @@ Missing character: There is no 6 in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no 5 in font nullfont! ! Undefined control sequence. -l.359 ... &\multirow{-4}*{11.8} & 56.5 & \multirow +l.361 ... &\multirow{-4}*{11.8} & 56.5 & \multirow {-4}*{63.8} \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -33155,7 +32695,7 @@ Missing character: There is no 2 in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no 0 in font nullfont! ! Undefined control sequence. -l.364 \rowcolor +l.366 \rowcolor {lightgray} 12a & 0.0 & W-H & 6.7 & 7.6 && 60.2 & \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -33194,7 +32734,7 @@ Missing character: There is no 2 in font nullfont! ! Undefined control sequence. \rowcolor -l.365 \rowcolor +l.367 \rowcolor {lightgray} 12b & 0.6 &W-H & 34.0 & 22.4 && 52.2 & \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -33235,7 +32775,7 @@ Missing character: There is no 2 in font nullfont! ! Undefined control sequence. \rowcolor -l.366 \rowcolor +l.368 \rowcolor {lightgray} \bf{12c} & 0.7 &W-H & 48.7 & 10.8 && 55.4 & \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -33253,7 +32793,7 @@ Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no y in font nullfont! ! Undefined control sequence. -l.366 \rowcolor{lightgray} \bf +l.368 \rowcolor{lightgray} \bf {12c} & 0.7 &W-H & 48.7 & 10.8 && 55.4 & \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -33285,7 +32825,7 @@ Missing character: There is no 4 in font nullfont! ! Undefined control sequence. \rowcolor -l.367 \rowcolor +l.369 \rowcolor {lightgray} 12d & 1.3 &W-H-U & 5.4 & 9.7 && 54.3 & \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -33326,7 +32866,7 @@ Missing character: There is no 3 in font nullfont! ! Undefined control sequence. \rowcolor -l.368 \rowcolor +l.370 \rowcolor {lightgray} 12e & 1.8 &W-H-U & 67.5 & 6.0 && 54.2 & \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -33368,7 +32908,7 @@ Missing character: There is no 2 in font nullfont! ! Undefined control sequence. \rowcolor -l.369 \rowcolor +l.371 \rowcolor {lightgray} 12f & 2.4 &W-H-U & 55.0 & 17.1 &\multirow{-6}*{... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -33405,7 +32945,7 @@ Missing character: There is no 7 in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no 1 in font nullfont! ! Undefined control sequence. -l.369 ...12f & 2.4 &W-H-U & 55.0 & 17.1 &\multirow +l.371 ...12f & 2.4 &W-H-U & 55.0 & 17.1 &\multirow {-6}*{12.2}& 54.1 & \multi... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -33425,7 +32965,7 @@ Missing character: There is no 4 in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no 1 in font nullfont! ! Undefined control sequence. -l.369 ...1 &\multirow{-6}*{12.2}& 54.1 & \multirow +l.371 ...1 &\multirow{-6}*{12.2}& 54.1 & \multirow {-6}*{77.0} \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -33441,72 +32981,72 @@ Missing character: There is no 7 in font nullfont! Missing character: There is no . in font nullfont! Missing character: There is no 0 in font nullfont! -Overfull \hbox (20.54877pt too wide) in paragraph at lines 326--372 +Overfull \hbox (20.54877pt too wide) in paragraph at lines 328--374 \OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (10.73615pt too wide) in paragraph at lines 326--372 +Overfull \hbox (10.73615pt too wide) in paragraph at lines 328--374 []$ [] -Overfull \hbox (19.28604pt too wide) in paragraph at lines 326--372 +Overfull \hbox (19.28604pt too wide) in paragraph at lines 328--374 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 326--372 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 328--374 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (23.31656pt too wide) in paragraph at lines 326--372 +Overfull \hbox (23.31656pt too wide) in paragraph at lines 328--374 \OML/cmm/m/it/10 ^^[[]$ [] -Overfull \hbox (11.98615pt too wide) in paragraph at lines 326--372 +Overfull \hbox (11.98615pt too wide) in paragraph at lines 328--374 []\/cmr/m/n/10 A$[]$ [] -Overfull \hbox (46.54184pt too wide) in paragraph at lines 326--372 +Overfull \hbox (46.54184pt too wide) in paragraph at lines 328--374 []$$[]$$[]$ [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 326--372 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 328--374 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (37.2312pt too wide) in paragraph at lines 326--372 +Overfull \hbox (37.2312pt too wide) in paragraph at lines 328--374 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (34.85855pt too wide) in paragraph at lines 326--372 +Overfull \hbox (34.85855pt too wide) in paragraph at lines 328--374 \OML/cmm/m/it/10 ^^[[]$ [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 326--372 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 328--374 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (23.31656pt too wide) in paragraph at lines 326--372 +Overfull \hbox (23.31656pt too wide) in paragraph at lines 328--374 \OML/cmm/m/it/10 ^^[[]$ [] -Overfull \hbox (19.5973pt too wide) in paragraph at lines 326--372 +Overfull \hbox (19.5973pt too wide) in paragraph at lines 328--374 []$$[]$$[]$ [] -Overfull \hbox (199.70374pt too wide) in paragraph at lines 326--372 +Overfull \hbox (199.70374pt too wide) in paragraph at lines 328--374 [] [] @@ -33517,7 +33057,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.373 \end{table*} +l.375 \end{table*} Your command was ignored. Type I to replace it with another command, @@ -34496,6 +34036,8 @@ Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no y in font nullfont! +Missing character: There is no I in font nullfont! +Missing character: There is no . in font nullfont! Missing character: There is no B in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! @@ -34506,7 +34048,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.376 ...d by Braud \textit{ al.} \cite{Braud2019} +l.378 .... Braud \textit{ et al.} \cite{Braud2019} This important finding ca... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -34515,7 +34057,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Braud2019' on page undefined on input line 376. +LaTeX Warning: Citation `Braud2019' on page undefined on input line 378. Missing character: There is no ] in font nullfont! Missing character: There is no T in font nullfont! @@ -34712,72 +34254,77 @@ Missing character: There is no o in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 375--377 +Overfull \hbox (20.0pt too wide) in paragraph at lines 377--379 [] [] -Overfull \hbox (23.31656pt too wide) in paragraph at lines 375--377 +Overfull \hbox (23.31656pt too wide) in paragraph at lines 377--379 \OML/cmm/m/it/10 ^^[[]$ [] -Overfull \hbox (47.28885pt too wide) in paragraph at lines 375--377 +Overfull \hbox (47.28885pt too wide) in paragraph at lines 377--379 []\/cmr/m/n/10 A$[]$ []A$[]$ $\OML/cmm/m/it/10 ^^[[]$ [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 375--377 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 377--379 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 375--377 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 377--379 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 375--377 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 377--379 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 375--377 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 377--379 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 375--377 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 377--379 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 375--377 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 377--379 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 375--377 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 377--379 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (25.84732pt too wide) in paragraph at lines 375--377 +Overfull \hbox (25.84732pt too wide) in paragraph at lines 377--379 []$$[]$$[]$ [] -Overfull \hbox (10.73328pt too wide) in paragraph at lines 375--377 +Overfull \hbox (7.92215pt too wide) in paragraph at lines 377--379 +\OT1/cmr/m/it/10 et + [] + + +Overfull \hbox (10.73328pt too wide) in paragraph at lines 377--379 \OT1/cmr/m/it/10 al. [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 375--377 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 377--379 [] [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 375--377 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 377--379 \OML/cmm/m/it/10 P[]$ [] @@ -35134,7 +34681,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...Reference `fig-1a-3b' on page \thepage \space undefined\on@line . -l.379 ...e, as displayed in Figure~\ref{fig-1a-3b} +l.381 ...e, as displayed in Figure~\ref{fig-1a-3b} , both being of U-H type s... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -35143,7 +34690,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `fig-1a-3b' on page undefined on input line 379. +LaTeX Warning: Reference `fig-1a-3b' on page undefined on input line 381. Missing character: There is no , in font nullfont! Missing character: There is no b in font nullfont! @@ -35678,7 +35225,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...Reference `fig-4a-5d' on page \thepage \space undefined\on@line . -l.379 ...ent to uracil (see Figure~\ref{fig-4a-5d} +l.381 ...ent to uracil (see Figure~\ref{fig-4a-5d} ). The case of (H$_2$O)$_5... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -35687,7 +35234,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `fig-4a-5d' on page undefined on input line 379. +LaTeX Warning: Reference `fig-4a-5d' on page undefined on input line 381. Missing character: There is no ) in font nullfont! Missing character: There is no . in font nullfont! @@ -35837,7 +35384,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...Reference `fig-4a-5d' on page \thepage \space undefined\on@line . -l.379 ... as can be seen on Figure~\ref{fig-4a-5d} +l.381 ... as can be seen on Figure~\ref{fig-4a-5d} . This implies very differ... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -35846,7 +35393,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `fig-4a-5d' on page undefined on input line 379. +LaTeX Warning: Reference `fig-4a-5d' on page undefined on input line 381. Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! @@ -36164,92 +35711,92 @@ Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 378--381 +Overfull \hbox (20.0pt too wide) in paragraph at lines 380--383 [] [] -Overfull \hbox (25.84732pt too wide) in paragraph at lines 378--381 +Overfull \hbox (25.84732pt too wide) in paragraph at lines 380--383 []$$[]$$[]$ [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 378--381 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 380--383 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 378--381 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 380--383 []$$[]$$[]$ [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 378--381 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 380--383 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (10.73615pt too wide) in paragraph at lines 378--381 +Overfull \hbox (10.73615pt too wide) in paragraph at lines 380--383 []$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 378--381 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 380--383 [] [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 378--381 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 380--383 []$$[]$$[]$ [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 378--381 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 380--383 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (10.73615pt too wide) in paragraph at lines 378--381 +Overfull \hbox (10.73615pt too wide) in paragraph at lines 380--383 []$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 378--381 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 380--383 [] [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 378--381 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 380--383 []$$[]$$[]$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 378--381 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 380--383 [] [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 378--381 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 380--383 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 378--381 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 380--383 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 378--381 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 380--383 []$$[]$$[]$ [] -Overfull \hbox (10.73615pt too wide) in paragraph at lines 378--381 +Overfull \hbox (10.73615pt too wide) in paragraph at lines 380--383 []$ [] ! Undefined control sequence. -l.382 \figuremacro +l.384 \figuremacro {fig-1a-3b}{Selected low-energy configurations of (H$_2$O)... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -36360,22 +35907,22 @@ Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 382--383 +Overfull \hbox (20.0pt too wide) in paragraph at lines 384--385 [] [] -Overfull \hbox (25.84732pt too wide) in paragraph at lines 382--383 +Overfull \hbox (25.84732pt too wide) in paragraph at lines 384--385 []$$[]$$[]$ [] -Overfull \hbox (10.73615pt too wide) in paragraph at lines 382--383 +Overfull \hbox (10.73615pt too wide) in paragraph at lines 384--385 []$ [] ! Undefined control sequence. -l.384 \figuremacro +l.386 \figuremacro {fig-4a-5d}{Selected low-energy configurations of (H$_2$O)... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -36486,17 +36033,17 @@ Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 384--385 +Overfull \hbox (20.0pt too wide) in paragraph at lines 386--387 [] [] -Overfull \hbox (25.84732pt too wide) in paragraph at lines 384--385 +Overfull \hbox (25.84732pt too wide) in paragraph at lines 386--387 []$$[]$$[]$ [] -Overfull \hbox (10.73615pt too wide) in paragraph at lines 384--385 +Overfull \hbox (10.73615pt too wide) in paragraph at lines 386--387 []$ [] @@ -36779,7 +36326,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...Reference `fig-6a-6f' on page \thepage \space undefined\on@line . -l.389 and 6e (see Figure~\ref{fig-6a-6f} +l.391 and 6e (see Figure~\ref{fig-6a-6f} ) are all W-H type structures which... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -36788,7 +36335,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `fig-6a-6f' on page undefined on input line 389. +LaTeX Warning: Reference `fig-6a-6f' on page undefined on input line 391. Missing character: There is no ) in font nullfont! Missing character: There is no a in font nullfont! @@ -37609,7 +37156,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...Reference `fig-6a-6f' on page \thepage \space undefined\on@line . -l.395 ...rally similar (see Figure~\ref{fig-6a-6f} +l.397 ...rally similar (see Figure~\ref{fig-6a-6f} ) but display different $P... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -37618,7 +37165,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `fig-6a-6f' on page undefined on input line 395. +LaTeX Warning: Reference `fig-6a-6f' on page undefined on input line 397. Missing character: There is no ) in font nullfont! Missing character: There is no b in font nullfont! @@ -38123,7 +37670,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...Reference `fig-7a-7d' on page \thepage \space undefined\on@line . -l.396 ...energy isomer (see Figure~\ref{fig-7a-7d} +l.398 ...energy isomer (see Figure~\ref{fig-7a-7d} ), has a $P_{NUL}$ value o... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -38132,7 +37679,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `fig-7a-7d' on page undefined on input line 396. +LaTeX Warning: Reference `fig-7a-7d' on page undefined on input line 398. Missing character: There is no ) in font nullfont! Missing character: There is no , in font nullfont! @@ -38319,117 +37866,117 @@ Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (35.61118pt too wide) in paragraph at lines 386--397 +Overfull \hbox (35.61118pt too wide) in paragraph at lines 388--399 []$[]$$[]$$[]$ [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 386--397 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 388--399 []$$[]$$[]$ [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 386--397 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 388--399 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (6.00235pt too wide) in paragraph at lines 386--397 +Overfull \hbox (6.00235pt too wide) in paragraph at lines 388--399 \OML/cmm/m/it/10 n$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 386--397 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 388--399 [] [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 386--397 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 388--399 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 386--397 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 388--399 []$$[]$$[]$ [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 386--397 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 388--399 []$$[]$$[]$ [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 386--397 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 388--399 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 386--397 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 388--399 []$$[]$$[]$ [] -Overfull \hbox (7.50002pt too wide) in paragraph at lines 386--397 +Overfull \hbox (7.50002pt too wide) in paragraph at lines 388--399 []\/cmr/m/n/10 A [] -Overfull \hbox (7.50002pt too wide) in paragraph at lines 386--397 +Overfull \hbox (7.50002pt too wide) in paragraph at lines 388--399 []\/cmr/m/n/10 A [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 386--397 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 388--399 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 386--397 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 388--399 [] [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 386--397 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 388--399 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (6.00235pt too wide) in paragraph at lines 386--397 +Overfull \hbox (6.00235pt too wide) in paragraph at lines 388--399 \OML/cmm/m/it/10 n$ [] -Overfull \hbox (10.73326pt too wide) in paragraph at lines 386--397 +Overfull \hbox (10.73326pt too wide) in paragraph at lines 388--399 \OT1/cmr/m/it/10 i.e [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 386--397 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 388--399 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 386--397 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 388--399 []$$[]$$[]$ [] -Overfull \hbox (10.73615pt too wide) in paragraph at lines 386--397 +Overfull \hbox (10.73615pt too wide) in paragraph at lines 388--399 []$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 386--397 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 388--399 [] [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 386--397 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 388--399 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 386--397 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 388--399 \OML/cmm/m/it/10 P[]$ [] @@ -39015,7 +38562,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ... Reference `tab:full' on page \thepage \space undefined\on@line . -l.400 ...nce 5a, 6d and 7c in Table~\ref{tab:full} +l.402 ...nce 5a, 6d and 7c in Table~\ref{tab:full} . This demonstrates that u... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -39024,7 +38571,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `tab:full' on page undefined on input line 400. +LaTeX Warning: Reference `tab:full' on page undefined on input line 402. Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! @@ -39127,47 +38674,47 @@ Missing character: There is no l in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 398--401 +Overfull \hbox (20.0pt too wide) in paragraph at lines 400--403 [] [] -Overfull \hbox (13.79991pt too wide) in paragraph at lines 398--401 +Overfull \hbox (13.79991pt too wide) in paragraph at lines 400--403 \OT1/cmr/m/it/10 i.e. [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 398--401 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 400--403 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (25.84732pt too wide) in paragraph at lines 398--401 +Overfull \hbox (25.84732pt too wide) in paragraph at lines 400--403 []$$[]$$[]$ [] -Overfull \hbox (25.84732pt too wide) in paragraph at lines 398--401 +Overfull \hbox (25.84732pt too wide) in paragraph at lines 400--403 []$$[]$$[]$ [] -Overfull \hbox (19.28604pt too wide) in paragraph at lines 398--401 +Overfull \hbox (19.28604pt too wide) in paragraph at lines 400--403 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (19.28604pt too wide) in paragraph at lines 398--401 +Overfull \hbox (19.28604pt too wide) in paragraph at lines 400--403 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 398--401 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 400--403 [] [] ! Undefined control sequence. -l.402 \figuremacro +l.404 \figuremacro {fig-6a-6f}{Selected low-energy configurations of (H$_2$O)... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -39278,22 +38825,22 @@ Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 402--403 +Overfull \hbox (20.0pt too wide) in paragraph at lines 404--405 [] [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 402--403 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 404--405 []$$[]$$[]$ [] -Overfull \hbox (10.73615pt too wide) in paragraph at lines 402--403 +Overfull \hbox (10.73615pt too wide) in paragraph at lines 404--405 []$ [] ! Undefined control sequence. -l.404 \figuremacro +l.406 \figuremacro {fig-7a-7d}{Selected low-energy configurations of (H$_2$O)... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -39404,17 +38951,17 @@ Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 404--405 +Overfull \hbox (20.0pt too wide) in paragraph at lines 406--407 [] [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 404--405 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 406--407 []$$[]$$[]$ [] -Overfull \hbox (10.73615pt too wide) in paragraph at lines 404--405 +Overfull \hbox (10.73615pt too wide) in paragraph at lines 406--407 []$ [] @@ -39757,8 +39304,6 @@ Missing character: There is no y in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! -Missing character: There is no w in font nullfont! -Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no u in font nullfont! @@ -39881,8 +39426,7 @@ Missing character: There is no w in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! -Missing character: There is no w in font nullfont! -Missing character: There is no e in font nullfont! +Missing character: There is no I in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no o in font nullfont! @@ -40034,8 +39578,7 @@ Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no z in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no w in font nullfont! -Missing character: There is no e in font nullfont! +Missing character: There is no I in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no v in font nullfont! @@ -40338,7 +39881,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ... `neutralUloss-Ne-Ar' on page \thepage \space undefined\on@line . -l.410 ...ighted on Figure~\ref{neutralUloss-Ne-Ar} +l.412 ...ighted on Figure~\ref{neutralUloss-Ne-Ar} , which presents the exper... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -40348,7 +39891,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `neutralUloss-Ne-Ar' on page undefined on input line -410. +412. Missing character: There is no , in font nullfont! Missing character: There is no w in font nullfont! @@ -40739,7 +40282,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...`cross-section-Ne-Ar' on page \thepage \space undefined\on@line . -l.411 (see Figure~\ref{cross-section-Ne-Ar} +l.413 (see Figure~\ref{cross-section-Ne-Ar} ), a good agreement with the expe... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -40749,7 +40292,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `cross-section-Ne-Ar' on page undefined on input line - 411. + 413. Missing character: There is no ) in font nullfont! Missing character: There is no , in font nullfont! @@ -40832,7 +40375,7 @@ Missing character: There is no a in font nullfont! ! Undefined control sequence. ...e `cross-section-geo' on page \thepage \space undefined\on@line . -l.411 ...ated from formula \ref{cross-section-geo} +l.413 ...ated from formula \ref{cross-section-geo} )is also obtained with the... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -40842,7 +40385,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `cross-section-geo' on page undefined on input line 4 -11. +13. Missing character: There is no ) in font nullfont! Missing character: There is no i in font nullfont! @@ -40928,67 +40471,67 @@ Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 406--412 +Overfull \hbox (20.0pt too wide) in paragraph at lines 408--414 [] [] -Overfull \hbox (10.73615pt too wide) in paragraph at lines 406--412 +Overfull \hbox (10.73615pt too wide) in paragraph at lines 408--414 []$ [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 406--412 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 408--414 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 406--412 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 408--414 [] [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 406--412 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 408--414 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (6.00235pt too wide) in paragraph at lines 406--412 +Overfull \hbox (6.00235pt too wide) in paragraph at lines 408--414 \OML/cmm/m/it/10 n$ [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 406--412 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 408--414 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (23.31656pt too wide) in paragraph at lines 406--412 +Overfull \hbox (23.31656pt too wide) in paragraph at lines 408--414 \OML/cmm/m/it/10 ^^[[]$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 406--412 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 408--414 [] [] -Overfull \hbox (18.10791pt too wide) in paragraph at lines 406--412 +Overfull \hbox (18.10791pt too wide) in paragraph at lines 408--414 \OML/cmm/m/it/10 ^^[[]$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 406--412 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 408--414 [] [] -Overfull \hbox (23.31656pt too wide) in paragraph at lines 406--412 +Overfull \hbox (23.31656pt too wide) in paragraph at lines 408--414 \OML/cmm/m/it/10 ^^[[]$ [] ! Undefined control sequence. -l.413 \figuremacro +l.415 \figuremacro {neutralUloss-Ne-Ar}{Theoretical (green and blue lines) an... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -41232,27 +40775,27 @@ Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 413--415 +Overfull \hbox (20.0pt too wide) in paragraph at lines 415--417 [] [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 413--415 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 415--417 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (46.54184pt too wide) in paragraph at lines 413--415 +Overfull \hbox (46.54184pt too wide) in paragraph at lines 415--417 []$$[]$$[]$ [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 413--415 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 415--417 \OML/cmm/m/it/10 P[]$ [] ! Undefined control sequence. -l.416 \figuremacro +l.418 \figuremacro {cross-section-Ne-Ar}{Theoretical (green and blue lines) a... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -41497,27 +41040,27 @@ Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 416--418 +Overfull \hbox (20.0pt too wide) in paragraph at lines 418--420 [] [] -Overfull \hbox (23.31656pt too wide) in paragraph at lines 416--418 +Overfull \hbox (23.31656pt too wide) in paragraph at lines 418--420 \OML/cmm/m/it/10 ^^[[]$ [] -Overfull \hbox (46.54184pt too wide) in paragraph at lines 416--418 +Overfull \hbox (46.54184pt too wide) in paragraph at lines 418--420 []$$[]$$[]$ [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 416--418 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 418--420 \OML/cmm/m/it/10 P[]$ [] ! Undefined control sequence. -l.419 \subsection +l.421 \subsection {Behaviour at Larger Sizes, the Cases of (H$_2$O)$_{11, 12}... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -41565,12 +41108,12 @@ Missing character: There is no ) in font nullfont! Missing character: There is no U in font nullfont! Missing character: There is no H in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 419--420 +Overfull \hbox (20.0pt too wide) in paragraph at lines 421--422 [] [] -Overfull \hbox (29.94456pt too wide) in paragraph at lines 419--420 +Overfull \hbox (29.94456pt too wide) in paragraph at lines 421--422 []$$[]$$[]$ [] @@ -41601,6 +41144,8 @@ Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no y in font nullfont! +Missing character: There is no I in font nullfont! +Missing character: There is no . in font nullfont! Missing character: There is no B in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no a in font nullfont! @@ -41612,7 +41157,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.421 ...by Braud \textit{et al.},\cite{Braud2019} +l.423 ...I. Braud \textit{et al.},\cite{Braud2019} $P_{NUL}$ starts to decre... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -41621,7 +41166,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Braud2019' on page undefined on input line 421. +LaTeX Warning: Citation `Braud2019' on page undefined on input line 423. Missing character: There is no ] in font nullfont! Missing character: There is no s in font nullfont! @@ -42015,7 +41560,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ... `neutralUloss-Ne-Ar' on page \thepage \space undefined\on@line . -l.423 As shown in Figure~\ref{neutralUloss-Ne-Ar} +l.425 As shown in Figure~\ref{neutralUloss-Ne-Ar} , experimental $P_{NUL}$ va... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -42025,7 +41570,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `neutralUloss-Ne-Ar' on page undefined on input line -423. +425. Missing character: There is no , in font nullfont! Missing character: There is no e in font nullfont! @@ -42234,57 +41779,57 @@ Missing character: There is no A in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 421--425 +Overfull \hbox (20.0pt too wide) in paragraph at lines 423--427 [] [] -Overfull \hbox (7.92215pt too wide) in paragraph at lines 421--425 +Overfull \hbox (7.92215pt too wide) in paragraph at lines 423--427 \OT1/cmr/m/it/10 et [] -Overfull \hbox (16.1638pt too wide) in paragraph at lines 421--425 +Overfull \hbox (16.1638pt too wide) in paragraph at lines 423--427 \OT1/cmr/m/it/10 al.[] [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 421--425 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 423--427 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (6.00235pt too wide) in paragraph at lines 421--425 +Overfull \hbox (6.00235pt too wide) in paragraph at lines 423--427 \OML/cmm/m/it/10 n$ [] -Overfull \hbox (29.94456pt too wide) in paragraph at lines 421--425 +Overfull \hbox (29.94456pt too wide) in paragraph at lines 423--427 []$$[]$$[]$ [] -Overfull \hbox (19.5973pt too wide) in paragraph at lines 421--425 +Overfull \hbox (19.5973pt too wide) in paragraph at lines 423--427 []$$[]$$[]$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 421--425 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 423--427 [] [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 421--425 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 423--427 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (19.5973pt too wide) in paragraph at lines 421--425 +Overfull \hbox (19.5973pt too wide) in paragraph at lines 423--427 []$$[]$$[]$ [] -Overfull \hbox (36.19458pt too wide) in paragraph at lines 421--425 +Overfull \hbox (36.19458pt too wide) in paragraph at lines 423--427 []$$[]$$[]$ [] @@ -42652,7 +42197,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...Reference `fig-11a-f' on page \thepage \space undefined\on@line . -l.428 ...uration as seen in Figure~\ref{fig-11a-f} +l.430 ...uration as seen in Figure~\ref{fig-11a-f} . $P_{PU}$ is very small f... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -42661,7 +42206,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `fig-11a-f' on page undefined on input line 428. +LaTeX Warning: Reference `fig-11a-f' on page undefined on input line 430. Missing character: There is no . in font nullfont! Missing character: There is no i in font nullfont! @@ -42772,62 +42317,62 @@ Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 426--429 +Overfull \hbox (20.0pt too wide) in paragraph at lines 428--431 [] [] -Overfull \hbox (19.5973pt too wide) in paragraph at lines 426--429 +Overfull \hbox (19.5973pt too wide) in paragraph at lines 428--431 []$$[]$$[]$ [] -Overfull \hbox (19.5973pt too wide) in paragraph at lines 426--429 +Overfull \hbox (19.5973pt too wide) in paragraph at lines 428--431 []$$[]$$[]$ [] -Overfull \hbox (19.5973pt too wide) in paragraph at lines 426--429 +Overfull \hbox (19.5973pt too wide) in paragraph at lines 428--431 []$$[]$$[]$ [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 426--429 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 428--431 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 426--429 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 428--431 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 426--429 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 428--431 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 426--429 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 428--431 []$$[]$$[]$ [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 426--429 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 428--431 []$$[]$$[]$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 426--429 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 428--431 [] [] -Overfull \hbox (19.28604pt too wide) in paragraph at lines 426--429 +Overfull \hbox (19.28604pt too wide) in paragraph at lines 428--431 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (19.5973pt too wide) in paragraph at lines 426--429 +Overfull \hbox (19.5973pt too wide) in paragraph at lines 428--431 []$$[]$$[]$ [] @@ -42893,7 +42438,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...Reference `fig-12a-f' on page \thepage \space undefined\on@line . -l.430 ...configuration (see Figure~\ref{fig-12a-f} +l.432 ...configuration (see Figure~\ref{fig-12a-f} ), has a $P_{NUL}$ value w... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -42902,7 +42447,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `fig-12a-f' on page undefined on input line 430. +LaTeX Warning: Reference `fig-12a-f' on page undefined on input line 432. Missing character: There is no ) in font nullfont! Missing character: There is no , in font nullfont! @@ -43015,7 +42560,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...Reference `fig-12a-f' on page \thepage \space undefined\on@line . -l.430 ...configuration (see Figure~\ref{fig-12a-f} +l.432 ...configuration (see Figure~\ref{fig-12a-f} ), has a $P_{NUL}$ value e... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -43024,7 +42569,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `fig-12a-f' on page undefined on input line 430. +LaTeX Warning: Reference `fig-12a-f' on page undefined on input line 432. Missing character: There is no ) in font nullfont! Missing character: There is no , in font nullfont! @@ -44043,7 +43588,7 @@ Missing character: There is no n in font nullfont! ! Undefined control sequence. ...ing: Reference `time' on page \thepage \space undefined\on@line . -l.436 ...onclusions obtained in section~\ref{time} +l.438 ...onclusions obtained in section~\ref{time} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -44052,7 +43597,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `time' on page undefined on input line 436. +LaTeX Warning: Reference `time' on page undefined on input line 438. Missing character: There is no f in font nullfont! Missing character: There is no r in font nullfont! @@ -44068,7 +43613,7 @@ Missing character: There is no s in font nullfont! ! Undefined control sequence. ...porEachFrag-11a-zoom' on page \thepage \space undefined\on@line . -l.437 from Figures~\ref{proporEachFrag-11a-zoom} +l.439 from Figures~\ref{proporEachFrag-11a-zoom} ,\ref{proporEachFrag-7a12a-z... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -44078,13 +43623,13 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `proporEachFrag-11a-zoom' on page undefined on input -line 437. +line 439. Missing character: There is no , in font nullfont! ! Undefined control sequence. ...rEachFrag-7a12a-zoom' on page \thepage \space undefined\on@line . -l.437 ...11a-zoom},\ref{proporEachFrag-7a12a-zoom} +l.439 ...11a-zoom},\ref{proporEachFrag-7a12a-zoom} and \ref{proporEachFrag-7... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -44094,7 +43639,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `proporEachFrag-7a12a-zoom' on page undefined on inpu -t line 437. +t line 439. Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! @@ -44102,7 +43647,7 @@ Missing character: There is no d in font nullfont! ! Undefined control sequence. ...rEachFrag-7d12c-zoom' on page \thepage \space undefined\on@line . -l.437 ...zoom} and \ref{proporEachFrag-7d12c-zoom} +l.439 ...zoom} and \ref{proporEachFrag-7d12c-zoom} . To further support this ... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -44112,7 +43657,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `proporEachFrag-7d12c-zoom' on page undefined on inpu -t line 437. +t line 439. Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! @@ -44146,8 +43691,7 @@ Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no , in font nullfont! -Missing character: There is no w in font nullfont! -Missing character: There is no e in font nullfont! +Missing character: There is no I in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! @@ -45014,152 +44558,152 @@ Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 430--444 +Overfull \hbox (20.0pt too wide) in paragraph at lines 432--446 [] [] -Overfull \hbox (19.5973pt too wide) in paragraph at lines 430--444 +Overfull \hbox (19.5973pt too wide) in paragraph at lines 432--446 []$$[]$$[]$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 430--444 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 432--446 [] [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 430--444 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 432--446 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 430--444 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 432--446 [] [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 430--444 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 432--446 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 430--444 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 432--446 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (19.5973pt too wide) in paragraph at lines 430--444 +Overfull \hbox (19.5973pt too wide) in paragraph at lines 432--446 []$$[]$$[]$ [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 430--444 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 432--446 []$$[]$$[]$ [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 430--444 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 432--446 []$$[]$$[]$ [] -Overfull \hbox (25.84732pt too wide) in paragraph at lines 430--444 +Overfull \hbox (25.84732pt too wide) in paragraph at lines 432--446 []$$[]$$[]$ [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 430--444 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 432--446 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 430--444 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 432--446 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (19.5973pt too wide) in paragraph at lines 430--444 +Overfull \hbox (19.5973pt too wide) in paragraph at lines 432--446 []$$[]$$[]$ [] -Overfull \hbox (19.5973pt too wide) in paragraph at lines 430--444 +Overfull \hbox (19.5973pt too wide) in paragraph at lines 432--446 []$$[]$$[]$ [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 430--444 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 432--446 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (19.5973pt too wide) in paragraph at lines 430--444 +Overfull \hbox (19.5973pt too wide) in paragraph at lines 432--446 []$$[]$$[]$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 430--444 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 432--446 [] [] -Overfull \hbox (21.7221pt too wide) in paragraph at lines 430--444 +Overfull \hbox (21.7221pt too wide) in paragraph at lines 432--446 [][] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 430--444 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 432--446 [] [] -Overfull \hbox (19.5973pt too wide) in paragraph at lines 430--444 +Overfull \hbox (19.5973pt too wide) in paragraph at lines 432--446 []$$[]$$[]$ [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 430--444 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 432--446 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (23.31656pt too wide) in paragraph at lines 430--444 +Overfull \hbox (23.31656pt too wide) in paragraph at lines 432--446 \OML/cmm/m/it/10 ^^[[]$ [] -Overfull \hbox (19.5973pt too wide) in paragraph at lines 430--444 +Overfull \hbox (19.5973pt too wide) in paragraph at lines 432--446 []$$[]$$[]$ [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 430--444 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 432--446 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (19.28604pt too wide) in paragraph at lines 430--444 +Overfull \hbox (19.28604pt too wide) in paragraph at lines 432--446 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (19.5973pt too wide) in paragraph at lines 430--444 +Overfull \hbox (19.5973pt too wide) in paragraph at lines 432--446 []$$[]$$[]$ [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 430--444 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 432--446 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 430--444 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 432--446 []$$[]$$[]$ [] ! Undefined control sequence. -l.445 \figuremacro +l.447 \figuremacro {fig-11a-f}{Selected low-energy configurations of (H$_2$O)... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -45270,22 +44814,22 @@ Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 445--447 +Overfull \hbox (20.0pt too wide) in paragraph at lines 447--449 [] [] -Overfull \hbox (19.5973pt too wide) in paragraph at lines 445--447 +Overfull \hbox (19.5973pt too wide) in paragraph at lines 447--449 []$$[]$$[]$ [] -Overfull \hbox (10.73615pt too wide) in paragraph at lines 445--447 +Overfull \hbox (10.73615pt too wide) in paragraph at lines 447--449 []$ [] ! Undefined control sequence. -l.448 \figuremacro +l.450 \figuremacro {fig-12a-f}{Selected low-energy configurations of (H$_2$O)... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -45396,22 +44940,22 @@ Missing character: There is no o in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 448--450 +Overfull \hbox (20.0pt too wide) in paragraph at lines 450--452 [] [] -Overfull \hbox (19.5973pt too wide) in paragraph at lines 448--450 +Overfull \hbox (19.5973pt too wide) in paragraph at lines 450--452 []$$[]$$[]$ [] -Overfull \hbox (10.73615pt too wide) in paragraph at lines 448--450 +Overfull \hbox (10.73615pt too wide) in paragraph at lines 450--452 []$ [] ! Undefined control sequence. -l.452 \subsection +l.454 \subsection {Mass Spectra of Fragments with Excess Proton} \label{mass-... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -45458,7 +45002,7 @@ Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 452--453 +Overfull \hbox (20.0pt too wide) in paragraph at lines 454--455 [] [] @@ -45704,7 +45248,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.454 ...s shaped as mass spectra.\cite{Braud2019} +l.456 ...s shaped as mass spectra.\cite{Braud2019} For each cluster size, on... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -45713,7 +45257,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Braud2019' on page undefined on input line 454. +LaTeX Warning: Citation `Braud2019' on page undefined on input line 456. Missing character: There is no ] in font nullfont! Missing character: There is no F in font nullfont! @@ -45886,7 +45430,7 @@ Missing character: There is no s in font nullfont! ! Undefined control sequence. ...R-1w-4w-Ne-Ar-branch' on page \thepage \space undefined\on@line . -l.454 ...n Figures~\ref{MS-BR-1w-4w-Ne-Ar-branch} +l.456 ...n Figures~\ref{MS-BR-1w-4w-Ne-Ar-branch} , \ref{MS-BR-5w-11w-Ne-Ar-... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -45896,13 +45440,13 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `MS-BR-1w-4w-Ne-Ar-branch' on page undefined on input - line 454. + line 456. Missing character: There is no , in font nullfont! ! Undefined control sequence. ...-5w-11w-Ne-Ar-branch' on page \thepage \space undefined\on@line . -l.454 ...-branch}, \ref{MS-BR-5w-11w-Ne-Ar-branch} +l.456 ...-branch}, \ref{MS-BR-5w-11w-Ne-Ar-branch} and \ref{MS-BR-12w-Ne-bra... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -45912,7 +45456,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `MS-BR-5w-11w-Ne-Ar-branch' on page undefined on inpu -t line 454. +t line 456. Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! @@ -45920,7 +45464,7 @@ Missing character: There is no d in font nullfont! ! Undefined control sequence. ...`MS-BR-12w-Ne-branch' on page \thepage \space undefined\on@line . -l.454 ...-Ar-branch} and \ref{MS-BR-12w-Ne-branch} +l.456 ...-Ar-branch} and \ref{MS-BR-12w-Ne-branch} . For cluster (H$_2$O)$_{1... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -45930,7 +45474,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `MS-BR-12w-Ne-branch' on page undefined on input line - 454. + 456. Missing character: There is no . in font nullfont! Missing character: There is no F in font nullfont! @@ -46333,57 +45877,57 @@ Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 454--456 +Overfull \hbox (20.0pt too wide) in paragraph at lines 456--458 [] [] -Overfull \hbox (46.54184pt too wide) in paragraph at lines 454--456 +Overfull \hbox (46.54184pt too wide) in paragraph at lines 456--458 []$$[]$$[]$ [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 454--456 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 456--458 [] [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 454--456 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 456--458 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 454--456 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 456--458 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 454--456 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 456--458 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 454--456 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 456--458 [] [] -Overfull \hbox (19.5973pt too wide) in paragraph at lines 454--456 +Overfull \hbox (19.5973pt too wide) in paragraph at lines 456--458 []$$[]$$[]$ [] -Overfull \hbox (19.5973pt too wide) in paragraph at lines 454--456 +Overfull \hbox (19.5973pt too wide) in paragraph at lines 456--458 []$$[]$$[]$ [] -Overfull \hbox (19.5973pt too wide) in paragraph at lines 454--456 +Overfull \hbox (19.5973pt too wide) in paragraph at lines 456--458 []$$[]$$[]$ [] ! Undefined control sequence. -l.457 \figuremacro +l.459 \figuremacro {MS-BR-1w-4w-Ne-Ar-branch}{Simulated mass spectra (positiv... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -46660,32 +46204,32 @@ Missing character: There is no a in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 457--458 +Overfull \hbox (20.0pt too wide) in paragraph at lines 459--460 [] [] -Overfull \hbox (16.56837pt too wide) in paragraph at lines 457--458 +Overfull \hbox (16.56837pt too wide) in paragraph at lines 459--460 []$$[]$$[]$ [] -Overfull \hbox (16.56837pt too wide) in paragraph at lines 457--458 +Overfull \hbox (16.56837pt too wide) in paragraph at lines 459--460 []$$[]$$[]$ [] -Overfull \hbox (16.56837pt too wide) in paragraph at lines 457--458 +Overfull \hbox (16.56837pt too wide) in paragraph at lines 459--460 []$$[]$$[]$ [] -Overfull \hbox (16.56837pt too wide) in paragraph at lines 457--458 +Overfull \hbox (16.56837pt too wide) in paragraph at lines 459--460 []$$[]$$[]$ [] ! Undefined control sequence. -l.459 \figuremacro +l.461 \figuremacro {MS-BR-5w-11w-Ne-Ar-branch}{Simulated mass spectra (positi... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -46924,22 +46468,22 @@ Missing character: There is no a in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 459--460 +Overfull \hbox (20.0pt too wide) in paragraph at lines 461--462 [] [] -Overfull \hbox (16.56837pt too wide) in paragraph at lines 459--460 +Overfull \hbox (16.56837pt too wide) in paragraph at lines 461--462 []$$[]$$[]$ [] -Overfull \hbox (16.56837pt too wide) in paragraph at lines 459--460 +Overfull \hbox (16.56837pt too wide) in paragraph at lines 461--462 []$$[]$$[]$ [] ! Undefined control sequence. -l.461 \figuremacro +l.463 \figuremacro {MS-BR-12w-Ne-branch}{Simulated mass spectra (positive are... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -47204,27 +46748,27 @@ Missing character: There is no n in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 461--462 +Overfull \hbox (20.0pt too wide) in paragraph at lines 463--464 [] [] -Overfull \hbox (16.56837pt too wide) in paragraph at lines 461--462 +Overfull \hbox (16.56837pt too wide) in paragraph at lines 463--464 []$$[]$$[]$ [] -Overfull \hbox (16.56837pt too wide) in paragraph at lines 461--462 +Overfull \hbox (16.56837pt too wide) in paragraph at lines 463--464 []$$[]$$[]$ [] -Overfull \hbox (16.56837pt too wide) in paragraph at lines 461--462 +Overfull \hbox (16.56837pt too wide) in paragraph at lines 463--464 []$$[]$$[]$ [] -Overfull \hbox (16.56837pt too wide) in paragraph at lines 461--462 +Overfull \hbox (16.56837pt too wide) in paragraph at lines 463--464 []$$[]$$[]$ [] @@ -47665,7 +47209,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ... Reference `tab:full' on page \thepage \space undefined\on@line . -l.464 in Table~\ref{tab:full} +l.466 in Table~\ref{tab:full} ; (iv) Pure protonated water fragments only app... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -47674,7 +47218,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `tab:full' on page undefined on input line 464. +LaTeX Warning: Reference `tab:full' on page undefined on input line 466. Missing character: There is no ; in font nullfont! Missing character: There is no ( in font nullfont! @@ -47959,22 +47503,22 @@ Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 463--466 +Overfull \hbox (20.0pt too wide) in paragraph at lines 465--468 [] [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 463--466 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 465--468 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 463--466 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 465--468 [] [] -Overfull \hbox (6.00235pt too wide) in paragraph at lines 463--466 +Overfull \hbox (6.00235pt too wide) in paragraph at lines 465--468 \OML/cmm/m/it/10 n$ [] @@ -48519,7 +48063,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...-5w-11w-Ne-Ar-branch' on page \thepage \space undefined\on@line . -l.468 ...in Figure \ref{MS-BR-5w-11w-Ne-Ar-branch} +l.470 ...in Figure \ref{MS-BR-5w-11w-Ne-Ar-branch} (e). The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -48529,7 +48073,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `MS-BR-5w-11w-Ne-Ar-branch' on page undefined on inpu -t line 468. +t line 470. Missing character: There is no ( in font nullfont! Missing character: There is no e in font nullfont! @@ -48600,62 +48144,62 @@ Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 467--470 +Overfull \hbox (20.0pt too wide) in paragraph at lines 469--472 [] [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 467--470 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 469--472 []$$[]$$[]$ [] -Overfull \hbox (11.12505pt too wide) in paragraph at lines 467--470 +Overfull \hbox (11.12505pt too wide) in paragraph at lines 469--472 []$$[]$ [] -Overfull \hbox (6.63892pt too wide) in paragraph at lines 467--470 +Overfull \hbox (6.63892pt too wide) in paragraph at lines 469--472 []$ [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 467--470 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 469--472 []$$[]$$[]$ [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 467--470 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 469--472 []$$[]$$[]$ [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 467--470 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 469--472 []$$[]$$[]$ [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 467--470 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 469--472 []$$[]$$[]$ [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 467--470 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 469--472 []$$[]$$[]$ [] -Overfull \hbox (7.7778pt too wide) in paragraph at lines 467--470 +Overfull \hbox (7.7778pt too wide) in paragraph at lines 469--472 \/cmr/m/n/10 +$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 467--470 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 469--472 [] [] -Overfull \hbox (36.3057pt too wide) in paragraph at lines 467--470 +Overfull \hbox (36.3057pt too wide) in paragraph at lines 469--472 []$$[]$$[]$ [] @@ -48673,7 +48217,7 @@ Missing character: There is no s in font nullfont! ! Undefined control sequence. ...R-1w-4w-Ne-Ar-branch' on page \thepage \space undefined\on@line . -l.471 From Figures \ref{MS-BR-1w-4w-Ne-Ar-branch} +l.473 From Figures \ref{MS-BR-1w-4w-Ne-Ar-branch} , \ref{MS-BR-5w-11w-Ne-Ar-b... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -48683,13 +48227,13 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `MS-BR-1w-4w-Ne-Ar-branch' on page undefined on input - line 471. + line 473. Missing character: There is no , in font nullfont! ! Undefined control sequence. ...-5w-11w-Ne-Ar-branch' on page \thepage \space undefined\on@line . -l.471 ...-branch}, \ref{MS-BR-5w-11w-Ne-Ar-branch} +l.473 ...-branch}, \ref{MS-BR-5w-11w-Ne-Ar-branch} and \ref{MS-BR-12w-Ne-bra... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -48699,7 +48243,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `MS-BR-5w-11w-Ne-Ar-branch' on page undefined on inpu -t line 471. +t line 473. Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! @@ -48707,7 +48251,7 @@ Missing character: There is no d in font nullfont! ! Undefined control sequence. ...`MS-BR-12w-Ne-branch' on page \thepage \space undefined\on@line . -l.471 ...-Ar-branch} and \ref{MS-BR-12w-Ne-branch} +l.473 ...-Ar-branch} and \ref{MS-BR-12w-Ne-branch} , it is clear that the sma... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -48717,7 +48261,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `MS-BR-12w-Ne-branch' on page undefined on input line - 471. + 473. Missing character: There is no , in font nullfont! Missing character: There is no i in font nullfont! @@ -48769,7 +48313,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...R-1w-4w-Ne-Ar-branch' on page \thepage \space undefined\on@line . -l.471 ...ept Figure \ref{MS-BR-1w-4w-Ne-Ar-branch} +l.473 ...ept Figure \ref{MS-BR-1w-4w-Ne-Ar-branch} (b)) is, the better the a... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -48779,7 +48323,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `MS-BR-1w-4w-Ne-Ar-branch' on page undefined on input - line 471. + line 473. Missing character: There is no ( in font nullfont! Missing character: There is no b in font nullfont! @@ -49320,7 +48864,7 @@ Missing character: There is no n in font nullfont! ! Undefined control sequence. ...ng: Reference `large' on page \thepage \space undefined\on@line . -l.473 ...nclusions obtained in section~\ref{large} +l.475 ...nclusions obtained in section~\ref{large} for (H$_2$O)$_{12}$UH$^+$ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -49329,7 +48873,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `large' on page undefined on input line 473. +LaTeX Warning: Reference `large' on page undefined on input line 475. Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! @@ -49383,7 +48927,7 @@ Missing character: There is no n in font nullfont! ! Undefined control sequence. ...ng: Reference `small' on page \thepage \space undefined\on@line . -l.474 ...terpretation given in section~\ref{small} +l.476 ...terpretation given in section~\ref{small} for (H$_2$O)$_{7}$UH$^+$.... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -49392,7 +48936,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `small' on page undefined on input line 474. +LaTeX Warning: Reference `small' on page undefined on input line 476. Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! @@ -49457,7 +49001,7 @@ Missing character: There is no n in font nullfont! ! Undefined control sequence. ...ng: Reference `large' on page \thepage \space undefined\on@line . -l.475 in section~\ref{large} +l.477 in section~\ref{large} for (H$_2$O)$_{11}$UH$^+$ do no evidence the co... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -49466,7 +49010,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `large' on page undefined on input line 475. +LaTeX Warning: Reference `large' on page undefined on input line 477. Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! @@ -49587,92 +49131,92 @@ Missing character: There is no U in font nullfont! Missing character: There is no H in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 471--477 +Overfull \hbox (20.0pt too wide) in paragraph at lines 473--479 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 471--477 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 473--479 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 471--477 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 473--479 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 471--477 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 473--479 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 471--477 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 473--479 [] [] -Overfull \hbox (13.79991pt too wide) in paragraph at lines 471--477 +Overfull \hbox (13.79991pt too wide) in paragraph at lines 473--479 \OT1/cmr/m/it/10 i.e. [] -Overfull \hbox (16.55786pt too wide) in paragraph at lines 471--477 +Overfull \hbox (16.55786pt too wide) in paragraph at lines 473--479 \OML/cmm/m/it/10 n \/cmr/m/n/10 = [] -Overfull \hbox (12.77782pt too wide) in paragraph at lines 471--477 +Overfull \hbox (12.77782pt too wide) in paragraph at lines 473--479 \/cmr/m/n/10 1 \OMS/cmsy/m/n/10 ^^@ [] -Overfull \hbox (5.00002pt too wide) in paragraph at lines 471--477 +Overfull \hbox (5.00002pt too wide) in paragraph at lines 473--479 \/cmr/m/n/10 6$ [] -Overfull \hbox (6.00235pt too wide) in paragraph at lines 471--477 +Overfull \hbox (6.00235pt too wide) in paragraph at lines 473--479 \OML/cmm/m/it/10 n$ [] -Overfull \hbox (13.79991pt too wide) in paragraph at lines 471--477 +Overfull \hbox (13.79991pt too wide) in paragraph at lines 473--479 \OT1/cmr/m/it/10 i.e. [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 471--477 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 473--479 [] [] -Overfull \hbox (19.5973pt too wide) in paragraph at lines 471--477 +Overfull \hbox (19.5973pt too wide) in paragraph at lines 473--479 []$$[]$$[]$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 471--477 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 473--479 [] [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 471--477 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 473--479 []$$[]$$[]$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 471--477 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 473--479 [] [] -Overfull \hbox (19.5973pt too wide) in paragraph at lines 471--477 +Overfull \hbox (19.5973pt too wide) in paragraph at lines 473--479 []$$[]$$[]$ [] -Overfull \hbox (19.5973pt too wide) in paragraph at lines 471--477 +Overfull \hbox (19.5973pt too wide) in paragraph at lines 473--479 []$$[]$$[]$ [] @@ -50006,7 +49550,7 @@ Missing character: There is no n in font nullfont! ! Undefined control sequence. ...ing: Reference `time' on page \thepage \space undefined\on@line . -l.480 ...lected trajectories in section~\ref{time} +l.482 ...lected trajectories in section~\ref{time} . To certify this, the tot... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -50015,7 +49559,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `time' on page undefined on input line 480. +LaTeX Warning: Reference `time' on page undefined on input line 482. Missing character: There is no . in font nullfont! Missing character: There is no T in font nullfont! @@ -50338,7 +49882,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...ence `tab:fragenergy' on page \thepage \space undefined\on@line . -l.481 ...re reported in Table~\ref{tab:fragenergy} +l.483 ...re reported in Table~\ref{tab:fragenergy} for five cases. When $\De... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -50347,7 +49891,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `tab:fragenergy' on page undefined on input line 481. +LaTeX Warning: Reference `tab:fragenergy' on page undefined on input line 483. Missing character: There is no f in font nullfont! @@ -50629,87 +50173,87 @@ Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 479--484 +Overfull \hbox (20.0pt too wide) in paragraph at lines 481--486 [] [] -Overfull \hbox (6.02548pt too wide) in paragraph at lines 479--484 +Overfull \hbox (6.02548pt too wide) in paragraph at lines 481--486 \OML/cmm/m/it/10 ^^V$ [] -Overfull \hbox (29.83345pt too wide) in paragraph at lines 479--484 +Overfull \hbox (29.83345pt too wide) in paragraph at lines 481--486 []$$[]$$[]$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 479--484 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 481--486 [] [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 479--484 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 481--486 []$$[]$$[]$ [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 479--484 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 481--486 []$$[]$$[]$ [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 479--484 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 481--486 []$$[]$$[]$ [] -Overfull \hbox (7.7778pt too wide) in paragraph at lines 479--484 +Overfull \hbox (7.7778pt too wide) in paragraph at lines 481--486 \OMS/cmsy/m/n/10 ^^B$ [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 479--484 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 481--486 []$$[]$$[]$ [] -Overfull \hbox (4.48613pt too wide) in paragraph at lines 479--484 +Overfull \hbox (4.48613pt too wide) in paragraph at lines 481--486 []$ [] -Overfull \hbox (16.29167pt too wide) in paragraph at lines 479--484 +Overfull \hbox (16.29167pt too wide) in paragraph at lines 481--486 \/cmr/m/n/10 ^^A\OML/cmm/m/it/10 E$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 479--484 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 481--486 [] [] -Overfull \hbox (16.29167pt too wide) in paragraph at lines 479--484 +Overfull \hbox (16.29167pt too wide) in paragraph at lines 481--486 \/cmr/m/n/10 ^^A\OML/cmm/m/it/10 E$ [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 479--484 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 481--486 []$$[]$$[]$ [] -Overfull \hbox (16.29167pt too wide) in paragraph at lines 479--484 +Overfull \hbox (16.29167pt too wide) in paragraph at lines 481--486 \/cmr/m/n/10 ^^A\OML/cmm/m/it/10 E$ [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 479--484 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 481--486 []$$[]$$[]$ [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 479--484 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 481--486 []$$[]$$[]$ [] @@ -50720,14 +50264,14 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.485 \begin{table} +l.487 \begin{table} Your command was ignored. Type I to replace it with another command, or to continue without it. -Overfull \hbox (20.0pt too wide) in paragraph at lines 486--486 +Overfull \hbox (20.0pt too wide) in paragraph at lines 488--488 [] [] @@ -50738,7 +50282,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.487 \caption +l.489 \caption {Energies of different (H$_2$O)$_6$UH$^+$ fragments select... You're in trouble here. Try typing to proceed. @@ -50928,7 +50472,7 @@ Missing character: There is no . in font nullfont! ! Undefined control sequence. \boldm -l.491 \textbf{\boldm{$E_{(H_2O)_6UH^+}$}} +l.493 \textbf{\boldm{$E_{(H_2O)_6UH^+}$}} & \textbf{\boldm{$E_{(H_2O)_... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -50939,7 +50483,7 @@ and I'll forget about whatever was undefined. ! Undefined control sequence. \boldm -l.491 ...$}} & \textbf{\boldm{$E_{(H_2O)_5UH^+}$}} +l.493 ...$}} & \textbf{\boldm{$E_{(H_2O)_5UH^+}$}} & \textbf{\boldm{$E_{H_2O... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -50950,7 +50494,7 @@ and I'll forget about whatever was undefined. ! Undefined control sequence. \boldm -l.491 ...)_5UH^+}$}} & \textbf{\boldm{$E_{H_2O}$}} +l.493 ...)_5UH^+}$}} & \textbf{\boldm{$E_{H_2O}$}} & \textbf{\boldm{$\Delta ... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -50961,7 +50505,7 @@ and I'll forget about whatever was undefined. ! Undefined control sequence. \boldm -l.491 ...E_{H_2O}$}} & \textbf{\boldm{$\Delta E$}} +l.493 ...E_{H_2O}$}} & \textbf{\boldm{$\Delta E$}} \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -51096,42 +50640,42 @@ Missing character: There is no 1 in font nullfont! Missing character: There is no 0 in font nullfont! Missing character: There is no 9 in font nullfont! -Overfull \hbox (15.61118pt too wide) in paragraph at lines 487--504 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 489--506 []$$[]$$[]$ [] -Overfull \hbox (15.61118pt too wide) in paragraph at lines 487--504 +Overfull \hbox (15.61118pt too wide) in paragraph at lines 489--506 []$$[]$$[]$ [] -Overfull \hbox (4.48613pt too wide) in paragraph at lines 487--504 +Overfull \hbox (4.48613pt too wide) in paragraph at lines 489--506 []$ [] -Overfull \hbox (16.29167pt too wide) in paragraph at lines 487--504 +Overfull \hbox (16.29167pt too wide) in paragraph at lines 489--506 \/cmr/m/n/10 ^^A\OML/cmm/m/it/10 E$ [] -Overfull \hbox (53.70665pt too wide) in paragraph at lines 487--504 +Overfull \hbox (53.70665pt too wide) in paragraph at lines 489--506 \OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (53.70665pt too wide) in paragraph at lines 487--504 +Overfull \hbox (53.70665pt too wide) in paragraph at lines 489--506 \OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (24.63188pt too wide) in paragraph at lines 487--504 +Overfull \hbox (24.63188pt too wide) in paragraph at lines 489--506 \OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (148.33685pt too wide) in paragraph at lines 487--504 +Overfull \hbox (148.33685pt too wide) in paragraph at lines 489--506 [] [] @@ -51142,14 +50686,14 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.505 \end{table} +l.507 \end{table} Your command was ignored. Type I to replace it with another command, or to continue without it. ! Undefined control sequence. -l.507 \subsection +l.509 \subsection {Conclusions about CID of (H$_2$O)$_{n}$UH$^+$} \label{Concl} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -51185,12 +50729,12 @@ Missing character: There is no ) in font nullfont! Missing character: There is no U in font nullfont! Missing character: There is no H in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 507--508 +Overfull \hbox (20.0pt too wide) in paragraph at lines 509--510 [] [] -Overfull \hbox (16.56837pt too wide) in paragraph at lines 507--508 +Overfull \hbox (16.56837pt too wide) in paragraph at lines 509--510 []$$[]$$[]$ [] @@ -51535,22 +51079,22 @@ Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 509--513 +Overfull \hbox (20.0pt too wide) in paragraph at lines 511--515 [] [] -Overfull \hbox (46.54184pt too wide) in paragraph at lines 509--513 +Overfull \hbox (46.54184pt too wide) in paragraph at lines 511--515 []$$[]$$[]$ [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 509--513 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 511--515 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (23.31656pt too wide) in paragraph at lines 509--513 +Overfull \hbox (23.31656pt too wide) in paragraph at lines 511--515 \OML/cmm/m/it/10 ^^[[]$ [] @@ -53225,92 +52769,92 @@ Missing character: There is no U in font nullfont! Missing character: There is no H in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 514--518 +Overfull \hbox (20.0pt too wide) in paragraph at lines 516--520 [] [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 514--518 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 516--520 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (25.84732pt too wide) in paragraph at lines 514--518 +Overfull \hbox (25.84732pt too wide) in paragraph at lines 516--520 []$$[]$$[]$ [] -Overfull \hbox (25.84732pt too wide) in paragraph at lines 514--518 +Overfull \hbox (25.84732pt too wide) in paragraph at lines 516--520 []$$[]$$[]$ [] -Overfull \hbox (13.79991pt too wide) in paragraph at lines 514--518 +Overfull \hbox (13.79991pt too wide) in paragraph at lines 516--520 \OT1/cmr/m/it/10 i.e. [] -Overfull \hbox (10.73615pt too wide) in paragraph at lines 514--518 +Overfull \hbox (10.73615pt too wide) in paragraph at lines 516--520 []$ [] -Overfull \hbox (32.20845pt too wide) in paragraph at lines 514--518 +Overfull \hbox (32.20845pt too wide) in paragraph at lines 516--520 []$$[]$$[]$ [] -Overfull \hbox (10.73615pt too wide) in paragraph at lines 514--518 +Overfull \hbox (10.73615pt too wide) in paragraph at lines 516--520 []$ [] -Overfull \hbox (21.9723pt too wide) in paragraph at lines 514--518 +Overfull \hbox (21.9723pt too wide) in paragraph at lines 516--520 []$$[]$$[]$ [] -Overfull \hbox (29.94456pt too wide) in paragraph at lines 514--518 +Overfull \hbox (29.94456pt too wide) in paragraph at lines 516--520 []$$[]$$[]$ [] -Overfull \hbox (29.94456pt too wide) in paragraph at lines 514--518 +Overfull \hbox (29.94456pt too wide) in paragraph at lines 516--520 []$$[]$$[]$ [] -Overfull \hbox (25.84732pt too wide) in paragraph at lines 514--518 +Overfull \hbox (25.84732pt too wide) in paragraph at lines 516--520 []$$[]$$[]$ [] -Overfull \hbox (25.84732pt too wide) in paragraph at lines 514--518 +Overfull \hbox (25.84732pt too wide) in paragraph at lines 516--520 []$$[]$$[]$ [] -Overfull \hbox (25.84732pt too wide) in paragraph at lines 514--518 +Overfull \hbox (25.84732pt too wide) in paragraph at lines 516--520 []$$[]$$[]$ [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 514--518 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 516--520 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (29.94456pt too wide) in paragraph at lines 514--518 +Overfull \hbox (29.94456pt too wide) in paragraph at lines 516--520 []$$[]$$[]$ [] -Overfull \hbox (25.68921pt too wide) in paragraph at lines 514--518 +Overfull \hbox (25.68921pt too wide) in paragraph at lines 516--520 \OML/cmm/m/it/10 P[]$ [] -Overfull \hbox (29.94456pt too wide) in paragraph at lines 514--518 +Overfull \hbox (29.94456pt too wide) in paragraph at lines 516--520 []$$[]$$[]$ [] @@ -53701,12 +53245,12 @@ Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 519--522 +Overfull \hbox (20.0pt too wide) in paragraph at lines 521--524 [] [] ! Undefined control sequence. -l.525 \section +l.527 \section {Dynamical Simulation of Collision-Induced Dissociation for Py... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -53785,12 +53329,12 @@ Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 525--526 +Overfull \hbox (20.0pt too wide) in paragraph at lines 527--528 [] [] ! Undefined control sequence. -l.527 \subsection +l.529 \subsection {Introduction} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -53811,7 +53355,7 @@ Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 527--528 +Overfull \hbox (20.0pt too wide) in paragraph at lines 529--530 [] [] @@ -54034,7 +53578,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.530 ...aggese2015, Eaves2015, Mao2017, Wang2018} +l.532 ...aggese2015, Eaves2015, Mao2017, Wang2018} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -54043,14 +53587,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Chung2011' on page undefined on input line 530. +LaTeX Warning: Citation `Chung2011' on page undefined on input line 532. Missing character: There is no , in font nullfont! \citation{Saggese2015} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.530 ...aggese2015, Eaves2015, Mao2017, Wang2018} +l.532 ...aggese2015, Eaves2015, Mao2017, Wang2018} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -54059,14 +53603,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Saggese2015' on page undefined on input line 530. +LaTeX Warning: Citation `Saggese2015' on page undefined on input line 532. Missing character: There is no , in font nullfont! \citation{Eaves2015} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.530 ...aggese2015, Eaves2015, Mao2017, Wang2018} +l.532 ...aggese2015, Eaves2015, Mao2017, Wang2018} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -54075,14 +53619,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Eaves2015' on page undefined on input line 530. +LaTeX Warning: Citation `Eaves2015' on page undefined on input line 532. Missing character: There is no , in font nullfont! \citation{Mao2017} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.530 ...aggese2015, Eaves2015, Mao2017, Wang2018} +l.532 ...aggese2015, Eaves2015, Mao2017, Wang2018} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -54091,14 +53635,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Mao2017' on page undefined on input line 530. +LaTeX Warning: Citation `Mao2017' on page undefined on input line 532. Missing character: There is no , in font nullfont! \citation{Wang2018} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.530 ...aggese2015, Eaves2015, Mao2017, Wang2018} +l.532 ...aggese2015, Eaves2015, Mao2017, Wang2018} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -54107,7 +53651,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Wang2018' on page undefined on input line 530. +LaTeX Warning: Citation `Wang2018' on page undefined on input line 532. Missing character: There is no ] in font nullfont! Missing character: There is no I in font nullfont! @@ -54335,7 +53879,6 @@ Missing character: There is no d in font nullfont! Missing character: There is no u in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! -Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! Missing character: There is no c in font nullfont! Missing character: There is no h in font nullfont! @@ -54364,7 +53907,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.531 ...tions. \cite{Kyrtopoulos2001, Farmer2003} +l.533 ...tions. \cite{Kyrtopoulos2001, Farmer2003} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -54373,7 +53916,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Kyrtopoulos2001' on page undefined on input line 531. +LaTeX Warning: Citation `Kyrtopoulos2001' on page undefined on input line 533. Missing character: There is no , in font nullfont! @@ -54381,7 +53924,7 @@ Missing character: There is no , in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.531 ...tions. \cite{Kyrtopoulos2001, Farmer2003} +l.533 ...tions. \cite{Kyrtopoulos2001, Farmer2003} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -54390,7 +53933,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Farmer2003' on page undefined on input line 531. +LaTeX Warning: Citation `Farmer2003' on page undefined on input line 533. Missing character: There is no ] in font nullfont! Missing character: There is no I in font nullfont! @@ -54554,7 +54097,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.532 ...ted as the prototypes.\cite{Aumaitre2019} +l.534 ...ted as the prototypes.\cite{Aumaitre2019} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -54563,7 +54106,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Aumaitre2019' on page undefined on input line 532. +LaTeX Warning: Citation `Aumaitre2019' on page undefined on input line 534. Missing character: There is no ] in font nullfont! Missing character: There is no I in font nullfont! @@ -54696,7 +54239,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.533 ... and stable structure. \cite{Tielens2008} +l.535 ... and stable structure. \cite{Tielens2008} The PAH clusters are impo... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -54705,7 +54248,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Tielens2008' on page undefined on input line 533. +LaTeX Warning: Citation `Tielens2008' on page undefined on input line 535. Missing character: There is no ] in font nullfont! Missing character: There is no T in font nullfont! @@ -54914,7 +54457,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.533 ...niverse. \cite{Leger1984,Allamandola1985} +l.535 ...niverse. \cite{Leger1984,Allamandola1985} The broadening of these b... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -54923,14 +54466,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Leger1984' on page undefined on input line 533. +LaTeX Warning: Citation `Leger1984' on page undefined on input line 535. Missing character: There is no , in font nullfont! \citation{Allamandola1985} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.533 ...niverse. \cite{Leger1984,Allamandola1985} +l.535 ...niverse. \cite{Leger1984,Allamandola1985} The broadening of these b... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -54939,7 +54482,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Allamandola1985' on page undefined on input line 533. +LaTeX Warning: Citation `Allamandola1985' on page undefined on input line 535. Missing character: There is no ] in font nullfont! @@ -55157,7 +54700,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.533 ...d region. \cite{Rapacioli2005, Berne2008} +l.535 ...d region. \cite{Rapacioli2005, Berne2008} For all these topics, i... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -55166,14 +54709,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Rapacioli2005' on page undefined on input line 533. +LaTeX Warning: Citation `Rapacioli2005' on page undefined on input line 535. Missing character: There is no , in font nullfont! \citation{Berne2008} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.533 ...d region. \cite{Rapacioli2005, Berne2008} +l.535 ...d region. \cite{Rapacioli2005, Berne2008} For all these topics, i... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -55182,7 +54725,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Berne2008' on page undefined on input line 533. +LaTeX Warning: Citation `Berne2008' on page undefined on input line 535. Missing character: There is no ] in font nullfont! Missing character: There is no F in font nullfont! @@ -55415,72 +54958,72 @@ Missing character: There is no z in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 529--534 +Overfull \hbox (20.0pt too wide) in paragraph at lines 531--536 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 529--534 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 531--536 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 529--534 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 531--536 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 529--534 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 531--536 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 529--534 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 531--536 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 529--534 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 531--536 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 529--534 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 531--536 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 529--534 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 531--536 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 529--534 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 531--536 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 529--534 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 531--536 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 529--534 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 531--536 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 529--534 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 531--536 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 529--534 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 531--536 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 529--534 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 531--536 [] [] @@ -55660,7 +55203,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.536 ...midt2006, Goulart2017, Wang2018, Lei2019} +l.538 ...midt2006, Goulart2017, Wang2018, Lei2019} . Their energetic properti... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -55669,14 +55212,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Eschenbach1998' on page undefined on input line 536. +LaTeX Warning: Citation `Eschenbach1998' on page undefined on input line 538. Missing character: There is no , in font nullfont! \citation{Schmidt2006} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.536 ...midt2006, Goulart2017, Wang2018, Lei2019} +l.538 ...midt2006, Goulart2017, Wang2018, Lei2019} . Their energetic properti... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -55685,14 +55228,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Schmidt2006' on page undefined on input line 536. +LaTeX Warning: Citation `Schmidt2006' on page undefined on input line 538. Missing character: There is no , in font nullfont! \citation{Goulart2017} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.536 ...midt2006, Goulart2017, Wang2018, Lei2019} +l.538 ...midt2006, Goulart2017, Wang2018, Lei2019} . Their energetic properti... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -55701,14 +55244,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Goulart2017' on page undefined on input line 536. +LaTeX Warning: Citation `Goulart2017' on page undefined on input line 538. Missing character: There is no , in font nullfont! \citation{Wang2018} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.536 ...midt2006, Goulart2017, Wang2018, Lei2019} +l.538 ...midt2006, Goulart2017, Wang2018, Lei2019} . Their energetic properti... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -55717,14 +55260,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Wang2018' on page undefined on input line 536. +LaTeX Warning: Citation `Wang2018' on page undefined on input line 538. Missing character: There is no , in font nullfont! \citation{Lei2019} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.536 ...midt2006, Goulart2017, Wang2018, Lei2019} +l.538 ...midt2006, Goulart2017, Wang2018, Lei2019} . Their energetic properti... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -55733,7 +55276,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Lei2019' on page undefined on input line 536. +LaTeX Warning: Citation `Lei2019' on page undefined on input line 538. Missing character: There is no ] in font nullfont! Missing character: There is no . in font nullfont! @@ -55808,7 +55351,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.536 ...ials have been recorded \cite{Joblin2017} +l.538 ...ials have been recorded \cite{Joblin2017} as well as their spectral... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -55817,7 +55360,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Joblin2017' on page undefined on input line 536. +LaTeX Warning: Citation `Joblin2017' on page undefined on input line 538. Missing character: There is no ] in font nullfont! Missing character: There is no a in font nullfont! @@ -55856,7 +55399,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.536 ...l properties \cite{Roser2015,Lemmens2019} +l.538 ...l properties \cite{Roser2015,Lemmens2019} . The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -55865,14 +55408,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Roser2015' on page undefined on input line 536. +LaTeX Warning: Citation `Roser2015' on page undefined on input line 538. Missing character: There is no , in font nullfont! \citation{Lemmens2019} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.536 ...l properties \cite{Roser2015,Lemmens2019} +l.538 ...l properties \cite{Roser2015,Lemmens2019} . The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -55881,7 +55424,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Lemmens2019' on page undefined on input line 536. +LaTeX Warning: Citation `Lemmens2019' on page undefined on input line 538. Missing character: There is no ] in font nullfont! Missing character: There is no . in font nullfont! @@ -56355,7 +55898,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.539 ...lin2017, Gatchell2017, Zamith2019thermal} +l.541 ...lin2017, Gatchell2017, Zamith2019thermal} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -56364,14 +55907,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Schmidt2006' on page undefined on input line 539. +LaTeX Warning: Citation `Schmidt2006' on page undefined on input line 541. Missing character: There is no , in font nullfont! \citation{Holm2010} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.539 ...lin2017, Gatchell2017, Zamith2019thermal} +l.541 ...lin2017, Gatchell2017, Zamith2019thermal} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -56380,14 +55923,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Holm2010' on page undefined on input line 539. +LaTeX Warning: Citation `Holm2010' on page undefined on input line 541. Missing character: There is no , in font nullfont! \citation{Gatchell2015} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.539 ...lin2017, Gatchell2017, Zamith2019thermal} +l.541 ...lin2017, Gatchell2017, Zamith2019thermal} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -56396,14 +55939,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Gatchell2015' on page undefined on input line 539. +LaTeX Warning: Citation `Gatchell2015' on page undefined on input line 541. Missing character: There is no , in font nullfont! \citation{Joblin2017} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.539 ...lin2017, Gatchell2017, Zamith2019thermal} +l.541 ...lin2017, Gatchell2017, Zamith2019thermal} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -56412,14 +55955,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Joblin2017' on page undefined on input line 539. +LaTeX Warning: Citation `Joblin2017' on page undefined on input line 541. Missing character: There is no , in font nullfont! \citation{Gatchell2017} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.539 ...lin2017, Gatchell2017, Zamith2019thermal} +l.541 ...lin2017, Gatchell2017, Zamith2019thermal} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -56428,14 +55971,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Gatchell2017' on page undefined on input line 539. +LaTeX Warning: Citation `Gatchell2017' on page undefined on input line 541. Missing character: There is no , in font nullfont! \citation{Zamith2019thermal} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.539 ...lin2017, Gatchell2017, Zamith2019thermal} +l.541 ...lin2017, Gatchell2017, Zamith2019thermal} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -56444,8 +55987,8 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Zamith2019thermal' on page undefined on input line 53 -9. +LaTeX Warning: Citation `Zamith2019thermal' on page undefined on input line 54 +1. Missing character: There is no ] in font nullfont! Missing character: There is no T in font nullfont! @@ -56633,7 +56176,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.540 ...ciation energies \cite{Zamith2019thermal} +l.542 ...ciation energies \cite{Zamith2019thermal} whereas the oligomerizati... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -56643,7 +56186,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Citation `Zamith2019thermal' on page undefined on input line 54 -0. +2. Missing character: There is no ] in font nullfont! Missing character: There is no w in font nullfont! @@ -56727,7 +56270,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.540 ...igh energy collisions \cite{Delaunay2015} +l.542 ...igh energy collisions \cite{Delaunay2015} or photoabsorption \cite{... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -56736,7 +56279,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Delaunay2015' on page undefined on input line 540. +LaTeX Warning: Citation `Delaunay2015' on page undefined on input line 542. Missing character: There is no ] in font nullfont! Missing character: There is no o in font nullfont! @@ -56761,7 +56304,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.540 ...y2015} or photoabsorption \cite{Zhen2018} +l.542 ...y2015} or photoabsorption \cite{Zhen2018} suggests the possible rol... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -56770,7 +56313,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Zhen2018' on page undefined on input line 540. +LaTeX Warning: Citation `Zhen2018' on page undefined on input line 542. Missing character: There is no ] in font nullfont! Missing character: There is no s in font nullfont! @@ -56845,7 +56388,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.540 ...ellar PAHs growth process \cite{Chen2018} +l.542 ...ellar PAHs growth process \cite{Chen2018} . The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -56854,102 +56397,102 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Chen2018' on page undefined on input line 540. +LaTeX Warning: Citation `Chen2018' on page undefined on input line 542. Missing character: There is no ] in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 535--541 +Overfull \hbox (20.0pt too wide) in paragraph at lines 537--543 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 535--541 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 537--543 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 535--541 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 537--543 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 535--541 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 537--543 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 535--541 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 537--543 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 535--541 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 537--543 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 535--541 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 537--543 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 535--541 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 537--543 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 535--541 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 537--543 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 535--541 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 537--543 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 535--541 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 537--543 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 535--541 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 537--543 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 535--541 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 537--543 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 535--541 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 537--543 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 535--541 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 537--543 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 535--541 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 537--543 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 535--541 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 537--543 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 535--541 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 537--543 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 535--541 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 537--543 [] [] @@ -57125,7 +56668,7 @@ Missing character: There is no e in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! ! Undefined control sequence. -l.542 ...ize of the systems limits the use of {\it +l.544 ...ize of the systems limits the use of {\it ab initio} wave function ... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -57229,7 +56772,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.542 ...ely dimers \cite{Piacenza2005, Birer2015} +l.544 ...ely dimers \cite{Piacenza2005, Birer2015} , whereas larger clusters ... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -57238,14 +56781,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Piacenza2005' on page undefined on input line 542. +LaTeX Warning: Citation `Piacenza2005' on page undefined on input line 544. Missing character: There is no , in font nullfont! \citation{Birer2015} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.542 ...ely dimers \cite{Piacenza2005, Birer2015} +l.544 ...ely dimers \cite{Piacenza2005, Birer2015} , whereas larger clusters ... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -57254,7 +56797,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Birer2015' on page undefined on input line 542. +LaTeX Warning: Citation `Birer2015' on page undefined on input line 544. Missing character: There is no ] in font nullfont! Missing character: There is no , in font nullfont! @@ -57348,7 +56891,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.542 ..., Rapacioli2009corr, Mao2017, Bowal2019} +l.544 ..., Rapacioli2009corr, Mao2017, Bowal2019} . Many of these studies, f... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -57357,7 +56900,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Zhao2008truhlar' on page undefined on input line 542. +LaTeX Warning: Citation `Zhao2008truhlar' on page undefined on input line 544. Missing character: There is no , in font nullfont! @@ -57365,7 +56908,7 @@ Missing character: There is no , in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.542 ..., Rapacioli2009corr, Mao2017, Bowal2019} +l.544 ..., Rapacioli2009corr, Mao2017, Bowal2019} . Many of these studies, f... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -57375,14 +56918,14 @@ and I'll forget about whatever was undefined. LaTeX Warning: Citation `Rapacioli2009corr' on page undefined on input line 54 -2. +4. Missing character: There is no , in font nullfont! \citation{Mao2017} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.542 ..., Rapacioli2009corr, Mao2017, Bowal2019} +l.544 ..., Rapacioli2009corr, Mao2017, Bowal2019} . Many of these studies, f... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -57391,14 +56934,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Mao2017' on page undefined on input line 542. +LaTeX Warning: Citation `Mao2017' on page undefined on input line 544. Missing character: There is no , in font nullfont! \citation{Bowal2019} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.542 ..., Rapacioli2009corr, Mao2017, Bowal2019} +l.544 ..., Rapacioli2009corr, Mao2017, Bowal2019} . Many of these studies, f... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -57407,7 +56950,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Bowal2019' on page undefined on input line 542. +LaTeX Warning: Citation `Bowal2019' on page undefined on input line 544. Missing character: There is no ] in font nullfont! Missing character: There is no . in font nullfont! @@ -57582,7 +57125,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.542 ...eported at the DFT level \cite{Ricca2013} +l.544 ...eported at the DFT level \cite{Ricca2013} . Most of the theoretical ... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -57591,7 +57134,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Ricca2013' on page undefined on input line 542. +LaTeX Warning: Citation `Ricca2013' on page undefined on input line 544. Missing character: There is no ] in font nullfont! Missing character: There is no . in font nullfont! @@ -57744,7 +57287,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.542 ... DFT based methods \cite{Grafenstein2009} +l.544 ... DFT based methods \cite{Grafenstein2009} . The singly charged PAH c... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -57753,7 +57296,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Grafenstein2009' on page undefined on input line 542. +LaTeX Warning: Citation `Grafenstein2009' on page undefined on input line 544. Missing character: There is no ] in font nullfont! @@ -57865,7 +57408,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.542 ...onance stabilization.\cite{Rapacioli2009} +l.544 ...onance stabilization.\cite{Rapacioli2009} Cationic PAH clusters are... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -57874,7 +57417,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Rapacioli2009' on page undefined on input line 542. +LaTeX Warning: Citation `Rapacioli2009' on page undefined on input line 544. Missing character: There is no ] in font nullfont! Missing character: There is no C in font nullfont! @@ -58228,7 +57771,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.542 ...g ionisation potentials \cite{Joblin2017} +l.544 ...g ionisation potentials \cite{Joblin2017} as well as structural \ci... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -58237,7 +57780,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Joblin2017' on page undefined on input line 542. +LaTeX Warning: Citation `Joblin2017' on page undefined on input line 544. Missing character: There is no ] in font nullfont! Missing character: There is no a in font nullfont! @@ -58263,7 +57806,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.542 ...} as well as structural \cite{Dontot2019} +l.544 ...} as well as structural \cite{Dontot2019} and spectral (electronic ... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -58272,7 +57815,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Dontot2019' on page undefined on input line 542. +LaTeX Warning: Citation `Dontot2019' on page undefined on input line 544. Missing character: There is no ] in font nullfont! Missing character: There is no a in font nullfont! @@ -58302,7 +57845,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.542 ...nd spectral (electronic \cite{Dontot2016} +l.544 ...nd spectral (electronic \cite{Dontot2016} and vibrational \cite{Don... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -58311,7 +57854,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Dontot2016' on page undefined on input line 542. +LaTeX Warning: Citation `Dontot2016' on page undefined on input line 544. Missing character: There is no ] in font nullfont! Missing character: There is no a in font nullfont! @@ -58333,7 +57876,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.542 ...ot2016} and vibrational \cite{Dontot2020} +l.544 ...ot2016} and vibrational \cite{Dontot2020} ) properties of cations, p... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -58342,7 +57885,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Dontot2020' on page undefined on input line 542. +LaTeX Warning: Citation `Dontot2020' on page undefined on input line 544. Missing character: There is no ] in font nullfont! Missing character: There is no ) in font nullfont! @@ -58412,7 +57955,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.543 Seifert1996, Elstner1998, Spiegelman2020} +l.545 Seifert1996, Elstner1998, Spiegelman2020} with a configuration intera... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -58421,14 +57964,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Porezag1995' on page undefined on input line 543. +LaTeX Warning: Citation `Porezag1995' on page undefined on input line 545. Missing character: There is no , in font nullfont! \citation{Seifert1996} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.543 Seifert1996, Elstner1998, Spiegelman2020} +l.545 Seifert1996, Elstner1998, Spiegelman2020} with a configuration intera... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -58437,14 +57980,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Seifert1996' on page undefined on input line 543. +LaTeX Warning: Citation `Seifert1996' on page undefined on input line 545. Missing character: There is no , in font nullfont! \citation{Elstner1998} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.543 Seifert1996, Elstner1998, Spiegelman2020} +l.545 Seifert1996, Elstner1998, Spiegelman2020} with a configuration intera... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -58453,14 +57996,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Elstner1998' on page undefined on input line 543. +LaTeX Warning: Citation `Elstner1998' on page undefined on input line 545. Missing character: There is no , in font nullfont! \citation{Spiegelman2020} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.543 Seifert1996, Elstner1998, Spiegelman2020} +l.545 Seifert1996, Elstner1998, Spiegelman2020} with a configuration intera... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -58469,7 +58012,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Spiegelman2020' on page undefined on input line 543. +LaTeX Warning: Citation `Spiegelman2020' on page undefined on input line 545. Missing character: There is no ] in font nullfont! Missing character: There is no w in font nullfont! @@ -58512,7 +58055,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.543 ...on interaction scheme\cite{Rapacioli2011} +l.545 ...on interaction scheme\cite{Rapacioli2011} . The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -58521,102 +58064,102 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Rapacioli2011' on page undefined on input line 543. +LaTeX Warning: Citation `Rapacioli2011' on page undefined on input line 545. Missing character: There is no ] in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 542--544 +Overfull \hbox (20.0pt too wide) in paragraph at lines 544--546 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 542--544 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 544--546 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 542--544 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 544--546 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 542--544 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 544--546 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 542--544 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 544--546 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 542--544 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 544--546 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 542--544 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 544--546 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 542--544 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 544--546 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 542--544 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 544--546 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 542--544 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 544--546 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 542--544 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 544--546 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 542--544 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 544--546 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 542--544 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 544--546 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 542--544 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 544--546 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 542--544 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 544--546 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 542--544 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 544--546 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 542--544 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 544--546 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 542--544 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 544--546 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 542--544 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 544--546 [] [] @@ -58789,6 +58332,8 @@ Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no y in font nullfont! +Missing character: There is no M in font nullfont! +Missing character: There is no . in font nullfont! Missing character: There is no G in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no t in font nullfont! @@ -58805,7 +58350,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.545 ...\cite{Gatchell2016, Gatchell2016knockout} +l.547 ...\cite{Gatchell2016, Gatchell2016knockout} at the semi-empirical and... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -58814,14 +58359,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Gatchell2016' on page undefined on input line 545. +LaTeX Warning: Citation `Gatchell2016' on page undefined on input line 547. Missing character: There is no , in font nullfont! \citation{Gatchell2016knockout} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.545 ...\cite{Gatchell2016, Gatchell2016knockout} +l.547 ...\cite{Gatchell2016, Gatchell2016knockout} at the semi-empirical and... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -58831,7 +58376,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Citation `Gatchell2016knockout' on page undefined on input line - 545. + 547. Missing character: There is no ] in font nullfont! Missing character: There is no a in font nullfont! @@ -58925,26 +58470,20 @@ Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no y in font nullfont! +Missing character: There is no S in font nullfont! +Missing character: There is no . in font nullfont! Missing character: There is no Z in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! -Missing character: There is no f in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no m in font nullfont! -Missing character: There is no L in font nullfont! -Missing character: There is no C in font nullfont! -Missing character: There is no A in font nullfont! -Missing character: There is no R in font nullfont! Missing character: There is no [ in font nullfont! \citation{Zamith2020threshold} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.546 ...al.} from LCAR \cite{Zamith2020threshold} +l.548 ...extit{et al.} \cite{Zamith2020threshold} (the principle of this ex... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -58954,7 +58493,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Citation `Zamith2020threshold' on page undefined on input line -546. +548. Missing character: There is no ] in font nullfont! Missing character: There is no ( in font nullfont! @@ -59031,7 +58570,7 @@ Missing character: There is no s in font nullfont! ! Undefined control sequence. ...rence `principleTCID' on page \thepage \space undefined\on@line . -l.546 ...ere shown in sections \ref{principleTCID} +l.548 ...ere shown in sections \ref{principleTCID} and \ref{EXPsetup}), whic... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -59040,7 +58579,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `principleTCID' on page undefined on input line 546. +LaTeX Warning: Reference `principleTCID' on page undefined on input line 548. Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! @@ -59048,7 +58587,7 @@ Missing character: There is no d in font nullfont! ! Undefined control sequence. ... Reference `EXPsetup' on page \thepage \space undefined\on@line . -l.546 ...ns \ref{principleTCID} and \ref{EXPsetup} +l.548 ...ns \ref{principleTCID} and \ref{EXPsetup} ), which were analysed by ... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -59057,7 +58596,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `EXPsetup' on page undefined on input line 546. +LaTeX Warning: Reference `EXPsetup' on page undefined on input line 548. Missing character: There is no ) in font nullfont! Missing character: There is no , in font nullfont! @@ -59235,7 +58774,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.546 ...pace theory (PST)\cite{Zamith2019thermal} +l.548 ...pace theory (PST)\cite{Zamith2019thermal} . A fair agreement with ex... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -59245,7 +58784,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Citation `Zamith2019thermal' on page undefined on input line 54 -6. +8. Missing character: There is no ] in font nullfont! Missing character: There is no . in font nullfont! @@ -60058,57 +59597,57 @@ Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 545--547 +Overfull \hbox (20.0pt too wide) in paragraph at lines 547--549 [] [] -Overfull \hbox (4.59996pt too wide) in paragraph at lines 545--547 +Overfull \hbox (4.59996pt too wide) in paragraph at lines 547--549 \OT1/cmr/m/it/10 e [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 545--547 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 547--549 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 545--547 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 547--549 [] [] -Overfull \hbox (7.92215pt too wide) in paragraph at lines 545--547 +Overfull \hbox (7.92215pt too wide) in paragraph at lines 547--549 \OT1/cmr/m/it/10 et [] -Overfull \hbox (10.73328pt too wide) in paragraph at lines 545--547 +Overfull \hbox (10.73328pt too wide) in paragraph at lines 547--549 \OT1/cmr/m/it/10 al. [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 545--547 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 547--549 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 545--547 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 547--549 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 545--547 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 547--549 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 545--547 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 547--549 [] [] ! Undefined control sequence. -l.550 \subsection +l.552 \subsection {Calculation of Energies} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -60138,7 +59677,7 @@ Missing character: There is no i in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 550--551 +Overfull \hbox (20.0pt too wide) in paragraph at lines 552--553 [] [] @@ -60156,8 +59695,7 @@ Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! -Missing character: There is no w in font nullfont! -Missing character: There is no e in font nullfont! +Missing character: There is no I in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! @@ -60272,7 +59810,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.553 \begin{align} +l.555 \begin{align} Your command was ignored. Type I to replace it with another command, @@ -60282,13 +59820,13 @@ Missing character: There is no E in font nullfont! ! Missing $ inserted. $ -l.555 E^ +l.557 E^ k_{tot}&=E^k_{Ar} + E^k_{td} + E^k_{Py^1} + E^k_{Py^2} + E^k_{Re} \... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Misplaced alignment tab character &. -l.555 E^k_{tot}& +l.557 E^k_{tot}& =E^k_{Ar} + E^k_{td} + E^k_{Py^1} + E^k_{Py^2} + E^k_{Re} \... I can't figure out why you would want to use a tab mark here. If you just want an ampersand, the remedy is @@ -60298,7 +59836,7 @@ you're probably due for more error messages, and you might try typing `S' now just to see what is salvageable. ! Misplaced alignment tab character &. -l.556 E^k_{tot} & +l.558 E^k_{tot} & =\frac{1}{2}\sum_{i=1}^{52}m_i(\Vec{v}_i)^2 \nonumber \\ I can't figure out why you would want to use a tab mark here. If you just want an ampersand, the remedy is @@ -60308,7 +59846,7 @@ you're probably due for more error messages, and you might try typing `S' now just to see what is salvageable. ! Undefined control sequence. -l.556 ...tot} &=\frac{1}{2}\sum_{i=1}^{52}m_i(\Vec +l.558 ...tot} &=\frac{1}{2}\sum_{i=1}^{52}m_i(\Vec {v}_i)^2 \nonumber \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -60317,7 +59855,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Misplaced alignment tab character &. -l.557 E^k_{Ar} & +l.559 E^k_{Ar} & = \frac{1}{2}m_{Ar}\Vec{v}_{Ar}^2 \nonumber \\ I can't figure out why you would want to use a tab mark here. If you just want an ampersand, the remedy is @@ -60327,7 +59865,7 @@ you're probably due for more error messages, and you might try typing `S' now just to see what is salvageable. ! Undefined control sequence. -l.557 E^k_{Ar} &= \frac{1}{2}m_{Ar}\Vec +l.559 E^k_{Ar} &= \frac{1}{2}m_{Ar}\Vec {v}_{Ar}^2 \nonumber \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -60336,7 +59874,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Misplaced alignment tab character &. -l.558 E^k_{td} & +l.560 E^k_{td} & =\frac{1}{2}m_{Py_2}\Vec{v}_t^2(Py_2) \\ I can't figure out why you would want to use a tab mark here. If you just want an ampersand, the remedy is @@ -60346,7 +59884,7 @@ you're probably due for more error messages, and you might try typing `S' now just to see what is salvageable. ! Undefined control sequence. -l.558 E^k_{td} & =\frac{1}{2}m_{Py_2}\Vec +l.560 E^k_{td} & =\frac{1}{2}m_{Py_2}\Vec {v}_t^2(Py_2) \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -60355,7 +59893,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Misplaced alignment tab character &. -l.559 E^k_{Re} & +l.561 E^k_{Re} & = \frac{1}{2} \frac{m_{Py^1}m_{Py^2}}{m_{Py^1}+m_{Py^2}}(\V... I can't figure out why you would want to use a tab mark here. If you just want an ampersand, the remedy is @@ -60365,7 +59903,7 @@ you're probably due for more error messages, and you might try typing `S' now just to see what is salvageable. ! Undefined control sequence. -l.559 ...m_{Py^1}m_{Py^2}}{m_{Py^1}+m_{Py^2}}(\Vec +l.561 ...m_{Py^1}m_{Py^2}}{m_{Py^1}+m_{Py^2}}(\Vec {v}_t(Py^2)-\Vec{v}_t(Py^1... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -60374,7 +59912,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. -l.559 ...}{m_{Py^1}+m_{Py^2}}(\Vec{v}_t(Py^2)-\Vec +l.561 ...}{m_{Py^1}+m_{Py^2}}(\Vec{v}_t(Py^2)-\Vec {v}_t(Py^1))^2 \nonumber \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -60383,7 +59921,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Misplaced alignment tab character &. -l.560 E^k_{Py^n} & +l.562 E^k_{Py^n} & = \frac{1}{2}\sum_{i=1}^{{26}}m_i^n (\Vec{v}_i^n-\Vec{v}_... I can't figure out why you would want to use a tab mark here. If you just want an ampersand, the remedy is @@ -60393,7 +59931,7 @@ you're probably due for more error messages, and you might try typing `S' now just to see what is salvageable. ! Undefined control sequence. -l.560 ...= \frac{1}{2}\sum_{i=1}^{{26}}m_i^n (\Vec +l.562 ...= \frac{1}{2}\sum_{i=1}^{{26}}m_i^n (\Vec {v}_i^n-\Vec{v}_t(Py^n))^2... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -60402,7 +59940,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. -l.560 ...}\sum_{i=1}^{{26}}m_i^n (\Vec{v}_i^n-\Vec +l.562 ...}\sum_{i=1}^{{26}}m_i^n (\Vec{v}_i^n-\Vec {v}_t(Py^n))^2 \nonumber The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -60417,7 +59955,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.562 \end{align} +l.564 \end{align} Your command was ignored. Type I to replace it with another command, @@ -60426,7 +59964,7 @@ or to continue without it. ! Missing $ inserted. $ -l.562 \end{align} +l.564 \end{align} I've inserted something that you may have forgotten. (See the above.) @@ -60615,7 +60153,7 @@ Missing character: There is no s in font nullfont! ! Undefined control sequence. \Vec -l.563 ...m the masses $m_i^n$ and velocities $\Vec +l.565 ...m the masses $m_i^n$ and velocities $\Vec {v}_i$ of its atoms. $E^k_... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -60691,7 +60229,7 @@ Missing character: There is no y in font nullfont! ! Undefined control sequence. \Vec -l.563 ...on (with mass $m_{Ar}$ and velocity $\Vec +l.565 ...on (with mass $m_{Ar}$ and velocity $\Vec {v}_{Ar}$). The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -60763,7 +60301,7 @@ Missing character: There is no y in font nullfont! ! Undefined control sequence. \Vec -l.564 ... (with mass $m_{Py_2}$ and velocity $\Vec +l.566 ... (with mass $m_{Py_2}$ and velocity $\Vec {v}_t(Py_2)$). The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -60887,8 +60425,8 @@ Missing character: There is no s in font nullfont! ! Undefined control sequence. \Vec -l.565 ...nomer global translation velocities $\Vec - {v}_t(Py^{n=1,2})$. +l.567 ...nomer global translation velocities $\Vec + {v}_t(Py^{1,2})$. The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct @@ -60990,7 +60528,7 @@ Missing character: There is no d in font nullfont! ! Undefined control sequence. \Vec -l.566 ...locities of its atoms ($m_i^n$ and $\Vec +l.568 ...locities of its atoms ($m_i^n$ and $\Vec {v}_i^n$, respectively). The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -61014,205 +60552,205 @@ Missing character: There is no y in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 552--567 +Overfull \hbox (20.0pt too wide) in paragraph at lines 554--569 [] [] -Overfull \hbox (17.87085pt too wide) in paragraph at lines 552--567 +Overfull \hbox (17.87085pt too wide) in paragraph at lines 554--569 \OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (21.04442pt too wide) in paragraph at lines 552--567 +Overfull \hbox (21.04442pt too wide) in paragraph at lines 554--569 [] \/cmr/m/n/10 = [] -Overfull \hbox (25.60191pt too wide) in paragraph at lines 552--567 +Overfull \hbox (25.60191pt too wide) in paragraph at lines 554--569 \OML/cmm/m/it/10 E[] \/cmr/m/n/10 + [] -Overfull \hbox (22.84346pt too wide) in paragraph at lines 552--567 +Overfull \hbox (22.84346pt too wide) in paragraph at lines 554--569 \OML/cmm/m/it/10 E[] \/cmr/m/n/10 + [] -Overfull \hbox (30.03703pt too wide) in paragraph at lines 552--567 +Overfull \hbox (30.03703pt too wide) in paragraph at lines 554--569 \OML/cmm/m/it/10 E[] \/cmr/m/n/10 + [] -Overfull \hbox (30.03703pt too wide) in paragraph at lines 552--567 +Overfull \hbox (30.03703pt too wide) in paragraph at lines 554--569 \OML/cmm/m/it/10 E[] \/cmr/m/n/10 + [] -Overfull \hbox (17.73615pt too wide) in paragraph at lines 552--567 +Overfull \hbox (17.73615pt too wide) in paragraph at lines 554--569 \OML/cmm/m/it/10 E[][] [] -Overfull \hbox (28.42636pt too wide) in paragraph at lines 552--567 +Overfull \hbox (28.42636pt too wide) in paragraph at lines 554--569 \OML/cmm/m/it/10 E[] \/cmr/m/n/10 = [] -Overfull \hbox (66.27916pt too wide) in paragraph at lines 552--567 +Overfull \hbox (66.27916pt too wide) in paragraph at lines 554--569 [] [][] \OML/cmm/m/it/10 m[]\/cmr/m/n/10 (\OML/cmm/m/it/10 v[]\/cmr/m/n/10 )[][ ] [] -Overfull \hbox (28.37962pt too wide) in paragraph at lines 552--567 +Overfull \hbox (28.37962pt too wide) in paragraph at lines 554--569 \OML/cmm/m/it/10 E[] \/cmr/m/n/10 = [] -Overfull \hbox (40.89783pt too wide) in paragraph at lines 552--567 +Overfull \hbox (40.89783pt too wide) in paragraph at lines 554--569 []\OML/cmm/m/it/10 m[]v[][] [] -Overfull \hbox (25.62117pt too wide) in paragraph at lines 552--567 +Overfull \hbox (25.62117pt too wide) in paragraph at lines 554--569 \OML/cmm/m/it/10 E[] \/cmr/m/n/10 = [] -Overfull \hbox (64.46031pt too wide) in paragraph at lines 552--567 +Overfull \hbox (64.46031pt too wide) in paragraph at lines 554--569 []\OML/cmm/m/it/10 m[]v[]\/cmr/m/n/10 (\OML/cmm/m/it/10 Py[]\/cmr/m/n/10 )[] [] -Overfull \hbox (28.29166pt too wide) in paragraph at lines 552--567 +Overfull \hbox (28.29166pt too wide) in paragraph at lines 554--569 \OML/cmm/m/it/10 E[] \/cmr/m/n/10 = [] -Overfull \hbox (101.44635pt too wide) in paragraph at lines 552--567 +Overfull \hbox (101.44635pt too wide) in paragraph at lines 554--569 [][]\/cmr/m/n/10 (\OML/cmm/m/it/10 v[]\/cmr/m/n/10 (\OML/cmm/m/it/10 Py[]\/cmr/ m/n/10 ) \OMS/cmsy/m/n/10 ^^@ [] -Overfull \hbox (42.07767pt too wide) in paragraph at lines 552--567 +Overfull \hbox (42.07767pt too wide) in paragraph at lines 554--569 \OML/cmm/m/it/10 v[]\/cmr/m/n/10 (\OML/cmm/m/it/10 Py[]\/cmr/m/n/10 ))[][] [] -Overfull \hbox (33.8159pt too wide) in paragraph at lines 552--567 +Overfull \hbox (33.8159pt too wide) in paragraph at lines 554--569 \OML/cmm/m/it/10 E[] \/cmr/m/n/10 = [] -Overfull \hbox (70.2688pt too wide) in paragraph at lines 552--567 +Overfull \hbox (70.2688pt too wide) in paragraph at lines 554--569 [] [][] \OML/cmm/m/it/10 m[]\/cmr/m/n/10 (\OML/cmm/m/it/10 v[] \OMS/cmsy/m/n/10 ^^@ [] -Overfull \hbox (43.03487pt too wide) in paragraph at lines 552--567 +Overfull \hbox (43.03487pt too wide) in paragraph at lines 554--569 \OML/cmm/m/it/10 v[]\/cmr/m/n/10 (\OML/cmm/m/it/10 Py[]\/cmr/m/n/10 ))[]$ [] -Overfull \hbox (17.19798pt too wide) in paragraph at lines 552--567 +Overfull \hbox (17.19798pt too wide) in paragraph at lines 554--569 \OML/cmm/m/it/10 Py[]$ [] -Overfull \hbox (17.55676pt too wide) in paragraph at lines 552--567 +Overfull \hbox (17.55676pt too wide) in paragraph at lines 554--569 \OML/cmm/m/it/10 Py[]$ [] -Overfull \hbox (17.55676pt too wide) in paragraph at lines 552--567 +Overfull \hbox (17.55676pt too wide) in paragraph at lines 554--569 \OML/cmm/m/it/10 Py[]$ [] -Overfull \hbox (17.87085pt too wide) in paragraph at lines 552--567 +Overfull \hbox (17.87085pt too wide) in paragraph at lines 554--569 \OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (14.22346pt too wide) in paragraph at lines 552--567 +Overfull \hbox (14.22346pt too wide) in paragraph at lines 554--569 \OML/cmm/m/it/10 m[]$ [] -Overfull \hbox (8.17651pt too wide) in paragraph at lines 552--567 +Overfull \hbox (8.17651pt too wide) in paragraph at lines 554--569 \OML/cmm/m/it/10 v[]$ [] -Overfull \hbox (17.82411pt too wide) in paragraph at lines 552--567 +Overfull \hbox (17.82411pt too wide) in paragraph at lines 554--569 \OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (19.2223pt too wide) in paragraph at lines 552--567 +Overfull \hbox (19.2223pt too wide) in paragraph at lines 554--569 \OML/cmm/m/it/10 m[]$ [] -Overfull \hbox (15.2894pt too wide) in paragraph at lines 552--567 +Overfull \hbox (15.2894pt too wide) in paragraph at lines 554--569 \OML/cmm/m/it/10 v[]$ [] -Overfull \hbox (15.06566pt too wide) in paragraph at lines 552--567 +Overfull \hbox (15.06566pt too wide) in paragraph at lines 554--569 \OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (23.40627pt too wide) in paragraph at lines 552--567 +Overfull \hbox (23.40627pt too wide) in paragraph at lines 554--569 \OML/cmm/m/it/10 m[]$ [] -Overfull \hbox (33.34386pt too wide) in paragraph at lines 552--567 +Overfull \hbox (33.34386pt too wide) in paragraph at lines 554--569 \OML/cmm/m/it/10 v[]\/cmr/m/n/10 (\OML/cmm/m/it/10 Py[]\/cmr/m/n/10 )$ [] -Overfull \hbox (17.73615pt too wide) in paragraph at lines 552--567 +Overfull \hbox (17.73615pt too wide) in paragraph at lines 554--569 \OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (34.21294pt too wide) in paragraph at lines 552--567 +Overfull \hbox (34.21294pt too wide) in paragraph at lines 554--569 \OML/cmm/m/it/10 m[] \/cmr/m/n/10 = [] -Overfull \hbox (23.65742pt too wide) in paragraph at lines 552--567 +Overfull \hbox (23.65742pt too wide) in paragraph at lines 554--569 \OML/cmm/m/it/10 m[]$ [] -Overfull \hbox (51.14601pt too wide) in paragraph at lines 552--567 +Overfull \hbox (40.06377pt too wide) in paragraph at lines 554--569 \OML/cmm/m/it/10 v[]\/cmr/m/n/10 (\OML/cmm/m/it/10 Py[]\/cmr/m/n/10 )$ [] -Overfull \hbox (23.26039pt too wide) in paragraph at lines 552--567 +Overfull \hbox (23.26039pt too wide) in paragraph at lines 554--569 \OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (6.00235pt too wide) in paragraph at lines 552--567 +Overfull \hbox (6.00235pt too wide) in paragraph at lines 554--569 \OML/cmm/m/it/10 n$ [] -Overfull \hbox (14.22346pt too wide) in paragraph at lines 552--567 +Overfull \hbox (14.22346pt too wide) in paragraph at lines 554--569 \OML/cmm/m/it/10 m[]$ [] -Overfull \hbox (10.64934pt too wide) in paragraph at lines 552--567 +Overfull \hbox (10.64934pt too wide) in paragraph at lines 554--569 \OML/cmm/m/it/10 v[]$ [] @@ -61383,7 +60921,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.569 \begin{align} +l.571 \begin{align} Your command was ignored. Type I to replace it with another command, @@ -61393,13 +60931,13 @@ Missing character: There is no E in font nullfont! ! Missing $ inserted. $ -l.570 E^ +l.572 E^ k_{intra^n}&= I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Misplaced alignment tab character &. -l.570 E^k_{intra^n}& +l.572 E^k_{intra^n}& = I can't figure out why you would want to use a tab mark here. If you just want an ampersand, the remedy is @@ -61409,7 +60947,7 @@ you're probably due for more error messages, and you might try typing `S' now just to see what is salvageable. ! Undefined control sequence. -l.571 \frac{1}{2}\sum_{i=1}^{{26}}m_i^n (\Vec +l.573 \frac{1}{2}\sum_{i=1}^{{26}}m_i^n (\Vec {v}_i^n-\Vec{v}_t(Py^n)-\Vec{v... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -61418,7 +60956,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. -l.571 ...}\sum_{i=1}^{{26}}m_i^n (\Vec{v}_i^n-\Vec +l.573 ...}\sum_{i=1}^{{26}}m_i^n (\Vec{v}_i^n-\Vec {v}_t(Py^n)-\Vec{v}_{ir}^n)^2 The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -61427,7 +60965,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. -l.571 ...}}m_i^n (\Vec{v}_i^n-\Vec{v}_t(Py^n)-\Vec +l.573 ...}}m_i^n (\Vec{v}_i^n-\Vec{v}_t(Py^n)-\Vec {v}_{ir}^n)^2 The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -61442,7 +60980,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.573 \end{align} +l.575 \end{align} Your command was ignored. Type I to replace it with another command, @@ -61451,7 +60989,7 @@ or to continue without it. ! Missing $ inserted. $ -l.573 \end{align} +l.575 \end{align} I've inserted something that you may have forgotten. (See the above.) @@ -61467,7 +61005,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. \Vec -l.574 where $\Vec +l.576 where $\Vec {v}_{ir}^n$ is the velocity of atom $i$ associated to the m... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -61608,7 +61146,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.576 \begin{align} +l.578 \begin{align} Your command was ignored. Type I to replace it with another command, @@ -61618,13 +61156,13 @@ Missing character: There is no E in font nullfont! ! Missing $ inserted. $ -l.577 E^ +l.579 E^ k_{inter}&=E^k_{tot}-E^k_{Ar}-E^k_{td}-E^k_r-E^k_{intra^1}-E^k_{int... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Misplaced alignment tab character &. -l.577 E^k_{inter}& +l.579 E^k_{inter}& =E^k_{tot}-E^k_{Ar}-E^k_{td}-E^k_r-E^k_{intra^1}-E^k_{int... I can't figure out why you would want to use a tab mark here. If you just want an ampersand, the remedy is @@ -61640,7 +61178,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.579 \end{align} +l.581 \end{align} Your command was ignored. Type I to replace it with another command, @@ -61649,7 +61187,7 @@ or to continue without it. ! Missing $ inserted. $ -l.579 \end{align} +l.581 \end{align} I've inserted something that you may have forgotten. (See the above.) @@ -61708,7 +61246,7 @@ Missing character: There is no . in font nullfont! ! Undefined control sequence. \Vec -l.581 $\Vec +l.583 $\Vec {v}_{ir}^n$ and $E^k_r$ are calculated using the following formulas. The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -61765,14 +61303,14 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.582 \begin{align} +l.584 \begin{align} Your command was ignored. Type I to replace it with another command, or to continue without it. ! Undefined control sequence. -l.583 \Vec +l.585 \Vec {L}(Py^n) &= \sum_{i=1}^{26}m_i^n (\Vec{r}_i^n-\Vec{r}_{_{CM}}(Py^... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -61787,13 +61325,13 @@ Missing character: There is no y in font nullfont! ! Missing $ inserted. $ -l.583 \Vec{L}(Py^ +l.585 \Vec{L}(Py^ n) &= \sum_{i=1}^{26}m_i^n (\Vec{r}_i^n-\Vec{r}_{_{CM}}(Py^... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Misplaced alignment tab character &. -l.583 \Vec{L}(Py^n) & +l.585 \Vec{L}(Py^n) & = \sum_{i=1}^{26}m_i^n (\Vec{r}_i^n-\Vec{r}_{_{CM}}(Py^... I can't figure out why you would want to use a tab mark here. If you just want an ampersand, the remedy is @@ -61803,7 +61341,7 @@ you're probably due for more error messages, and you might try typing `S' now just to see what is salvageable. ! Undefined control sequence. -l.583 \Vec{L}(Py^n) &= \sum_{i=1}^{26}m_i^n (\Vec +l.585 \Vec{L}(Py^n) &= \sum_{i=1}^{26}m_i^n (\Vec {r}_i^n-\Vec{r}_{_{CM}}(Py^... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -61812,7 +61350,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. -l.583 ...&= \sum_{i=1}^{26}m_i^n (\Vec{r}_i^n-\Vec +l.585 ...&= \sum_{i=1}^{26}m_i^n (\Vec{r}_i^n-\Vec {r}_{_{CM}}(Py^n)) \times ... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -61821,7 +61359,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. -l.583 ...}_i^n-\Vec{r}_{_{CM}}(Py^n)) \times (\Vec +l.585 ...}_i^n-\Vec{r}_{_{CM}}(Py^n)) \times (\Vec {v}_i^n-\Vec{v}_t(Py^{n}))... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -61830,7 +61368,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. -l.583 ...}_{_{CM}}(Py^n)) \times (\Vec{v}_i^n-\Vec +l.585 ...}_{_{CM}}(Py^n)) \times (\Vec{v}_i^n-\Vec {v}_t(Py^{n})) \nonumber \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -61841,7 +61379,7 @@ and I'll forget about whatever was undefined. ! Undefined control sequence. \Vec -l.584 \Vec +l.586 \Vec {L}(Py_2) &= \sum_{i=1}^{52} m_i (\Vec{r}_i-\Vec{r}_{_{CM}}(Py_2))... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -61850,7 +61388,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Misplaced alignment tab character &. -l.584 \Vec{L}(Py_2) & +l.586 \Vec{L}(Py_2) & = \sum_{i=1}^{52} m_i (\Vec{r}_i-\Vec{r}_{_{CM}}(Py_2))... I can't figure out why you would want to use a tab mark here. If you just want an ampersand, the remedy is @@ -61860,7 +61398,7 @@ you're probably due for more error messages, and you might try typing `S' now just to see what is salvageable. ! Undefined control sequence. -l.584 \Vec{L}(Py_2) &= \sum_{i=1}^{52} m_i (\Vec +l.586 \Vec{L}(Py_2) &= \sum_{i=1}^{52} m_i (\Vec {r}_i-\Vec{r}_{_{CM}}(Py_2))... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -61869,7 +61407,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. -l.584 ...2) &= \sum_{i=1}^{52} m_i (\Vec{r}_i-\Vec +l.586 ...2) &= \sum_{i=1}^{52} m_i (\Vec{r}_i-\Vec {r}_{_{CM}}(Py_2)) \times ... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -61878,7 +61416,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. -l.584 ...{r}_i-\Vec{r}_{_{CM}}(Py_2)) \times (\Vec +l.586 ...{r}_i-\Vec{r}_{_{CM}}(Py_2)) \times (\Vec {v}_i-\Vec{v}_t(Py_{2})) \... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -61887,7 +61425,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. -l.584 ...{r}_{_{CM}}(Py_2)) \times (\Vec{v}_i-\Vec +l.586 ...{r}_{_{CM}}(Py_2)) \times (\Vec{v}_i-\Vec {v}_t(Py_{2})) \nonumber \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -61896,7 +61434,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Misplaced alignment tab character &. -l.585 I & +l.587 I & = mr^2 \nonumber \\ I can't figure out why you would want to use a tab mark here. If you just want an ampersand, the remedy is @@ -61908,7 +61446,7 @@ might try typing `S' now just to see what is salvageable. ! Undefined control sequence. \Vec -l.586 \Vec +l.588 \Vec {\omega} &= [I]^{-1} \times \Vec{L} \nonumber \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -61917,7 +61455,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Misplaced alignment tab character &. -l.586 \Vec{\omega} & +l.588 \Vec{\omega} & = [I]^{-1} \times \Vec{L} \nonumber \\ I can't figure out why you would want to use a tab mark here. If you just want an ampersand, the remedy is @@ -61927,7 +61465,7 @@ you're probably due for more error messages, and you might try typing `S' now just to see what is salvageable. ! Undefined control sequence. -l.586 \Vec{\omega} &= [I]^{-1} \times \Vec +l.588 \Vec{\omega} &= [I]^{-1} \times \Vec {L} \nonumber \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -61938,7 +61476,7 @@ and I'll forget about whatever was undefined. ! Undefined control sequence. \Vec -l.587 \Vec +l.589 \Vec {v}_{ir}^n &= \Vec{\omega}(Py^n) \times (\Vec{r}_i^n - \Vec{r}_{_... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -61947,7 +61485,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Misplaced alignment tab character &. -l.587 \Vec{v}_{ir}^n & +l.589 \Vec{v}_{ir}^n & = \Vec{\omega}(Py^n) \times (\Vec{r}_i^n - \Vec{r}_{_... I can't figure out why you would want to use a tab mark here. If you just want an ampersand, the remedy is @@ -61957,7 +61495,7 @@ you're probably due for more error messages, and you might try typing `S' now just to see what is salvageable. ! Undefined control sequence. -l.587 \Vec{v}_{ir}^n &= \Vec +l.589 \Vec{v}_{ir}^n &= \Vec {\omega}(Py^n) \times (\Vec{r}_i^n - \Vec{r}_{_... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -61966,7 +61504,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. -l.587 ...ir}^n &= \Vec{\omega}(Py^n) \times (\Vec +l.589 ...ir}^n &= \Vec{\omega}(Py^n) \times (\Vec {r}_i^n - \Vec{r}_{_{CM}}(... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -61975,7 +61513,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. -l.587 ...\omega}(Py^n) \times (\Vec{r}_i^n - \Vec +l.589 ...\omega}(Py^n) \times (\Vec{r}_i^n - \Vec {r}_{_{CM}}(Py^n)) \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -61984,7 +61522,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Misplaced alignment tab character &. -l.588 E^k_{tot^n} & +l.590 E^k_{tot^n} & =E^k_{r^n} + E^k_{td^n} + E^k_{intra^n} \nonumber \\ I can't figure out why you would want to use a tab mark here. If you just want an ampersand, the remedy is @@ -61994,7 +61532,7 @@ you're probably due for more error messages, and you might try typing `S' now just to see what is salvageable. ! Misplaced alignment tab character &. -l.589 E^k_{tot^n} & +l.591 E^k_{tot^n} & =\frac{1}{2}\sum_{i=1}^{26}m_i^n(\Vec{v}_i^n)^2 \nonumber \\ I can't figure out why you would want to use a tab mark here. If you just want an ampersand, the remedy is @@ -62004,7 +61542,7 @@ you're probably due for more error messages, and you might try typing `S' now just to see what is salvageable. ! Undefined control sequence. -l.589 ...n} &=\frac{1}{2}\sum_{i=1}^{26}m_i^n(\Vec +l.591 ...n} &=\frac{1}{2}\sum_{i=1}^{26}m_i^n(\Vec {v}_i^n)^2 \nonumber \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -62013,7 +61551,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Misplaced alignment tab character &. -l.590 E^k_{td^n} & +l.592 E^k_{td^n} & =\frac{1}{2}m_{Py^n}\Vec{v}_t^2(Py^n) \nonumber \\ I can't figure out why you would want to use a tab mark here. If you just want an ampersand, the remedy is @@ -62023,7 +61561,7 @@ you're probably due for more error messages, and you might try typing `S' now just to see what is salvageable. ! Undefined control sequence. -l.590 E^k_{td^n} &=\frac{1}{2}m_{Py^n}\Vec +l.592 E^k_{td^n} &=\frac{1}{2}m_{Py^n}\Vec {v}_t^2(Py^n) \nonumber \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -62032,7 +61570,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Misplaced alignment tab character &. -l.591 E^k_{r} & +l.593 E^k_{r} & = \frac{1}{2} \Vec{\omega}(Py_2) \times [I](Py_2) \times\Vec{... I can't figure out why you would want to use a tab mark here. If you just want an ampersand, the remedy is @@ -62042,7 +61580,7 @@ you're probably due for more error messages, and you might try typing `S' now just to see what is salvageable. ! Undefined control sequence. -l.591 E^k_{r} &= \frac{1}{2} \Vec +l.593 E^k_{r} &= \frac{1}{2} \Vec {\omega}(Py_2) \times [I](Py_2) \times\Vec{... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -62051,7 +61589,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. -l.591 ...\omega}(Py_2) \times [I](Py_2) \times\Vec +l.593 ...\omega}(Py_2) \times [I](Py_2) \times\Vec {\omega}(Py_2) = \frac{1}{... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -62060,7 +61598,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. -l.591 ...imes\Vec{\omega}(Py_2) = \frac{1}{2} \Vec +l.593 ...imes\Vec{\omega}(Py_2) = \frac{1}{2} \Vec {L}(Py_2) \times [I]^{-1}(... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -62069,7 +61607,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. -l.591 ...}(Py_2) \times [I]^{-1}(Py_2) \times \Vec +l.593 ...}(Py_2) \times [I]^{-1}(Py_2) \times \Vec {L}(Py_2) \nonumber \\ The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -62084,7 +61622,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.593 \end{align} +l.595 \end{align} Your command was ignored. Type I to replace it with another command, @@ -62093,7 +61631,7 @@ or to continue without it. ! Missing $ inserted. $ -l.593 \end{align} +l.595 \end{align} I've inserted something that you may have forgotten. (See the above.) @@ -62182,7 +61720,7 @@ Missing character: There is no . in font nullfont! ! Undefined control sequence. \Vec -l.596 $\Vec +l.598 $\Vec {L}(Py^n)$ is the angular momentum of pyrene monomer $n$. The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -62229,7 +61767,7 @@ Missing character: There is no . in font nullfont! ! Undefined control sequence. \Vec -l.597 $\Vec +l.599 $\Vec {L}(Py_2)$ is the angular momentum of the dimer. The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -62319,7 +61857,7 @@ Missing character: There is no . in font nullfont! ! Undefined control sequence. \Vec -l.600 $\Vec +l.602 $\Vec {\omega}$ is the angular velocity. The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -62351,7 +61889,7 @@ Missing character: There is no . in font nullfont! ! Undefined control sequence. \Vec -l.601 $\Vec +l.603 $\Vec {r}_{i}^n$ and $\Vec{r}_{_{CM}}(Py^n)$ denote the coordinates of ... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -62365,7 +61903,7 @@ Missing character: There is no d in font nullfont! ! Undefined control sequence. \Vec -l.601 $\Vec{r}_{i}^n$ and $\Vec +l.603 $\Vec{r}_{i}^n$ and $\Vec {r}_{_{CM}}(Py^n)$ denote the coordinates of ... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -62447,7 +61985,7 @@ Missing character: There is no . in font nullfont! ! Undefined control sequence. \Vec -l.602 $\Vec +l.604 $\Vec {r}_{i}$ and $\Vec{r}_{_{CM}}(Py_2)$ and denote the coordinates o... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -62461,7 +61999,7 @@ Missing character: There is no d in font nullfont! ! Undefined control sequence. \Vec -l.602 $\Vec{r}_{i}$ and $\Vec +l.604 $\Vec{r}_{i}$ and $\Vec {r}_{_{CM}}(Py_2)$ and denote the coordinates o... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -62535,374 +62073,374 @@ Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 568--603 +Overfull \hbox (20.0pt too wide) in paragraph at lines 570--605 [] [] -Overfull \hbox (31.84529pt too wide) in paragraph at lines 568--603 +Overfull \hbox (31.84529pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (6.00235pt too wide) in paragraph at lines 568--603 +Overfull \hbox (6.00235pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 n$ [] -Overfull \hbox (35.01886pt too wide) in paragraph at lines 568--603 +Overfull \hbox (35.01886pt too wide) in paragraph at lines 570--605 [] \/cmr/m/n/10 = [] -Overfull \hbox (70.2688pt too wide) in paragraph at lines 568--603 +Overfull \hbox (70.2688pt too wide) in paragraph at lines 570--605 [] [][] \OML/cmm/m/it/10 m[]\/cmr/m/n/10 (\OML/cmm/m/it/10 v[] \OMS/cmsy/m/n/10 ^^@ [] -Overfull \hbox (42.43764pt too wide) in paragraph at lines 568--603 +Overfull \hbox (42.43764pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 v[]\/cmr/m/n/10 (\OML/cmm/m/it/10 Py[]\/cmr/m/n/10 ) \OMS/cmsy /m/n/10 ^^@ [] -Overfull \hbox (20.4798pt too wide) in paragraph at lines 568--603 +Overfull \hbox (20.4798pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 v[]\/cmr/m/n/10 )[][]$ [] -Overfull \hbox (12.10477pt too wide) in paragraph at lines 568--603 +Overfull \hbox (12.10477pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 v[]$ [] -Overfull \hbox (3.44513pt too wide) in paragraph at lines 568--603 +Overfull \hbox (3.44513pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 i$ [] -Overfull \hbox (26.39777pt too wide) in paragraph at lines 568--603 +Overfull \hbox (26.39777pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (29.57133pt too wide) in paragraph at lines 568--603 +Overfull \hbox (29.57133pt too wide) in paragraph at lines 570--605 [] \/cmr/m/n/10 = [] -Overfull \hbox (25.64865pt too wide) in paragraph at lines 568--603 +Overfull \hbox (25.64865pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 E[] \OMS/cmsy/m/n/10 ^^@ [] -Overfull \hbox (25.60191pt too wide) in paragraph at lines 568--603 +Overfull \hbox (25.60191pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 E[] \OMS/cmsy/m/n/10 ^^@ [] -Overfull \hbox (22.84346pt too wide) in paragraph at lines 568--603 +Overfull \hbox (22.84346pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 E[] \OMS/cmsy/m/n/10 ^^@ [] -Overfull \hbox (20.65628pt too wide) in paragraph at lines 568--603 +Overfull \hbox (20.65628pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 E[] \OMS/cmsy/m/n/10 ^^@ [] -Overfull \hbox (38.62193pt too wide) in paragraph at lines 568--603 +Overfull \hbox (38.62193pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 E[] \OMS/cmsy/m/n/10 ^^@ [] -Overfull \hbox (30.84413pt too wide) in paragraph at lines 568--603 +Overfull \hbox (30.84413pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 E[][]$ [] -Overfull \hbox (12.87848pt too wide) in paragraph at lines 568--603 +Overfull \hbox (12.87848pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (12.10477pt too wide) in paragraph at lines 568--603 +Overfull \hbox (12.10477pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 v[]$ [] -Overfull \hbox (12.87848pt too wide) in paragraph at lines 568--603 +Overfull \hbox (12.87848pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (19.88774pt too wide) in paragraph at lines 568--603 +Overfull \hbox (19.88774pt too wide) in paragraph at lines 570--605 []\/cmr/m/n/10 ) = [] -Overfull \hbox (61.79941pt too wide) in paragraph at lines 568--603 +Overfull \hbox (61.79941pt too wide) in paragraph at lines 570--605 [][] \OML/cmm/m/it/10 m[]\/cmr/m/n/10 (\OML/cmm/m/it/10 r[] \OMS/cmsy/m/n/10 ^^ @ [] -Overfull \hbox (55.75558pt too wide) in paragraph at lines 568--603 +Overfull \hbox (55.75558pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 r[]\/cmr/m/n/10 (\OML/cmm/m/it/10 Py[]\/cmr/m/n/10 )) \OMS/cms y/m/n/10 ^^B [] -Overfull \hbox (22.31604pt too wide) in paragraph at lines 568--603 +Overfull \hbox (22.31604pt too wide) in paragraph at lines 570--605 \/cmr/m/n/10 (\OML/cmm/m/it/10 v[] \OMS/cmsy/m/n/10 ^^@ [] -Overfull \hbox (38.54874pt too wide) in paragraph at lines 568--603 +Overfull \hbox (38.54874pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 v[]\/cmr/m/n/10 (\OML/cmm/m/it/10 Py[]\/cmr/m/n/10 ))[] [] -Overfull \hbox (42.33687pt too wide) in paragraph at lines 568--603 +Overfull \hbox (42.33687pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 L\/cmr/m/n/10 (\OML/cmm/m/it/10 Py[]\/cmr/m/n/10 ) = [] -Overfull \hbox (57.29353pt too wide) in paragraph at lines 568--603 +Overfull \hbox (57.29353pt too wide) in paragraph at lines 570--605 [][] \OML/cmm/m/it/10 m[]\/cmr/m/n/10 (\OML/cmm/m/it/10 r[] \OMS/cmsy/m/n/10 ^^ @ [] -Overfull \hbox (54.4396pt too wide) in paragraph at lines 568--603 +Overfull \hbox (54.4396pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 r[]\/cmr/m/n/10 (\OML/cmm/m/it/10 Py[]\/cmr/m/n/10 )) \OMS/cms y/m/n/10 ^^B [] -Overfull \hbox (19.84322pt too wide) in paragraph at lines 568--603 +Overfull \hbox (19.84322pt too wide) in paragraph at lines 570--605 \/cmr/m/n/10 (\OML/cmm/m/it/10 v[] \OMS/cmsy/m/n/10 ^^@ [] -Overfull \hbox (37.23276pt too wide) in paragraph at lines 568--603 +Overfull \hbox (37.23276pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 v[]\/cmr/m/n/10 (\OML/cmm/m/it/10 Py[]\/cmr/m/n/10 ))[] [] -Overfull \hbox (15.73605pt too wide) in paragraph at lines 568--603 +Overfull \hbox (15.73605pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 I \/cmr/m/n/10 = [] -Overfull \hbox (18.05563pt too wide) in paragraph at lines 568--603 +Overfull \hbox (18.05563pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 mr[][] [] -Overfull \hbox (17.13882pt too wide) in paragraph at lines 568--603 +Overfull \hbox (17.13882pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 ! \/cmr/m/n/10 = [] -Overfull \hbox (29.25006pt too wide) in paragraph at lines 568--603 +Overfull \hbox (29.25006pt too wide) in paragraph at lines 570--605 \/cmr/m/n/10 [\OML/cmm/m/it/10 I\/cmr/m/n/10 ][] \OMS/cmsy/m/n/10 ^^B [] -Overfull \hbox (6.80557pt too wide) in paragraph at lines 568--603 +Overfull \hbox (6.80557pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 L[] [] -Overfull \hbox (22.66028pt too wide) in paragraph at lines 568--603 +Overfull \hbox (22.66028pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 v[] \/cmr/m/n/10 = [] -Overfull \hbox (40.65288pt too wide) in paragraph at lines 568--603 +Overfull \hbox (40.65288pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 !\/cmr/m/n/10 (\OML/cmm/m/it/10 Py[]\/cmr/m/n/10 ) \OMS/cmsy/m /n/10 ^^B [] -Overfull \hbox (21.8994pt too wide) in paragraph at lines 568--603 +Overfull \hbox (21.8994pt too wide) in paragraph at lines 570--605 \/cmr/m/n/10 (\OML/cmm/m/it/10 r[] \OMS/cmsy/m/n/10 ^^@ [] -Overfull \hbox (47.97778pt too wide) in paragraph at lines 568--603 +Overfull \hbox (47.97778pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 r[]\/cmr/m/n/10 (\OML/cmm/m/it/10 Py[]\/cmr/m/n/10 ))[] [] -Overfull \hbox (33.33035pt too wide) in paragraph at lines 568--603 +Overfull \hbox (33.33035pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 E[] \/cmr/m/n/10 = [] -Overfull \hbox (24.49199pt too wide) in paragraph at lines 568--603 +Overfull \hbox (24.49199pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 E[] \/cmr/m/n/10 + [] -Overfull \hbox (27.74745pt too wide) in paragraph at lines 568--603 +Overfull \hbox (27.74745pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 E[] \/cmr/m/n/10 + [] -Overfull \hbox (31.84529pt too wide) in paragraph at lines 568--603 +Overfull \hbox (31.84529pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 E[][] [] -Overfull \hbox (33.33035pt too wide) in paragraph at lines 568--603 +Overfull \hbox (33.33035pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 E[] \/cmr/m/n/10 = [] -Overfull \hbox (70.86603pt too wide) in paragraph at lines 568--603 +Overfull \hbox (70.86603pt too wide) in paragraph at lines 570--605 [] [][] \OML/cmm/m/it/10 m[]\/cmr/m/n/10 (\OML/cmm/m/it/10 v[]\/cmr/m/n/10 )[][ ] [] -Overfull \hbox (30.52516pt too wide) in paragraph at lines 568--603 +Overfull \hbox (30.52516pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 E[] \/cmr/m/n/10 = [] -Overfull \hbox (67.02861pt too wide) in paragraph at lines 568--603 +Overfull \hbox (67.02861pt too wide) in paragraph at lines 570--605 []\OML/cmm/m/it/10 m[]v[]\/cmr/m/n/10 (\OML/cmm/m/it/10 Py[]\/cmr/m/n/10 )[] [] -Overfull \hbox (23.43399pt too wide) in paragraph at lines 568--603 +Overfull \hbox (23.43399pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 E[] \/cmr/m/n/10 = [] -Overfull \hbox (45.72302pt too wide) in paragraph at lines 568--603 +Overfull \hbox (45.72302pt too wide) in paragraph at lines 570--605 []\OML/cmm/m/it/10 !\/cmr/m/n/10 (\OML/cmm/m/it/10 Py[]\/cmr/m/n/10 ) \OMS/cmsy /m/n/10 ^^B [] -Overfull \hbox (43.4897pt too wide) in paragraph at lines 568--603 +Overfull \hbox (43.4897pt too wide) in paragraph at lines 570--605 \/cmr/m/n/10 [\OML/cmm/m/it/10 I\/cmr/m/n/10 ](\OML/cmm/m/it/10 Py[]\/cmr/m/n/1 0 ) \OMS/cmsy/m/n/10 ^^B [] -Overfull \hbox (42.11461pt too wide) in paragraph at lines 568--603 +Overfull \hbox (42.11461pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 !\/cmr/m/n/10 (\OML/cmm/m/it/10 Py[]\/cmr/m/n/10 ) = [] -Overfull \hbox (45.94528pt too wide) in paragraph at lines 568--603 +Overfull \hbox (45.94528pt too wide) in paragraph at lines 570--605 []\OML/cmm/m/it/10 L\/cmr/m/n/10 (\OML/cmm/m/it/10 Py[]\/cmr/m/n/10 ) \OMS/cmsy /m/n/10 ^^B [] -Overfull \hbox (54.22585pt too wide) in paragraph at lines 568--603 +Overfull \hbox (54.22585pt too wide) in paragraph at lines 570--605 \/cmr/m/n/10 [\OML/cmm/m/it/10 I\/cmr/m/n/10 ][](\OML/cmm/m/it/10 Py[]\/cmr/m/n /10 ) \OMS/cmsy/m/n/10 ^^B [] -Overfull \hbox (31.78136pt too wide) in paragraph at lines 568--603 +Overfull \hbox (31.78136pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 L\/cmr/m/n/10 (\OML/cmm/m/it/10 Py[]\/cmr/m/n/10 )[] [] -Overfull \hbox (22.77484pt too wide) in paragraph at lines 568--603 +Overfull \hbox (22.77484pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (6.00235pt too wide) in paragraph at lines 568--603 +Overfull \hbox (6.00235pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 n$ [] -Overfull \hbox (19.96965pt too wide) in paragraph at lines 568--603 +Overfull \hbox (19.96965pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (6.00235pt too wide) in paragraph at lines 568--603 +Overfull \hbox (6.00235pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 n$ [] -Overfull \hbox (33.09734pt too wide) in paragraph at lines 568--603 +Overfull \hbox (33.09734pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 L\/cmr/m/n/10 (\OML/cmm/m/it/10 Py[]\/cmr/m/n/10 )$ [] -Overfull \hbox (6.00235pt too wide) in paragraph at lines 568--603 +Overfull \hbox (6.00235pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 n$ [] -Overfull \hbox (31.78136pt too wide) in paragraph at lines 568--603 +Overfull \hbox (31.78136pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 L\/cmr/m/n/10 (\OML/cmm/m/it/10 Py[]\/cmr/m/n/10 )$ [] -Overfull \hbox (10.73611pt too wide) in paragraph at lines 568--603 +Overfull \hbox (10.73611pt too wide) in paragraph at lines 570--605 \/cmr/m/n/10 [\OML/cmm/m/it/10 I\/cmr/m/n/10 ]$ [] -Overfull \hbox (21.47226pt too wide) in paragraph at lines 568--603 +Overfull \hbox (21.47226pt too wide) in paragraph at lines 570--605 \/cmr/m/n/10 [\OML/cmm/m/it/10 I\/cmr/m/n/10 ][]$ [] -Overfull \hbox (10.73611pt too wide) in paragraph at lines 568--603 +Overfull \hbox (10.73611pt too wide) in paragraph at lines 570--605 \/cmr/m/n/10 [\OML/cmm/m/it/10 I\/cmr/m/n/10 ]$ [] -Overfull \hbox (6.58331pt too wide) in paragraph at lines 568--603 +Overfull \hbox (6.58331pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 !$ [] -Overfull \hbox (10.2327pt too wide) in paragraph at lines 568--603 +Overfull \hbox (10.2327pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 r[]$ [] -Overfull \hbox (44.08888pt too wide) in paragraph at lines 568--603 +Overfull \hbox (44.08888pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 r[]\/cmr/m/n/10 (\OML/cmm/m/it/10 Py[]\/cmr/m/n/10 )$ [] -Overfull \hbox (3.44513pt too wide) in paragraph at lines 568--603 +Overfull \hbox (3.44513pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 i$ [] -Overfull \hbox (6.00235pt too wide) in paragraph at lines 568--603 +Overfull \hbox (6.00235pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 n$ [] -Overfull \hbox (7.84087pt too wide) in paragraph at lines 568--603 +Overfull \hbox (7.84087pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 r[]$ [] -Overfull \hbox (42.7729pt too wide) in paragraph at lines 568--603 +Overfull \hbox (42.7729pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 r[]\/cmr/m/n/10 (\OML/cmm/m/it/10 Py[]\/cmr/m/n/10 )$ [] -Overfull \hbox (3.44513pt too wide) in paragraph at lines 568--603 +Overfull \hbox (3.44513pt too wide) in paragraph at lines 570--605 \OML/cmm/m/it/10 i$ [] @@ -62937,22 +62475,6 @@ Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no , in font nullfont! -Missing character: There is no w in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no l in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no m in font nullfont! -Missing character: There is no p in font nullfont! -Missing character: There is no u in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! @@ -63027,16 +62549,33 @@ Missing character: There is no i in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no l in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no m in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no : in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 604--605 +Overfull \hbox (20.0pt too wide) in paragraph at lines 606--607 [] [] -Overfull \hbox (111.936pt too wide) detected at line 607 +Overfull \hbox (111.936pt too wide) detected at line 609 \/cmr/m/n/10 ^^A\OML/cmm/m/it/10 E[] \/cmr/m/n/10 = \OML/cmm/m/it/10 E[] \OMS/c msy/m/n/10 ^^@ \OML/cmm/m/it/10 E[] \OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 E[] [] @@ -63192,21 +62731,6 @@ Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no , in font nullfont! -Missing character: There is no w in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no l in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no d in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no d in font nullfont! -Missing character: There is no u in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! @@ -63261,33 +62785,45 @@ Missing character: There is no m in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no s in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no b in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no : in font nullfont! -Overfull \hbox (19.23961pt too wide) in paragraph at lines 607--610 +Overfull \hbox (19.23961pt too wide) in paragraph at lines 609--612 $\OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (17.82411pt too wide) in paragraph at lines 607--610 +Overfull \hbox (17.82411pt too wide) in paragraph at lines 609--612 \OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (15.06566pt too wide) in paragraph at lines 607--610 +Overfull \hbox (15.06566pt too wide) in paragraph at lines 609--612 \OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (158.21732pt too wide) detected at line 612 +Overfull \hbox (158.21732pt too wide) detected at line 614 \/cmr/m/n/10 ^^A\OML/cmm/m/it/10 E[] \/cmr/m/n/10 = \OML/cmm/m/it/10 E[] \OMS/c msy/m/n/10 ^^@ \OML/cmm/m/it/10 E[] \OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 E[] \ OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 E[] [] ! Undefined control sequence. -l.615 \subsection +l.617 \subsection {Simulation of the Experimental TOFMS} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -63328,7 +62864,7 @@ Missing character: There is no F in font nullfont! Missing character: There is no M in font nullfont! Missing character: There is no S in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 615--616 +Overfull \hbox (20.0pt too wide) in paragraph at lines 617--618 [] [] @@ -63727,7 +63263,7 @@ Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 617--618 +Overfull \hbox (20.0pt too wide) in paragraph at lines 619--620 [] [] @@ -63742,6 +63278,8 @@ Missing character: There is no r in font nullfont! Missing character: There is no k in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! +Missing character: There is no S in font nullfont! +Missing character: There is no . in font nullfont! Missing character: There is no Z in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no m in font nullfont! @@ -63758,7 +63296,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.619 ...extit et al.}, \cite{Zamith2020threshold} +l.621 ...extit et al.}, \cite{Zamith2020threshold} the energy transfer was t... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -63768,7 +63306,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Citation `Zamith2020threshold' on page undefined on input line -619. +621. Missing character: There is no ] in font nullfont! Missing character: There is no t in font nullfont! @@ -63848,7 +63386,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.619 ...e of Center model (LOC) \cite{Levine1987} +l.621 ...e of Center model (LOC) \cite{Levine1987} . In the LOC model, the tr... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -63857,7 +63395,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Levine1987' on page undefined on input line 619. +LaTeX Warning: Citation `Levine1987' on page undefined on input line 621. Missing character: There is no ] in font nullfont! Missing character: There is no . in font nullfont! @@ -64218,7 +63756,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.619 ...on experiments,\cite{Zamith2020threshold} +l.621 ...on experiments,\cite{Zamith2020threshold} it fails to reproduce in ... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -64228,7 +63766,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Citation `Zamith2020threshold' on page undefined on input line -619. +621. Missing character: There is no ] in font nullfont! Missing character: There is no i in font nullfont! @@ -64331,7 +63869,7 @@ Missing character: There is no n in font nullfont! ! Undefined control sequence. ...g: Reference `sec:MS' on page \thepage \space undefined\on@line . -l.619 ... as will be shown in section \ref{sec:MS} +l.621 ... as will be shown in section \ref{sec:MS} . The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -64340,36 +63878,36 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `sec:MS' on page undefined on input line 619. +LaTeX Warning: Reference `sec:MS' on page undefined on input line 621. Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 619--620 +Overfull \hbox (20.0pt too wide) in paragraph at lines 621--622 [] [] -Overfull \hbox (4.59996pt too wide) in paragraph at lines 619--620 +Overfull \hbox (4.59996pt too wide) in paragraph at lines 621--622 \OT1/cmr/m/it/10 e [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 619--620 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 621--622 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 619--620 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 621--622 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 619--620 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 621--622 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 619--620 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 621--622 [] [] @@ -64625,7 +64163,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...ng: Reference `MDPST' on page \thepage \space undefined\on@line . -l.621 ...MD+PST is displayed in Figure \ref{MDPST} +l.623 ...MD+PST is displayed in Figure \ref{MDPST} . The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -64634,21 +64172,21 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `MDPST' on page undefined on input line 621. +LaTeX Warning: Reference `MDPST' on page undefined on input line 623. Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 621--622 +Overfull \hbox (20.0pt too wide) in paragraph at lines 623--624 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 621--622 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 623--624 [] [] ! Undefined control sequence. -l.623 \figuremacrob +l.625 \figuremacrob {MDPST}{Principle of MD+PST.} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -64680,7 +64218,7 @@ Missing character: There is no S in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 623--624 +Overfull \hbox (20.0pt too wide) in paragraph at lines 625--626 [] [] @@ -64919,11 +64457,6 @@ Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! -Missing character: There is no w in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no u in font nullfont! -Missing character: There is no s in font nullfont! -Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! @@ -64958,6 +64491,13 @@ Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no f in font nullfont! @@ -65076,14 +64616,6 @@ Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no n in font nullfont! -Missing character: There is no w in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no u in font nullfont! -Missing character: There is no p in font nullfont! -Missing character: There is no d in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no e in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! @@ -65100,6 +64632,15 @@ Missing character: There is no c in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no y in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no u in font nullfont! +Missing character: There is no p in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no d in font nullfont! @@ -65551,27 +65092,27 @@ Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 625--628 +Overfull \hbox (20.0pt too wide) in paragraph at lines 627--630 [] [] -Overfull \hbox (4.29166pt too wide) in paragraph at lines 625--628 +Overfull \hbox (4.29166pt too wide) in paragraph at lines 627--630 \OML/cmm/m/it/10 b$ [] -Overfull \hbox (30.9178pt too wide) in paragraph at lines 625--628 +Overfull \hbox (30.9178pt too wide) in paragraph at lines 627--630 \/cmr/m/n/10 ^^A\OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (6.63892pt too wide) in paragraph at lines 625--628 +Overfull \hbox (6.63892pt too wide) in paragraph at lines 627--630 []$ [] -Overfull \hbox (6.63892pt too wide) in paragraph at lines 625--628 +Overfull \hbox (6.63892pt too wide) in paragraph at lines 627--630 []$ [] @@ -65579,8 +65120,7 @@ Missing character: There is no H in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no e in font nullfont! -Missing character: There is no w in font nullfont! -Missing character: There is no e in font nullfont! +Missing character: There is no I in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no p in font nullfont! @@ -65909,12 +65449,12 @@ Missing character: There is no S in font nullfont! Missing character: There is no T in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 629--630 +Overfull \hbox (20.0pt too wide) in paragraph at lines 631--632 [] [] ! Undefined control sequence. -l.631 \subsection +l.633 \subsection {\label{sec:results}Results and Discussion} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -65943,7 +65483,7 @@ Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 631--632 +Overfull \hbox (20.0pt too wide) in paragraph at lines 633--634 [] [] @@ -65962,8 +65502,7 @@ Missing character: There is no i in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no , in font nullfont! -Missing character: There is no w in font nullfont! -Missing character: There is no e in font nullfont! +Missing character: There is no I in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! @@ -66318,7 +65857,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.633 ...es \cite{Dontot2019, Zamith2020threshold} +l.635 ...es \cite{Dontot2019, Zamith2020threshold} ). It can be regarded as t... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -66327,14 +65866,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Dontot2019' on page undefined on input line 633. +LaTeX Warning: Citation `Dontot2019' on page undefined on input line 635. Missing character: There is no , in font nullfont! \citation{Zamith2020threshold} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.633 ...es \cite{Dontot2019, Zamith2020threshold} +l.635 ...es \cite{Dontot2019, Zamith2020threshold} ). It can be regarded as t... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -66344,7 +65883,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Citation `Zamith2020threshold' on page undefined on input line -633. +635. Missing character: There is no ] in font nullfont! Missing character: There is no ) in font nullfont! @@ -66481,27 +66020,27 @@ Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 633--634 +Overfull \hbox (20.0pt too wide) in paragraph at lines 635--636 [] [] -Overfull \hbox (30.9178pt too wide) in paragraph at lines 633--634 +Overfull \hbox (30.9178pt too wide) in paragraph at lines 635--636 \/cmr/m/n/10 ^^A\OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 633--634 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 635--636 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 633--634 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 635--636 [] [] ! Undefined control sequence. -l.635 \subsubsection +l.637 \subsubsection {\label{sec:MS}TOFMS Comparison} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -66525,7 +66064,7 @@ Missing character: There is no s in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 635--636 +Overfull \hbox (20.0pt too wide) in paragraph at lines 637--638 [] [] @@ -66563,7 +66102,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...g: Reference `expTOF' on page \thepage \space undefined\on@line . -l.637 ... of TOFMS is given in Figure~\ref{expTOF} +l.639 ... of TOFMS is given in Figure~\ref{expTOF} . Figure~\ref{expTOF}(a) i... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -66572,7 +66111,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `expTOF' on page undefined on input line 637. +LaTeX Warning: Reference `expTOF' on page undefined on input line 639. Missing character: There is no . in font nullfont! Missing character: There is no F in font nullfont! @@ -66584,7 +66123,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...g: Reference `expTOF' on page \thepage \space undefined\on@line . -l.637 ... Figure~\ref{expTOF}. Figure~\ref{expTOF} +l.639 ... Figure~\ref{expTOF}. Figure~\ref{expTOF} (a) is centered around the... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -66593,7 +66132,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `expTOF' on page undefined on input line 637. +LaTeX Warning: Reference `expTOF' on page undefined on input line 639. Missing character: There is no ( in font nullfont! Missing character: There is no a in font nullfont! @@ -66696,27 +66235,27 @@ Missing character: There is no y in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 637--638 +Overfull \hbox (20.0pt too wide) in paragraph at lines 639--640 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 637--638 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 639--640 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 637--638 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 639--640 [] [] -Overfull \hbox (6.63892pt too wide) in paragraph at lines 637--638 +Overfull \hbox (6.63892pt too wide) in paragraph at lines 639--640 []$ [] -Overfull \hbox (6.63892pt too wide) in paragraph at lines 637--638 +Overfull \hbox (6.63892pt too wide) in paragraph at lines 639--640 []$ [] @@ -66731,7 +66270,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...g: Reference `expTOF' on page \thepage \space undefined\on@line . -l.639 In Figure~\ref{expTOF} +l.641 In Figure~\ref{expTOF} (a) are displayed three curves corresponding to ... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -66740,7 +66279,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `expTOF' on page undefined on input line 639. +LaTeX Warning: Reference `expTOF' on page undefined on input line 641. Missing character: There is no ( in font nullfont! Missing character: There is no a in font nullfont! @@ -67157,17 +66696,17 @@ Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 639--640 +Overfull \hbox (20.0pt too wide) in paragraph at lines 641--642 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 639--640 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 641--642 [] [] ! Undefined control sequence. -l.641 \figuremacrob +l.643 \figuremacrob {expTOF}{Normalized time of flight mass spectra of the pa... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -67494,17 +67033,17 @@ Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 641--643 +Overfull \hbox (20.0pt too wide) in paragraph at lines 643--645 [] [] -Overfull \hbox (6.63892pt too wide) in paragraph at lines 641--643 +Overfull \hbox (6.63892pt too wide) in paragraph at lines 643--645 []$ [] -Overfull \hbox (6.63892pt too wide) in paragraph at lines 641--643 +Overfull \hbox (6.63892pt too wide) in paragraph at lines 643--645 []$ [] @@ -67519,7 +67058,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...g: Reference `expTOF' on page \thepage \space undefined\on@line . -l.644 In Figure~\ref{expTOF} +l.646 In Figure~\ref{expTOF} (b), the experimental result is compared to the ... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -67528,7 +67067,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `expTOF' on page undefined on input line 644. +LaTeX Warning: Reference `expTOF' on page undefined on input line 646. Missing character: There is no ( in font nullfont! Missing character: There is no b in font nullfont! @@ -68178,7 +67717,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...g: Reference `expTOF' on page \thepage \space undefined\on@line . -l.644 ...epresented in blue in Figure \ref{expTOF} +l.646 ...epresented in blue in Figure \ref{expTOF} (b). The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -68187,39 +67726,39 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `expTOF' on page undefined on input line 644. +LaTeX Warning: Reference `expTOF' on page undefined on input line 646. Missing character: There is no ( in font nullfont! Missing character: There is no b in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 644--645 +Overfull \hbox (20.0pt too wide) in paragraph at lines 646--647 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 644--645 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 646--647 [] [] -Overfull \hbox (13.65697pt too wide) in paragraph at lines 644--645 +Overfull \hbox (13.65697pt too wide) in paragraph at lines 646--647 \OML/cmm/m/it/10 i:e:$ [] -Overfull \hbox (13.65697pt too wide) in paragraph at lines 644--645 +Overfull \hbox (13.65697pt too wide) in paragraph at lines 646--647 \OML/cmm/m/it/10 i:e:$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 644--645 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 646--647 [] [] ! Undefined control sequence. -l.646 \subsubsection +l.648 \subsubsection {\label{sec:MDanalysis}Molecular Dynamics Analysis} The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -68253,47 +67792,47 @@ Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no s in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 646--647 +Overfull \hbox (20.0pt too wide) in paragraph at lines 648--649 [] [] -Overfull \hbox (77.8622pt too wide) in paragraph at lines 648--649 +Overfull \hbox (77.8622pt too wide) in paragraph at lines 650--651 []\OT1/cmr/bx/n/10 Description [] -Overfull \hbox (9.26384pt too wide) in paragraph at lines 648--649 +Overfull \hbox (9.26384pt too wide) in paragraph at lines 650--651 \OT1/cmr/bx/n/10 of [] -Overfull \hbox (13.6402pt too wide) in paragraph at lines 648--649 +Overfull \hbox (13.6402pt too wide) in paragraph at lines 650--651 \OT1/cmr/bx/n/10 se- [] -Overfull \hbox (29.70819pt too wide) in paragraph at lines 648--649 +Overfull \hbox (29.70819pt too wide) in paragraph at lines 650--651 \OT1/cmr/bx/n/10 lected [] -Overfull \hbox (18.63184pt too wide) in paragraph at lines 648--649 +Overfull \hbox (18.63184pt too wide) in paragraph at lines 650--651 \OT1/cmr/bx/n/10 tra- [] -Overfull \hbox (17.72908pt too wide) in paragraph at lines 648--649 +Overfull \hbox (17.72908pt too wide) in paragraph at lines 650--651 \OT1/cmr/bx/n/10 jec- [] -Overfull \hbox (14.05548pt too wide) in paragraph at lines 648--649 +Overfull \hbox (14.05548pt too wide) in paragraph at lines 650--651 \OT1/cmr/bx/n/10 to- [] -Overfull \hbox (17.73741pt too wide) in paragraph at lines 648--649 +Overfull \hbox (17.73741pt too wide) in paragraph at lines 650--651 \OT1/cmr/bx/n/10 ries [] @@ -68425,7 +67964,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...eference `collisions' on page \thepage \space undefined\on@line . -l.650 ... MD trajectories. Figure \ref{collisions} +l.652 ... MD trajectories. Figure \ref{collisions} (top and bottom) reports ... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -68434,7 +67973,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `collisions' on page undefined on input line 650. +LaTeX Warning: Reference `collisions' on page undefined on input line 652. Missing character: There is no ( in font nullfont! Missing character: There is no t in font nullfont! @@ -68621,15 +68160,6 @@ Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no , in font nullfont! -Missing character: There is no w in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no e in font nullfont! -Missing character: There is no x in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no r in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no t in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! @@ -68663,21 +68193,20 @@ Missing character: There is no t in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no y in font nullfont! -Missing character: There is no a in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no d in font nullfont! -Missing character: There is no c in font nullfont! -Missing character: There is no o in font nullfont! -Missing character: There is no n in font nullfont! -Missing character: There is no s in font nullfont! Missing character: There is no i in font nullfont! -Missing character: There is no d in font nullfont! +Missing character: There is no s in font nullfont! Missing character: There is no e in font nullfont! +Missing character: There is no x in font nullfont! +Missing character: There is no t in font nullfont! Missing character: There is no r in font nullfont! -Missing character: There is no t in font nullfont! -Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! +Missing character: There is no c in font nullfont! Missing character: There is no t in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no a in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no d in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no e in font nullfont! @@ -68700,6 +68229,18 @@ Missing character: There is no t in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no i in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no c in font nullfont! +Missing character: There is no o in font nullfont! +Missing character: There is no n in font nullfont! +Missing character: There is no s in font nullfont! +Missing character: There is no i in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no r in font nullfont! +Missing character: There is no e in font nullfont! +Missing character: There is no d in font nullfont! +Missing character: There is no i in font nullfont! Missing character: There is no f in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! @@ -68778,7 +68319,7 @@ Missing character: There is no s in font nullfont! ! Undefined control sequence. ...eference `collisions' on page \thepage \space undefined\on@line . -l.651 Figures \ref{collisions} +l.653 Figures \ref{collisions} -1/1* represent the system after its prelimina... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -68787,7 +68328,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `collisions' on page undefined on input line 651. +LaTeX Warning: Reference `collisions' on page undefined on input line 653. Missing character: There is no - in font nullfont! Missing character: There is no 1 in font nullfont! @@ -68920,7 +68461,7 @@ Missing character: There is no s in font nullfont! ! Undefined control sequence. ...eference `collisions' on page \thepage \space undefined\on@line . -l.652 Figures \ref{collisions} +l.654 Figures \ref{collisions} -2/2* and 3/3* represent the beginning and end... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -68929,7 +68470,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `collisions' on page undefined on input line 652. +LaTeX Warning: Reference `collisions' on page undefined on input line 654. Missing character: There is no - in font nullfont! Missing character: There is no 2 in font nullfont! @@ -69072,7 +68613,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...eference `collisions' on page \thepage \space undefined\on@line . -l.653 ...top trajectory in Figure \ref{collisions} +l.655 ...top trajectory in Figure \ref{collisions} , snapshot 5 corresponds t... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -69081,7 +68622,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `collisions' on page undefined on input line 653. +LaTeX Warning: Reference `collisions' on page undefined on input line 655. Missing character: There is no , in font nullfont! Missing character: There is no s in font nullfont! @@ -69271,7 +68812,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...eference `collisions' on page \thepage \space undefined\on@line . -l.653 ...tom trajectory in Figure \ref{collisions} +l.655 ...tom trajectory in Figure \ref{collisions} , Figures \ref{collisions}... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -69280,7 +68821,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `collisions' on page undefined on input line 653. +LaTeX Warning: Reference `collisions' on page undefined on input line 655. Missing character: There is no , in font nullfont! Missing character: There is no F in font nullfont! @@ -69293,7 +68834,7 @@ Missing character: There is no s in font nullfont! ! Undefined control sequence. ...eference `collisions' on page \thepage \space undefined\on@line . -l.653 ...ref{collisions}, Figures \ref{collisions} +l.655 ...ref{collisions}, Figures \ref{collisions} -5* and 6* correspond to t... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -69302,7 +68843,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `collisions' on page undefined on input line 653. +LaTeX Warning: Reference `collisions' on page undefined on input line 655. Missing character: There is no - in font nullfont! Missing character: There is no 5 in font nullfont! @@ -69549,57 +69090,57 @@ Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 650--654 +Overfull \hbox (20.0pt too wide) in paragraph at lines 652--656 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 650--654 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 652--656 [] [] -Overfull \hbox (7.50002pt too wide) in paragraph at lines 650--654 +Overfull \hbox (7.50002pt too wide) in paragraph at lines 652--656 []\/cmr/m/n/10 A [] -Overfull \hbox (6.63892pt too wide) in paragraph at lines 650--654 +Overfull \hbox (6.63892pt too wide) in paragraph at lines 652--656 []$ [] -Overfull \hbox (7.50002pt too wide) in paragraph at lines 650--654 +Overfull \hbox (7.50002pt too wide) in paragraph at lines 652--656 []\/cmr/m/n/10 A [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 650--654 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 652--656 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 650--654 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 652--656 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 650--654 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 652--656 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 650--654 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 652--656 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 650--654 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 652--656 [] [] ! Undefined control sequence. -l.655 \figuremacrob +l.657 \figuremacrob {collisions}{Snapshots for two different molecular dynam... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -69817,12 +69358,12 @@ Missing character: There is no y in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 655--656 +Overfull \hbox (20.0pt too wide) in paragraph at lines 657--658 [] [] -Overfull \hbox (7.50002pt too wide) in paragraph at lines 655--656 +Overfull \hbox (7.50002pt too wide) in paragraph at lines 657--658 []\/cmr/m/n/10 A [] @@ -70051,7 +69592,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...eference `collisions' on page \thepage \space undefined\on@line . -l.657 ...top trajectory in Figure \ref{collisions} +l.659 ...top trajectory in Figure \ref{collisions} , the argon atom is pushin... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -70060,7 +69601,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `collisions' on page undefined on input line 657. +LaTeX Warning: Reference `collisions' on page undefined on input line 659. Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! @@ -70237,7 +69778,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...eference `collisions' on page \thepage \space undefined\on@line . -l.657 ...tom trajectory in Figure \ref{collisions} +l.659 ...tom trajectory in Figure \ref{collisions} , the collision mostly inv... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -70246,7 +69787,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `collisions' on page undefined on input line 657. +LaTeX Warning: Reference `collisions' on page undefined on input line 659. Missing character: There is no , in font nullfont! Missing character: There is no t in font nullfont! @@ -70610,22 +70151,22 @@ Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 657--661 +Overfull \hbox (20.0pt too wide) in paragraph at lines 659--663 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 657--661 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 659--663 [] [] -Overfull \hbox (13.65697pt too wide) in paragraph at lines 657--661 +Overfull \hbox (13.65697pt too wide) in paragraph at lines 659--663 \OML/cmm/m/it/10 i:e:$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 657--661 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 659--663 [] [] @@ -70852,7 +70393,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...rc-Etf-175eV-d-bin03' on page \thepage \space undefined\on@line . -l.663 ...Figure~\ref{distriPerc-Etf-175eV-d-bin03} +l.665 ...Figure~\ref{distriPerc-Etf-175eV-d-bin03} where the distribution of... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -70862,7 +70403,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `distriPerc-Etf-175eV-d-bin03' on page undefined on i -nput line 663. +nput line 665. Missing character: There is no w in font nullfont! Missing character: There is no h in font nullfont! @@ -71287,7 +70828,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...rc-Etf-175eV-d-bin03' on page \thepage \space undefined\on@line . -l.664 ...Figure \ref{distriPerc-Etf-175eV-d-bin03} +l.666 ...Figure \ref{distriPerc-Etf-175eV-d-bin03} . In the distribution resu... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -71297,7 +70838,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `distriPerc-Etf-175eV-d-bin03' on page undefined on i -nput line 664. +nput line 666. Missing character: There is no . in font nullfont! Missing character: There is no I in font nullfont! @@ -71600,27 +71141,27 @@ Missing character: There is no t in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 662--667 +Overfull \hbox (20.0pt too wide) in paragraph at lines 664--669 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 662--667 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 664--669 [] [] -Overfull \hbox (30.9178pt too wide) in paragraph at lines 662--667 +Overfull \hbox (30.9178pt too wide) in paragraph at lines 664--669 \/cmr/m/n/10 ^^A\OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 662--667 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 664--669 [] [] ! Undefined control sequence. -l.668 \figuremacro +l.670 \figuremacro {distriPerc-Etf-175eV-d-bin03}{Distribution of transferred... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -71864,12 +71405,12 @@ Missing character: There is no e in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 668--669 +Overfull \hbox (20.0pt too wide) in paragraph at lines 670--671 [] [] -Overfull \hbox (30.9178pt too wide) in paragraph at lines 668--669 +Overfull \hbox (30.9178pt too wide) in paragraph at lines 670--671 \/cmr/m/n/10 ^^A\OML/cmm/m/it/10 E[]$ [] @@ -71881,8 +71422,7 @@ Missing character: There is no l in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no , in font nullfont! -Missing character: There is no w in font nullfont! -Missing character: There is no e in font nullfont! +Missing character: There is no I in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! @@ -72049,7 +71589,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...rence `fragmentation' on page \thepage \space undefined\on@line . -l.671 ...V are shown in Figure \ref{fragmentation} +l.673 ...V are shown in Figure \ref{fragmentation} . The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -72058,7 +71598,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `fragmentation' on page undefined on input line 671. +LaTeX Warning: Reference `fragmentation' on page undefined on input line 673. Missing character: There is no . in font nullfont! Missing character: There is no I in font nullfont! @@ -72263,8 +71803,7 @@ Missing character: There is no p in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no , in font nullfont! -Missing character: There is no w in font nullfont! -Missing character: There is no e in font nullfont! +Missing character: There is no I in font nullfont! Missing character: There is no w in font nullfont! Missing character: There is no i in font nullfont! Missing character: There is no l in font nullfont! @@ -72362,22 +71901,22 @@ Missing character: There is no n in font nullfont! Missing character: There is no g in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 670--674 +Overfull \hbox (20.0pt too wide) in paragraph at lines 672--676 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 670--674 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 672--676 [] [] -Overfull \hbox (4.48613pt too wide) in paragraph at lines 670--674 +Overfull \hbox (4.48613pt too wide) in paragraph at lines 672--676 []$ [] ! Undefined control sequence. -l.675 \figuremacrob +l.677 \figuremacrob {fragmentation}{Snapshots for molecular dynamics trajecto... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -72526,32 +72065,32 @@ Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 675--676 +Overfull \hbox (20.0pt too wide) in paragraph at lines 677--678 [] [] -Overfull \hbox (7.50002pt too wide) in paragraph at lines 675--676 +Overfull \hbox (7.50002pt too wide) in paragraph at lines 677--678 []\/cmr/m/n/10 A [] -Overfull \hbox (80.85657pt too wide) in paragraph at lines 677--678 +Overfull \hbox (80.85657pt too wide) in paragraph at lines 679--680 []\OT1/cmr/bx/n/10 Dissociation [] -Overfull \hbox (24.6693pt too wide) in paragraph at lines 677--678 +Overfull \hbox (24.6693pt too wide) in paragraph at lines 679--680 \OT1/cmr/bx/n/10 cross [] -Overfull \hbox (18.75128pt too wide) in paragraph at lines 677--678 +Overfull \hbox (18.75128pt too wide) in paragraph at lines 679--680 \OT1/cmr/bx/n/10 sec- [] -Overfull \hbox (19.80545pt too wide) in paragraph at lines 677--678 +Overfull \hbox (19.80545pt too wide) in paragraph at lines 679--680 \OT1/cmr/bx/n/10 tion [] @@ -72594,7 +72133,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...rence `opacitycurves' on page \thepage \space undefined\on@line . -l.679 ...e presented in Figure \ref{opacitycurves} +l.681 ...e presented in Figure \ref{opacitycurves} for various collision ene... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -72603,7 +72142,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `opacitycurves' on page undefined on input line 679. +LaTeX Warning: Reference `opacitycurves' on page undefined on input line 681. Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! @@ -74057,7 +73596,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.680 ...rks \cite{Chen2014, Gatchell2016knockout} +l.682 ...rks \cite{Chen2014, Gatchell2016knockout} which also pointed out th... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -74066,14 +73605,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Chen2014' on page undefined on input line 680. +LaTeX Warning: Citation `Chen2014' on page undefined on input line 682. Missing character: There is no , in font nullfont! \citation{Gatchell2016knockout} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.680 ...rks \cite{Chen2014, Gatchell2016knockout} +l.682 ...rks \cite{Chen2014, Gatchell2016knockout} which also pointed out th... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -74083,7 +73622,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Citation `Gatchell2016knockout' on page undefined on input line - 680. + 682. Missing character: There is no ] in font nullfont! Missing character: There is no w in font nullfont! @@ -74224,102 +73763,102 @@ Missing character: There is no s in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 679--681 +Overfull \hbox (20.0pt too wide) in paragraph at lines 681--683 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 679--681 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 681--683 [] [] -Overfull \hbox (7.50002pt too wide) in paragraph at lines 679--681 +Overfull \hbox (7.50002pt too wide) in paragraph at lines 681--683 []\/cmr/m/n/10 A [] -Overfull \hbox (7.50002pt too wide) in paragraph at lines 679--681 +Overfull \hbox (7.50002pt too wide) in paragraph at lines 681--683 []\/cmr/m/n/10 A [] -Overfull \hbox (7.50002pt too wide) in paragraph at lines 679--681 +Overfull \hbox (7.50002pt too wide) in paragraph at lines 681--683 []\/cmr/m/n/10 A [] -Overfull \hbox (7.50002pt too wide) in paragraph at lines 679--681 +Overfull \hbox (7.50002pt too wide) in paragraph at lines 681--683 []\/cmr/m/n/10 A [] -Overfull \hbox (7.50002pt too wide) in paragraph at lines 679--681 +Overfull \hbox (7.50002pt too wide) in paragraph at lines 681--683 []\/cmr/m/n/10 A [] -Overfull \hbox (7.50002pt too wide) in paragraph at lines 679--681 +Overfull \hbox (7.50002pt too wide) in paragraph at lines 681--683 []\/cmr/m/n/10 A [] -Overfull \hbox (7.50002pt too wide) in paragraph at lines 679--681 +Overfull \hbox (7.50002pt too wide) in paragraph at lines 681--683 []\/cmr/m/n/10 A [] -Overfull \hbox (7.50002pt too wide) in paragraph at lines 679--681 +Overfull \hbox (7.50002pt too wide) in paragraph at lines 681--683 []\/cmr/m/n/10 A [] -Overfull \hbox (7.50002pt too wide) in paragraph at lines 679--681 +Overfull \hbox (7.50002pt too wide) in paragraph at lines 681--683 []\/cmr/m/n/10 A [] -Overfull \hbox (7.50002pt too wide) in paragraph at lines 679--681 +Overfull \hbox (7.50002pt too wide) in paragraph at lines 681--683 []\/cmr/m/n/10 A [] -Overfull \hbox (7.50002pt too wide) in paragraph at lines 679--681 +Overfull \hbox (7.50002pt too wide) in paragraph at lines 681--683 []\/cmr/m/n/10 A [] -Overfull \hbox (7.50002pt too wide) in paragraph at lines 679--681 +Overfull \hbox (7.50002pt too wide) in paragraph at lines 681--683 []\/cmr/m/n/10 A [] -Overfull \hbox (7.50002pt too wide) in paragraph at lines 679--681 +Overfull \hbox (7.50002pt too wide) in paragraph at lines 681--683 []\/cmr/m/n/10 A [] -Overfull \hbox (7.50002pt too wide) in paragraph at lines 679--681 +Overfull \hbox (7.50002pt too wide) in paragraph at lines 681--683 []\/cmr/m/n/10 A [] -Overfull \hbox (7.50002pt too wide) in paragraph at lines 679--681 +Overfull \hbox (7.50002pt too wide) in paragraph at lines 681--683 []\/cmr/m/n/10 A [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 679--681 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 681--683 [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 679--681 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 681--683 [] [] ! Undefined control sequence. -l.682 \figuremacro +l.684 \figuremacro {opacitycurves}{Opacity curves as a function of the impact... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -74433,12 +73972,12 @@ Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 682--683 +Overfull \hbox (20.0pt too wide) in paragraph at lines 684--685 [] [] -Overfull \hbox (4.29166pt too wide) in paragraph at lines 682--683 +Overfull \hbox (4.29166pt too wide) in paragraph at lines 684--685 \OML/cmm/m/it/10 b$ [] @@ -74465,7 +74004,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...rence `cross-section' on page \thepage \space undefined\on@line . -l.684 The blue curve in Figure \ref{cross-section} +l.686 The blue curve in Figure \ref{cross-section} shows the MD dissociation... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -74474,7 +74013,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `cross-section' on page undefined on input line 684. +LaTeX Warning: Reference `cross-section' on page undefined on input line 686. Missing character: There is no s in font nullfont! Missing character: There is no h in font nullfont! @@ -74568,7 +74107,7 @@ Missing character: There is no . in font nullfont! ! Undefined control sequence. ...ng: Reference `integ' on page \thepage \space undefined\on@line . -l.684 ... opacity curves following eq. \ref{integ} +l.686 ... opacity curves following eq. \ref{integ} . It presents a steep incr... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -74577,7 +74116,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `integ' on page undefined on input line 684. +LaTeX Warning: Reference `integ' on page undefined on input line 686. Missing character: There is no . in font nullfont! Missing character: There is no I in font nullfont! @@ -74871,7 +74410,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...rence `cross-section' on page \thepage \space undefined\on@line . -l.685 ...te timescales. Figure \ref{cross-section} +l.687 ...te timescales. Figure \ref{cross-section} also reports the cross se... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -74880,7 +74419,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `cross-section' on page undefined on input line 685. +LaTeX Warning: Reference `cross-section' on page undefined on input line 687. Missing character: There is no a in font nullfont! Missing character: There is no l in font nullfont! @@ -75532,7 +75071,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...g: Reference `expTOF' on page \thepage \space undefined\on@line . -l.687 ...spectra analysis (see Figure \ref{expTOF} +l.689 ...spectra analysis (see Figure \ref{expTOF} ). The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -75541,47 +75080,46 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `expTOF' on page undefined on input line 687. +LaTeX Warning: Reference `expTOF' on page undefined on input line 689. Missing character: There is no ) in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 684--688 +Overfull \hbox (20.0pt too wide) in paragraph at lines 686--690 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 684--688 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 686--690 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 684--688 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 686--690 [] [] -Overfull \hbox (11.98615pt too wide) in paragraph at lines 684--688 +Overfull \hbox (11.98615pt too wide) in paragraph at lines 686--690 []\/cmr/m/n/10 A$[]$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 684--688 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 686--690 [] [] -Overfull \hbox (11.98615pt too wide) in paragraph at lines 684--688 +Overfull \hbox (11.98615pt too wide) in paragraph at lines 686--690 []\/cmr/m/n/10 A$[]$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 684--688 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 686--690 [] [] -Missing character: There is no W in font nullfont! -Missing character: There is no e in font nullfont! +Missing character: There is no I in font nullfont! Missing character: There is no h in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no v in font nullfont! @@ -75608,7 +75146,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...rence `cross-section' on page \thepage \space undefined\on@line . -l.689 ...lso plotted in Figure~\ref{cross-section} +l.691 ...lso plotted in Figure~\ref{cross-section} the model cross section $... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -75617,7 +75155,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `cross-section' on page undefined on input line 689. +LaTeX Warning: Reference `cross-section' on page undefined on input line 691. Missing character: There is no t in font nullfont! Missing character: There is no h in font nullfont! @@ -75730,7 +75268,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.689 ...mental results \cite{Zamith2020threshold} +l.691 ...mental results \cite{Zamith2020threshold} . This model cross section... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -75740,7 +75278,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Citation `Zamith2020threshold' on page undefined on input line -689. +691. Missing character: There is no ] in font nullfont! Missing character: There is no . in font nullfont! @@ -75883,27 +75421,27 @@ Missing character: There is no b in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no : in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 689--690 +Overfull \hbox (20.0pt too wide) in paragraph at lines 691--692 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 689--690 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 691--692 [] [] -Overfull \hbox (14.18637pt too wide) in paragraph at lines 689--690 +Overfull \hbox (14.18637pt too wide) in paragraph at lines 691--692 \OML/cmm/m/it/10 ^^[[]$ [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 689--690 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 691--692 [] [] -Overfull \hbox (149.12054pt too wide) detected at line 692 +Overfull \hbox (149.12054pt too wide) detected at line 694 \OML/cmm/m/it/10 ^^[[]\/cmr/m/n/10 (\OML/cmm/m/it/10 E[]\/cmr/m/n/10 ) = \OML/c mm/m/it/10 ^^[[]\/cmr/m/n/10 (\OML/cmm/m/it/10 E[] \OMS/cmsy/m/n/10 ^^@ \OML/cm m/m/it/10 D\/cmr/m/n/10 )\OML/cmm/m/it/10 =\/cmr/m/n/10 (\OML/cmm/m/it/10 E[]\/ @@ -75945,7 +75483,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.693 ...gy \cite{Dontot2019, Zamith2020threshold} +l.695 ...gy \cite{Dontot2019, Zamith2020threshold} and $\sigma_0=63$~\AA$^2$... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -75954,14 +75492,14 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Dontot2019' on page undefined on input line 693. +LaTeX Warning: Citation `Dontot2019' on page undefined on input line 695. Missing character: There is no , in font nullfont! \citation{Zamith2020threshold} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.693 ...gy \cite{Dontot2019, Zamith2020threshold} +l.695 ...gy \cite{Dontot2019, Zamith2020threshold} and $\sigma_0=63$~\AA$^2$... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -75971,7 +75509,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Citation `Zamith2020threshold' on page undefined on input line -693. +695. Missing character: There is no ] in font nullfont! Missing character: There is no a in font nullfont! @@ -76358,7 +75896,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...rence `cross-section' on page \thepage \space undefined\on@line . -l.693 ... purple one in Figure~\ref{cross-section} +l.695 ... purple one in Figure~\ref{cross-section} , namely the cross section... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -76367,7 +75905,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `cross-section' on page undefined on input line 693. +LaTeX Warning: Reference `cross-section' on page undefined on input line 695. Missing character: There is no , in font nullfont! Missing character: There is no n in font nullfont! @@ -76741,42 +76279,42 @@ Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (19.11246pt too wide) in paragraph at lines 692--695 +Overfull \hbox (19.11246pt too wide) in paragraph at lines 694--697 $\OML/cmm/m/it/10 D \/cmr/m/n/10 = [] -Overfull \hbox (23.20836pt too wide) in paragraph at lines 692--695 +Overfull \hbox (23.20836pt too wide) in paragraph at lines 694--697 \/cmr/m/n/10 1\OML/cmm/m/it/10 :\/cmr/m/n/10 08$ [] [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 692--695 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 694--697 [] [] -Overfull \hbox (20.75577pt too wide) in paragraph at lines 692--695 +Overfull \hbox (20.75577pt too wide) in paragraph at lines 694--697 \OML/cmm/m/it/10 ^^[[] \/cmr/m/n/10 = [] -Overfull \hbox (21.98618pt too wide) in paragraph at lines 692--695 +Overfull \hbox (21.98618pt too wide) in paragraph at lines 694--697 \/cmr/m/n/10 63$ []A$[]$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 692--695 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 694--697 [] [] -Overfull \hbox (11.98615pt too wide) in paragraph at lines 692--695 +Overfull \hbox (11.98615pt too wide) in paragraph at lines 694--697 []\/cmr/m/n/10 A$[]$ [] -Overfull \hbox (11.98615pt too wide) in paragraph at lines 692--695 +Overfull \hbox (11.98615pt too wide) in paragraph at lines 694--697 []\/cmr/m/n/10 A$[]$ [] @@ -76891,7 +76429,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...rence `cross-section' on page \thepage \space undefined\on@line . -l.696 ...{MD}$(0.1)) in Figure~\ref{cross-section} +l.698 ...{MD}$(0.1)) in Figure~\ref{cross-section} are close to the ones of ... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -76900,7 +76438,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `cross-section' on page undefined on input line 696. +LaTeX Warning: Reference `cross-section' on page undefined on input line 698. Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! @@ -77061,27 +76599,27 @@ Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 696--697 +Overfull \hbox (20.0pt too wide) in paragraph at lines 698--699 [] [] -Overfull \hbox (19.42947pt too wide) in paragraph at lines 696--697 +Overfull \hbox (19.42947pt too wide) in paragraph at lines 698--699 \OML/cmm/m/it/10 ^^[[]$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 696--697 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 698--699 [] [] -Overfull \hbox (19.42947pt too wide) in paragraph at lines 696--697 +Overfull \hbox (19.42947pt too wide) in paragraph at lines 698--699 \OML/cmm/m/it/10 ^^[[]$ [] ! Undefined control sequence. -l.698 \figuremacro +l.700 \figuremacro {cross-section}{Dissociation cross sections of Py$_2^+$ af... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -77386,37 +76924,37 @@ Missing character: There is no f in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 698--699 +Overfull \hbox (20.0pt too wide) in paragraph at lines 700--701 [] [] -Overfull \hbox (6.63892pt too wide) in paragraph at lines 698--699 +Overfull \hbox (6.63892pt too wide) in paragraph at lines 700--701 []$ [] -Overfull \hbox (19.42947pt too wide) in paragraph at lines 698--699 +Overfull \hbox (19.42947pt too wide) in paragraph at lines 700--701 \OML/cmm/m/it/10 ^^[[]$ [] -Overfull \hbox (55.77066pt too wide) in paragraph at lines 701--702 +Overfull \hbox (55.77066pt too wide) in paragraph at lines 703--704 []\OT1/cmr/bx/n/10 Energy [] -Overfull \hbox (20.5485pt too wide) in paragraph at lines 701--702 +Overfull \hbox (20.5485pt too wide) in paragraph at lines 703--704 \OT1/cmr/bx/n/10 par- [] -Overfull \hbox (11.49994pt too wide) in paragraph at lines 701--702 +Overfull \hbox (11.49994pt too wide) in paragraph at lines 703--704 \OT1/cmr/bx/n/10 ti- [] -Overfull \hbox (19.80545pt too wide) in paragraph at lines 701--702 +Overfull \hbox (19.80545pt too wide) in paragraph at lines 703--704 \OT1/cmr/bx/n/10 tion [] @@ -77541,7 +77079,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...`transferredE-Ar-300' on page \thepage \space undefined\on@line . -l.703 ...otted in Figure \ref{transferredE-Ar-300} +l.705 ...otted in Figure \ref{transferredE-Ar-300} as a function of the coll... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -77551,7 +77089,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `transferredE-Ar-300' on page undefined on input line - 703. + 705. Missing character: There is no a in font nullfont! Missing character: There is no s in font nullfont! @@ -78152,8 +77690,7 @@ Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no . in font nullfont! -Missing character: There is no W in font nullfont! -Missing character: There is no e in font nullfont! +Missing character: There is no I in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no t in font nullfont! @@ -78351,7 +77888,7 @@ Missing character: There is no u in font nullfont! Missing character: There is no e in font nullfont! Missing character: There is no , in font nullfont! ! Undefined control sequence. -l.706 ... arbitrarily chosen $b_{max}$ value, {\it +l.708 ... arbitrarily chosen $b_{max}$ value, {\it i.e.} increasing $b_{max}... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -78594,42 +78131,42 @@ Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 703--707 +Overfull \hbox (20.0pt too wide) in paragraph at lines 705--709 [] [] -Overfull \hbox (30.9178pt too wide) in paragraph at lines 703--707 +Overfull \hbox (30.9178pt too wide) in paragraph at lines 705--709 \/cmr/m/n/10 ^^A\OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 703--707 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 705--709 [] [] -Overfull \hbox (42.1497pt too wide) in paragraph at lines 703--707 +Overfull \hbox (42.1497pt too wide) in paragraph at lines 705--709 \/cmr/m/n/10 ^^A\OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (29.08829pt too wide) in paragraph at lines 703--707 +Overfull \hbox (29.08829pt too wide) in paragraph at lines 705--709 \OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (20.76015pt too wide) in paragraph at lines 703--707 +Overfull \hbox (20.76015pt too wide) in paragraph at lines 705--709 \OML/cmm/m/it/10 b[]$ [] -Overfull \hbox (20.76015pt too wide) in paragraph at lines 703--707 +Overfull \hbox (20.76015pt too wide) in paragraph at lines 705--709 \OML/cmm/m/it/10 b[]$ [] -Overfull \hbox (20.76015pt too wide) in paragraph at lines 703--707 +Overfull \hbox (20.76015pt too wide) in paragraph at lines 705--709 \OML/cmm/m/it/10 b[]$ [] @@ -78735,7 +78272,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...`transferredE-Ar-300' on page \thepage \space undefined\on@line . -l.708 ...rgies in Figure~\ref{transferredE-Ar-300} +l.710 ...rgies in Figure~\ref{transferredE-Ar-300} are close to the ones of ... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -78745,7 +78282,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `transferredE-Ar-300' on page undefined on input line - 708. + 710. Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! @@ -78917,17 +78454,17 @@ Missing character: There is no g in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 708--709 +Overfull \hbox (20.0pt too wide) in paragraph at lines 710--711 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 708--709 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 710--711 [] [] ! Undefined control sequence. -l.710 \figuremacro +l.712 \figuremacro {transferredE-Ar-300}{At the end of the MD collision simul... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -79246,27 +78783,27 @@ Missing character: There is no e in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 710--711 +Overfull \hbox (20.0pt too wide) in paragraph at lines 712--713 [] [] -Overfull \hbox (30.9178pt too wide) in paragraph at lines 710--711 +Overfull \hbox (30.9178pt too wide) in paragraph at lines 712--713 \/cmr/m/n/10 ^^A\OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (37.42165pt too wide) in paragraph at lines 710--711 +Overfull \hbox (37.42165pt too wide) in paragraph at lines 712--713 \/cmr/m/n/10 ^^A\OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (42.1497pt too wide) in paragraph at lines 710--711 +Overfull \hbox (42.1497pt too wide) in paragraph at lines 712--713 \/cmr/m/n/10 ^^A\OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (51.68517pt too wide) in paragraph at lines 710--711 +Overfull \hbox (51.68517pt too wide) in paragraph at lines 712--713 \/cmr/m/n/10 ^^A\OML/cmm/m/it/10 E[]$ [] @@ -79434,7 +78971,7 @@ Missing character: There is no . in font nullfont! ! Undefined control sequence. ...g: Reference `Eparti' on page \thepage \space undefined\on@line . -l.712 ...e modes) is easier (see eqs. \ref{Eparti} +l.714 ...e modes) is easier (see eqs. \ref{Eparti} ) than that of the potenti... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -79443,7 +78980,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `Eparti' on page undefined on input line 712. +LaTeX Warning: Reference `Eparti' on page undefined on input line 714. Missing character: There is no ) in font nullfont! Missing character: There is no t in font nullfont! @@ -79582,7 +79119,7 @@ Missing character: There is no . in font nullfont! ! Undefined control sequence. ...g: Reference `Eparti' on page \thepage \space undefined\on@line . -l.713 ...ergy sub-contributions (eqs. \ref{Eparti} +l.715 ...ergy sub-contributions (eqs. \ref{Eparti} ) are averaged over all th... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -79591,7 +79128,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `Eparti' on page undefined on input line 713. +LaTeX Warning: Reference `Eparti' on page undefined on input line 715. Missing character: There is no ) in font nullfont! Missing character: There is no a in font nullfont! @@ -79648,7 +79185,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...eference `tab:table1' on page \thepage \space undefined\on@line . -l.713 ...es and reported in Table \ref{tab:table1} +l.715 ...es and reported in Table \ref{tab:table1} and Figure \ref{Epartitio... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -79657,7 +79194,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `tab:table1' on page undefined on input line 713. +LaTeX Warning: Reference `tab:table1' on page undefined on input line 715. Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! @@ -79671,7 +79208,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...Epartition-Ar-300-SP' on page \thepage \space undefined\on@line . -l.713 ...e1} and Figure \ref{Epartition-Ar-300-SP} +l.715 ...e1} and Figure \ref{Epartition-Ar-300-SP} . The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -79681,7 +79218,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `Epartition-Ar-300-SP' on page undefined on input lin -e 713. +e 715. Missing character: There is no . in font nullfont! Missing character: There is no I in font nullfont! @@ -79928,7 +79465,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...Epartition-Ar-300-SP' on page \thepage \space undefined\on@line . -l.714 ...rves in Figure \ref{Epartition-Ar-300-SP} +l.716 ...rves in Figure \ref{Epartition-Ar-300-SP} ) calculated by the follow... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -79938,7 +79475,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `Epartition-Ar-300-SP' on page undefined on input lin -e 714. +e 716. Missing character: There is no ) in font nullfont! Missing character: There is no c in font nullfont! @@ -79971,7 +79508,7 @@ Missing character: There is no s in font nullfont! ! Undefined control sequence. ...eference `separately' on page \thepage \space undefined\on@line . -l.714 ...ted by the following eqs \ref{separately} +l.716 ...ted by the following eqs \ref{separately} , The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -79980,7 +79517,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `separately' on page undefined on input line 714. +LaTeX Warning: Reference `separately' on page undefined on input line 716. Missing character: There is no , in font nullfont! @@ -79990,7 +79527,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.715 \begin{align} +l.717 \begin{align} Your command was ignored. Type I to replace it with another command, @@ -80000,13 +79537,13 @@ Missing character: There is no E in font nullfont! ! Missing $ inserted. $ -l.717 E_ +l.719 E_ {1}^k &=E_{td-d}^k*P+E_{td-ud}^k*(1-P) \nonumber \\ I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Misplaced alignment tab character &. -l.717 E_{1}^k & +l.719 E_{1}^k & =E_{td-d}^k*P+E_{td-ud}^k*(1-P) \nonumber \\ I can't figure out why you would want to use a tab mark here. If you just want an ampersand, the remedy is @@ -80016,7 +79553,7 @@ you're probably due for more error messages, and you might try typing `S' now just to see what is salvageable. ! Misplaced alignment tab character &. -l.718 E_{2}^k & +l.720 E_{2}^k & =E_{Re-d}^k*P+E_{Re-ud}^k*(1-P) \\ I can't figure out why you would want to use a tab mark here. If you just want an ampersand, the remedy is @@ -80026,7 +79563,7 @@ you're probably due for more error messages, and you might try typing `S' now just to see what is salvageable. ! Misplaced alignment tab character &. -l.719 E_{3}^k & +l.721 E_{3}^k & =(E_{Py^1}^k + E_{Py^2}^k)_{-d}*P+(E_{Py^1}^k + E_{Py^2}^k)_{... I can't figure out why you would want to use a tab mark here. If you just want an ampersand, the remedy is @@ -80042,7 +79579,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.720 \end{align} +l.722 \end{align} Your command was ignored. Type I to replace it with another command, @@ -80051,7 +79588,7 @@ or to continue without it. ! Missing $ inserted. $ -l.720 \end{align} +l.722 \end{align} I've inserted something that you may have forgotten. (See the above.) @@ -80262,7 +79799,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...Epartition-Ar-300-SP' on page \thepage \space undefined\on@line . -l.722 ...es (see Figure \ref{Epartition-Ar-300-SP} +l.724 ...es (see Figure \ref{Epartition-Ar-300-SP} ). The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -80272,7 +79809,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `Epartition-Ar-300-SP' on page undefined on input lin -e 722. +e 724. Missing character: There is no ) in font nullfont! Missing character: There is no . in font nullfont! @@ -80352,147 +79889,147 @@ Missing character: There is no h in font nullfont! Missing character: There is no t in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 712--724 +Overfull \hbox (20.0pt too wide) in paragraph at lines 714--726 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 712--724 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 714--726 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 712--724 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 714--726 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 712--724 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 714--726 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 712--724 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 714--726 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 712--724 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 714--726 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 712--724 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 714--726 [] [] -Overfull \hbox (15.47568pt too wide) in paragraph at lines 712--724 +Overfull \hbox (15.47568pt too wide) in paragraph at lines 714--726 [] \/cmr/m/n/10 = [] -Overfull \hbox (30.47856pt too wide) in paragraph at lines 712--724 +Overfull \hbox (30.47856pt too wide) in paragraph at lines 714--726 \OML/cmm/m/it/10 E[] \OMS/cmsy/m/n/10 ^^C [] -Overfull \hbox (15.58684pt too wide) in paragraph at lines 712--724 +Overfull \hbox (15.58684pt too wide) in paragraph at lines 714--726 \OML/cmm/m/it/10 P \/cmr/m/n/10 + [] -Overfull \hbox (35.20662pt too wide) in paragraph at lines 712--724 +Overfull \hbox (35.20662pt too wide) in paragraph at lines 714--726 \OML/cmm/m/it/10 E[] \OMS/cmsy/m/n/10 ^^C [] -Overfull \hbox (16.66672pt too wide) in paragraph at lines 712--724 +Overfull \hbox (16.66672pt too wide) in paragraph at lines 714--726 \/cmr/m/n/10 (1 \OMS/cmsy/m/n/10 ^^@ [] -Overfull \hbox (11.69794pt too wide) in paragraph at lines 712--724 +Overfull \hbox (11.69794pt too wide) in paragraph at lines 714--726 \OML/cmm/m/it/10 P\/cmr/m/n/10 )[] [] -Overfull \hbox (23.43399pt too wide) in paragraph at lines 712--724 +Overfull \hbox (23.43399pt too wide) in paragraph at lines 714--726 \OML/cmm/m/it/10 E[] \/cmr/m/n/10 = [] -Overfull \hbox (33.14905pt too wide) in paragraph at lines 712--724 +Overfull \hbox (33.14905pt too wide) in paragraph at lines 714--726 \OML/cmm/m/it/10 E[] \OMS/cmsy/m/n/10 ^^C [] -Overfull \hbox (15.58684pt too wide) in paragraph at lines 712--724 +Overfull \hbox (15.58684pt too wide) in paragraph at lines 714--726 \OML/cmm/m/it/10 P \/cmr/m/n/10 + [] -Overfull \hbox (37.8771pt too wide) in paragraph at lines 712--724 +Overfull \hbox (37.8771pt too wide) in paragraph at lines 714--726 \OML/cmm/m/it/10 E[] \OMS/cmsy/m/n/10 ^^C [] -Overfull \hbox (16.66672pt too wide) in paragraph at lines 712--724 +Overfull \hbox (16.66672pt too wide) in paragraph at lines 714--726 \/cmr/m/n/10 (1 \OMS/cmsy/m/n/10 ^^@ [] -Overfull \hbox (11.69794pt too wide) in paragraph at lines 712--724 +Overfull \hbox (11.69794pt too wide) in paragraph at lines 714--726 \OML/cmm/m/it/10 P\/cmr/m/n/10 )[] [] -Overfull \hbox (23.43399pt too wide) in paragraph at lines 712--724 +Overfull \hbox (23.43399pt too wide) in paragraph at lines 714--726 \OML/cmm/m/it/10 E[] \/cmr/m/n/10 = [] -Overfull \hbox (33.92593pt too wide) in paragraph at lines 712--724 +Overfull \hbox (33.92593pt too wide) in paragraph at lines 714--726 \/cmr/m/n/10 (\OML/cmm/m/it/10 E[] \/cmr/m/n/10 + [] -Overfull \hbox (42.06104pt too wide) in paragraph at lines 712--724 +Overfull \hbox (42.06104pt too wide) in paragraph at lines 714--726 \OML/cmm/m/it/10 E[]\/cmr/m/n/10 )[] \OMS/cmsy/m/n/10 ^^C [] -Overfull \hbox (15.58684pt too wide) in paragraph at lines 712--724 +Overfull \hbox (15.58684pt too wide) in paragraph at lines 714--726 \OML/cmm/m/it/10 P \/cmr/m/n/10 + [] -Overfull \hbox (33.92593pt too wide) in paragraph at lines 712--724 +Overfull \hbox (33.92593pt too wide) in paragraph at lines 714--726 \/cmr/m/n/10 (\OML/cmm/m/it/10 E[] \/cmr/m/n/10 + [] -Overfull \hbox (46.7891pt too wide) in paragraph at lines 712--724 +Overfull \hbox (46.7891pt too wide) in paragraph at lines 714--726 \OML/cmm/m/it/10 E[]\/cmr/m/n/10 )[] \OMS/cmsy/m/n/10 ^^C [] -Overfull \hbox (16.66672pt too wide) in paragraph at lines 712--724 +Overfull \hbox (16.66672pt too wide) in paragraph at lines 714--726 \/cmr/m/n/10 (1 \OMS/cmsy/m/n/10 ^^@ [] -Overfull \hbox (11.69794pt too wide) in paragraph at lines 712--724 +Overfull \hbox (11.69794pt too wide) in paragraph at lines 714--726 \OML/cmm/m/it/10 P\/cmr/m/n/10 )$ [] -Overfull \hbox (7.80904pt too wide) in paragraph at lines 712--724 +Overfull \hbox (7.80904pt too wide) in paragraph at lines 714--726 \OML/cmm/m/it/10 P$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 712--724 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 714--726 [] [] @@ -80503,14 +80040,14 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.728 \begin{table} +l.730 \begin{table} Your command was ignored. Type I to replace it with another command, or to continue without it. -Overfull \hbox (20.0pt too wide) in paragraph at lines 729--729 +Overfull \hbox (20.0pt too wide) in paragraph at lines 731--731 [] [] @@ -80521,7 +80058,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.730 \caption +l.732 \caption {The kinetic energy partition after the collision of pyrene d... You're in trouble here. Try typing to proceed. @@ -80642,7 +80179,7 @@ Missing character: There is no . in font nullfont! ! Undefined control sequence. \boldm -l.734 \boldm +l.736 \boldm {$E_{col}$} & \boldm{$E^k_{td}$} & \boldm{$E^k_{Ar}$} & \boldm{... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -80651,7 +80188,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. -l.734 \boldm{$E_{col}$} & \boldm +l.736 \boldm{$E_{col}$} & \boldm {$E^k_{td}$} & \boldm{$E^k_{Ar}$} & \boldm{... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -80660,7 +80197,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. -l.734 ...{$E_{col}$} & \boldm{$E^k_{td}$} & \boldm +l.736 ...{$E_{col}$} & \boldm{$E^k_{td}$} & \boldm {$E^k_{Ar}$} & \boldm{$E^k... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -80669,7 +80206,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. -l.734 ...$E^k_{td}$} & \boldm{$E^k_{Ar}$} & \boldm +l.736 ...$E^k_{td}$} & \boldm{$E^k_{Ar}$} & \boldm {$E^k_{Py^1}$} & \boldm{$E... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -80678,7 +80215,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. -l.734 ...^k_{Ar}$} & \boldm{$E^k_{Py^1}$} & \boldm +l.736 ...^k_{Ar}$} & \boldm{$E^k_{Py^1}$} & \boldm {$E^k_{Py^2}$} & \boldm{$E... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -80687,7 +80224,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. -l.734 ..._{Py^1}$} & \boldm{$E^k_{Py^2}$} & \boldm +l.736 ..._{Py^1}$} & \boldm{$E^k_{Py^2}$} & \boldm {$E^k_{Re}$} \\ [0.08cm] The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -80938,12 +80475,12 @@ Missing character: There is no . in font nullfont! Missing character: There is no 4 in font nullfont! Missing character: There is no 5 in font nullfont! -Overfull \hbox (17.97237pt too wide) in paragraph at lines 730--761 +Overfull \hbox (17.97237pt too wide) in paragraph at lines 732--763 \OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (185.11674pt too wide) in paragraph at lines 730--761 +Overfull \hbox (185.11674pt too wide) in paragraph at lines 732--763 [] [] @@ -80954,14 +80491,14 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.762 \end{table} +l.764 \end{table} Your command was ignored. Type I to replace it with another command, or to continue without it. ! Undefined control sequence. -l.764 \figuremacro +l.766 \figuremacro {Epartition-Ar-300-SP}{Mean kinetic energy partition at th... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -81043,7 +80580,7 @@ Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 764--765 +Overfull \hbox (20.0pt too wide) in paragraph at lines 766--767 [] [] @@ -81170,7 +80707,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...eference `tab:table2' on page \thepage \space undefined\on@line . -l.766 ...ations is shown in Table \ref{tab:table2} +l.768 ...ations is shown in Table \ref{tab:table2} and Figure \ref{Epartitio... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -81179,7 +80716,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `tab:table2' on page undefined on input line 766. +LaTeX Warning: Reference `tab:table2' on page undefined on input line 768. Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! @@ -81193,7 +80730,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...tion-Ar-300-Tstep-01' on page \thepage \space undefined\on@line . -l.766 ...d Figure \ref{Epartition-Ar-300-Tstep-01} +l.768 ...d Figure \ref{Epartition-Ar-300-Tstep-01} , which indicate a time st... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -81203,7 +80740,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `Epartition-Ar-300-Tstep-01' on page undefined on inp -ut line 766. +ut line 768. Missing character: There is no , in font nullfont! Missing character: There is no w in font nullfont! @@ -81297,17 +80834,17 @@ Missing character: There is no n in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 766--767 +Overfull \hbox (20.0pt too wide) in paragraph at lines 768--769 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 766--767 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 768--769 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 766--767 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 768--769 [] [] @@ -81318,14 +80855,14 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.771 \begin{table} +l.773 \begin{table} Your command was ignored. Type I to replace it with another command, or to continue without it. -Overfull \hbox (20.0pt too wide) in paragraph at lines 772--772 +Overfull \hbox (20.0pt too wide) in paragraph at lines 774--774 [] [] @@ -81336,7 +80873,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.773 \caption +l.775 \caption {The kinetic energy partition and cross section at the end o... You're in trouble here. Try typing to proceed. @@ -81525,7 +81062,7 @@ Missing character: There is no . in font nullfont! ! Undefined control sequence. \boldm -l.777 \boldm +l.779 \boldm {$E_{col}$} & \boldm{$Tstep$} & \boldm{$E^k_{td}$} & \boldm{$E... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -81534,7 +81071,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. -l.777 \boldm{$E_{col}$} & \boldm +l.779 \boldm{$E_{col}$} & \boldm {$Tstep$} & \boldm{$E^k_{td}$} & \boldm{$E... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -81543,7 +81080,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. -l.777 ...dm{$E_{col}$} & \boldm{$Tstep$} & \boldm +l.779 ...dm{$E_{col}$} & \boldm{$Tstep$} & \boldm {$E^k_{td}$} & \boldm{$E^k... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -81552,7 +81089,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. -l.777 ...dm{$Tstep$} & \boldm{$E^k_{td}$} & \boldm +l.779 ...dm{$Tstep$} & \boldm{$E^k_{td}$} & \boldm {$E^k_{Ar}$} & \boldm{$E^k... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -81561,7 +81098,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. -l.777 ...$E^k_{td}$} & \boldm{$E^k_{Ar}$} & \boldm +l.779 ...$E^k_{td}$} & \boldm{$E^k_{Ar}$} & \boldm {$E^k_{Py^1}$} & \boldm{$E... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -81570,7 +81107,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. -l.777 ...^k_{Ar}$} & \boldm{$E^k_{Py^1}$} & \boldm +l.779 ...^k_{Ar}$} & \boldm{$E^k_{Py^1}$} & \boldm {$E^k_{Py^2}$} & \boldm{$E... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -81579,7 +81116,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. -l.777 ..._{Py^1}$} & \boldm{$E^k_{Py^2}$} & \boldm +l.779 ..._{Py^1}$} & \boldm{$E^k_{Py^2}$} & \boldm {$E^k_{Re}$} & \boldm{$\s... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -81588,7 +81125,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ! Undefined control sequence. -l.777 ...k_{Py^2}$} & \boldm{$E^k_{Re}$} & \boldm +l.779 ...k_{Py^2}$} & \boldm{$E^k_{Re}$} & \boldm {$\sigma_{_{MD}}$} \\ [0.0... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -81729,22 +81266,22 @@ Missing character: There is no . in font nullfont! Missing character: There is no 7 in font nullfont! Missing character: There is no 7 in font nullfont! -Overfull \hbox (25.21878pt too wide) in paragraph at lines 773--790 +Overfull \hbox (25.21878pt too wide) in paragraph at lines 775--792 \OML/cmm/m/it/10 Tstep$ [] -Overfull \hbox (19.40245pt too wide) in paragraph at lines 773--790 +Overfull \hbox (19.40245pt too wide) in paragraph at lines 775--792 \OML/cmm/m/it/10 ^^[[]$ [] -Overfull \hbox (7.50002pt too wide) in paragraph at lines 773--790 +Overfull \hbox (7.50002pt too wide) in paragraph at lines 775--792 []\/cmr/m/n/10 A [] -Overfull \hbox (253.73798pt too wide) in paragraph at lines 773--790 +Overfull \hbox (253.73798pt too wide) in paragraph at lines 775--792 [] [] @@ -81755,14 +81292,14 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.791 \end{table} +l.793 \end{table} Your command was ignored. Type I to replace it with another command, or to continue without it. ! Undefined control sequence. -l.793 \figuremacro +l.795 \figuremacro {Epartition-Ar-300-Tstep-01}{Mean kinetic energy partition... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -82043,7 +81580,7 @@ Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 793--794 +Overfull \hbox (20.0pt too wide) in paragraph at lines 795--796 [] [] @@ -82058,7 +81595,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...ference `prot-Ar-300' on page \thepage \space undefined\on@line . -l.795 In Figure~\ref{prot-Ar-300} +l.797 In Figure~\ref{prot-Ar-300} are reported the ratios of the pyrene dime... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -82067,7 +81604,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `prot-Ar-300' on page undefined on input line 795. +LaTeX Warning: Reference `prot-Ar-300' on page undefined on input line 797. Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! @@ -82656,52 +82193,52 @@ Missing character: There is no e in font nullfont! Missing character: There is no V in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 795--797 +Overfull \hbox (20.0pt too wide) in paragraph at lines 797--799 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 795--797 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 797--799 [] [] -Overfull \hbox (15.06566pt too wide) in paragraph at lines 795--797 +Overfull \hbox (15.06566pt too wide) in paragraph at lines 797--799 \OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (17.73615pt too wide) in paragraph at lines 795--797 +Overfull \hbox (17.73615pt too wide) in paragraph at lines 797--799 \OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (30.03703pt too wide) in paragraph at lines 795--797 +Overfull \hbox (30.03703pt too wide) in paragraph at lines 797--799 \OML/cmm/m/it/10 E[] \/cmr/m/n/10 + [] -Overfull \hbox (22.25923pt too wide) in paragraph at lines 795--797 +Overfull \hbox (22.25923pt too wide) in paragraph at lines 797--799 \OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (25.64865pt too wide) in paragraph at lines 795--797 +Overfull \hbox (25.64865pt too wide) in paragraph at lines 797--799 \OML/cmm/m/it/10 E[] \OMS/cmsy/m/n/10 ^^@ [] -Overfull \hbox (17.82411pt too wide) in paragraph at lines 795--797 +Overfull \hbox (17.82411pt too wide) in paragraph at lines 797--799 \OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (15.06566pt too wide) in paragraph at lines 795--797 +Overfull \hbox (15.06566pt too wide) in paragraph at lines 797--799 \OML/cmm/m/it/10 E[]$ [] ! Undefined control sequence. -l.798 \figuremacro +l.800 \figuremacro {prot-Ar-300}{Kinetic energy proportion after collision of... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -82800,12 +82337,12 @@ Missing character: There is no g in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 798--799 +Overfull \hbox (20.0pt too wide) in paragraph at lines 800--801 [] [] -Overfull \hbox (6.63892pt too wide) in paragraph at lines 798--799 +Overfull \hbox (6.63892pt too wide) in paragraph at lines 800--801 []$ [] @@ -82931,7 +82468,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...artition-Ar-300-d-ud' on page \thepage \space undefined\on@line . -l.800 ...ne in Figure \ref{Epartition-Ar-300-d-ud} +l.802 ...ne in Figure \ref{Epartition-Ar-300-d-ud} for $E^k_{td}$, $E^k_{Re}... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -82941,7 +82478,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `Epartition-Ar-300-d-ud' on page undefined on input l -ine 800. +ine 802. Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! @@ -83154,7 +82691,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...artition-Ar-300-d-ud' on page \thepage \space undefined\on@line . -l.801 ...wn in Figure \ref{Epartition-Ar-300-d-ud} +l.803 ...wn in Figure \ref{Epartition-Ar-300-d-ud} (black curves). This is e... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -83164,7 +82701,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `Epartition-Ar-300-d-ud' on page undefined on input l -ine 801. +ine 803. Missing character: There is no ( in font nullfont! Missing character: There is no b in font nullfont! @@ -83234,37 +82771,37 @@ Missing character: There is no e in font nullfont! Missing character: There is no m in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 800--803 +Overfull \hbox (20.0pt too wide) in paragraph at lines 802--805 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 800--803 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 802--805 [] [] -Overfull \hbox (15.06566pt too wide) in paragraph at lines 800--803 +Overfull \hbox (15.06566pt too wide) in paragraph at lines 802--805 \OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (17.73615pt too wide) in paragraph at lines 800--803 +Overfull \hbox (17.73615pt too wide) in paragraph at lines 802--805 \OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (30.03703pt too wide) in paragraph at lines 800--803 +Overfull \hbox (30.03703pt too wide) in paragraph at lines 802--805 \OML/cmm/m/it/10 E[] \/cmr/m/n/10 + [] -Overfull \hbox (22.25923pt too wide) in paragraph at lines 800--803 +Overfull \hbox (22.25923pt too wide) in paragraph at lines 802--805 \OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 800--803 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 802--805 [] [] @@ -83640,7 +83177,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...`transferredE-Ar-300' on page \thepage \space undefined\on@line . -l.804 ...red from Figure \ref{transferredE-Ar-300} +l.806 ...red from Figure \ref{transferredE-Ar-300} . The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -83650,7 +83187,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `transferredE-Ar-300' on page undefined on input line - 804. + 806. Missing character: There is no . in font nullfont! Missing character: There is no O in font nullfont! @@ -83973,7 +83510,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...`transferredE-Ar-300' on page \thepage \space undefined\on@line . -l.805 ...lysis of Figure \ref{transferredE-Ar-300} +l.807 ...lysis of Figure \ref{transferredE-Ar-300} , which shows the amount o... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -83983,7 +83520,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `transferredE-Ar-300' on page undefined on input line - 805. + 807. Missing character: There is no , in font nullfont! Missing character: There is no w in font nullfont! @@ -84133,57 +83670,57 @@ Missing character: There is no g in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 804--806 +Overfull \hbox (20.0pt too wide) in paragraph at lines 806--808 [] [] -Overfull \hbox (32.87709pt too wide) in paragraph at lines 804--806 +Overfull \hbox (32.87709pt too wide) in paragraph at lines 806--808 \OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 804--806 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 806--808 [] [] -Overfull \hbox (28.14903pt too wide) in paragraph at lines 804--806 +Overfull \hbox (28.14903pt too wide) in paragraph at lines 806--808 \OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (33.92593pt too wide) in paragraph at lines 804--806 +Overfull \hbox (33.92593pt too wide) in paragraph at lines 806--808 \/cmr/m/n/10 (\OML/cmm/m/it/10 E[] \/cmr/m/n/10 + [] -Overfull \hbox (37.06102pt too wide) in paragraph at lines 804--806 +Overfull \hbox (37.06102pt too wide) in paragraph at lines 806--808 \OML/cmm/m/it/10 E[]\/cmr/m/n/10 )[]$ [] -Overfull \hbox (33.92593pt too wide) in paragraph at lines 804--806 +Overfull \hbox (33.92593pt too wide) in paragraph at lines 806--808 \/cmr/m/n/10 (\OML/cmm/m/it/10 E[] \/cmr/m/n/10 + [] -Overfull \hbox (37.06102pt too wide) in paragraph at lines 804--806 +Overfull \hbox (37.06102pt too wide) in paragraph at lines 806--808 \OML/cmm/m/it/10 E[]\/cmr/m/n/10 )[]$ [] -Overfull \hbox (28.14903pt too wide) in paragraph at lines 804--806 +Overfull \hbox (28.14903pt too wide) in paragraph at lines 806--808 \OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 804--806 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 806--808 [] [] ! Undefined control sequence. -l.807 \figuremacro +l.809 \figuremacro {Epartition-Ar-300-d-ud}{Kinetic energy partition for diss... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -84341,7 +83878,7 @@ Missing character: There is no g in font nullfont! Missing character: There is no y in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 807--808 +Overfull \hbox (20.0pt too wide) in paragraph at lines 809--810 [] [] @@ -84421,7 +83958,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...nce `figuretimescale' on page \thepage \space undefined\on@line . -l.809 ...presented in Figure \ref{figuretimescale} +l.811 ...presented in Figure \ref{figuretimescale} . They correspond to the t... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -84430,7 +83967,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `figuretimescale' on page undefined on input line 809 +LaTeX Warning: Reference `figuretimescale' on page undefined on input line 811 . Missing character: There is no . in font nullfont! @@ -84847,7 +84384,7 @@ Missing character: There is no [ in font nullfont! ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.810 spectral range \cite{Dontot2020} +l.812 spectral range \cite{Dontot2020} with corresponding half-periods of 13... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -84856,7 +84393,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Dontot2020' on page undefined on input line 810. +LaTeX Warning: Citation `Dontot2020' on page undefined on input line 812. Missing character: There is no ] in font nullfont! Missing character: There is no w in font nullfont! @@ -85835,7 +85372,7 @@ Missing character: There is no s in font nullfont! ! Undefined control sequence. ...`transferredE-Ar-300' on page \thepage \space undefined\on@line . -l.813 ...alysis (Figures~\ref{transferredE-Ar-300} +l.815 ...alysis (Figures~\ref{transferredE-Ar-300} , \ref{prot-Ar-300} and \r... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -85845,13 +85382,13 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `transferredE-Ar-300' on page undefined on input line - 813. + 815. Missing character: There is no , in font nullfont! ! Undefined control sequence. ...ference `prot-Ar-300' on page \thepage \space undefined\on@line . -l.813 ...f{transferredE-Ar-300}, \ref{prot-Ar-300} +l.815 ...f{transferredE-Ar-300}, \ref{prot-Ar-300} and \ref{Epartition-Ar-30... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -85860,7 +85397,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `prot-Ar-300' on page undefined on input line 813. +LaTeX Warning: Reference `prot-Ar-300' on page undefined on input line 815. Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! @@ -85868,7 +85405,7 @@ Missing character: There is no d in font nullfont! ! Undefined control sequence. ...artition-Ar-300-d-ud' on page \thepage \space undefined\on@line . -l.813 ...-Ar-300} and \ref{Epartition-Ar-300-d-ud} +l.815 ...-Ar-300} and \ref{Epartition-Ar-300-d-ud} ). The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -85878,72 +85415,72 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `Epartition-Ar-300-d-ud' on page undefined on input l -ine 813. +ine 815. Missing character: There is no ) in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 809--814 +Overfull \hbox (20.0pt too wide) in paragraph at lines 811--816 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 809--814 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 811--816 [] [] -Overfull \hbox (7.50002pt too wide) in paragraph at lines 809--814 +Overfull \hbox (7.50002pt too wide) in paragraph at lines 811--816 []\/cmr/m/n/10 A [] -Overfull \hbox (7.50002pt too wide) in paragraph at lines 809--814 +Overfull \hbox (7.50002pt too wide) in paragraph at lines 811--816 []\/cmr/m/n/10 A [] -Overfull \hbox (7.50002pt too wide) in paragraph at lines 809--814 +Overfull \hbox (7.50002pt too wide) in paragraph at lines 811--816 []\/cmr/m/n/10 A [] -Overfull \hbox (23.84384pt too wide) in paragraph at lines 809--814 +Overfull \hbox (23.84384pt too wide) in paragraph at lines 811--816 \OML/cmm/m/it/10 cm[]$ [] -Overfull \hbox (5.43053pt too wide) in paragraph at lines 809--814 +Overfull \hbox (5.43053pt too wide) in paragraph at lines 811--816 [] [] -Overfull \hbox (23.84384pt too wide) in paragraph at lines 809--814 +Overfull \hbox (23.84384pt too wide) in paragraph at lines 811--816 \OML/cmm/m/it/10 cm[]$ [] -Overfull \hbox (23.84384pt too wide) in paragraph at lines 809--814 +Overfull \hbox (23.84384pt too wide) in paragraph at lines 811--816 \OML/cmm/m/it/10 cm[]$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 809--814 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 811--816 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 809--814 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 811--816 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 809--814 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 811--816 [] [] ! Undefined control sequence. -l.815 \figuremacro +l.817 \figuremacro {figuretimescale}{Timescales, as a function of center of m... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -86158,57 +85695,57 @@ Missing character: There is no e in font nullfont! Missing character: There is no ) in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 815--816 +Overfull \hbox (20.0pt too wide) in paragraph at lines 817--818 [] [] -Overfull \hbox (68.28447pt too wide) in paragraph at lines 817--818 +Overfull \hbox (68.28447pt too wide) in paragraph at lines 819--820 []\OT1/cmr/bx/n/10 Efficiency [] -Overfull \hbox (9.26384pt too wide) in paragraph at lines 817--818 +Overfull \hbox (9.26384pt too wide) in paragraph at lines 819--820 \OT1/cmr/bx/n/10 of [] -Overfull \hbox (15.49298pt too wide) in paragraph at lines 817--818 +Overfull \hbox (15.49298pt too wide) in paragraph at lines 819--820 \OT1/cmr/bx/n/10 en- [] -Overfull \hbox (21.8263pt too wide) in paragraph at lines 817--818 +Overfull \hbox (21.8263pt too wide) in paragraph at lines 819--820 \OT1/cmr/bx/n/10 ergy [] -Overfull \hbox (29.55676pt too wide) in paragraph at lines 817--818 +Overfull \hbox (29.55676pt too wide) in paragraph at lines 819--820 \OT1/cmr/bx/n/10 trans- [] -Overfull \hbox (13.52078pt too wide) in paragraph at lines 817--818 +Overfull \hbox (13.52078pt too wide) in paragraph at lines 819--820 \OT1/cmr/bx/n/10 fer [] -Overfull \hbox (31.94427pt too wide) in paragraph at lines 817--818 +Overfull \hbox (31.94427pt too wide) in paragraph at lines 819--820 \OT1/cmr/bx/n/10 within [] -Overfull \hbox (16.13187pt too wide) in paragraph at lines 817--818 +Overfull \hbox (16.13187pt too wide) in paragraph at lines 819--820 \OT1/cmr/bx/n/10 the [] -Overfull \hbox (29.17348pt too wide) in paragraph at lines 817--818 +Overfull \hbox (29.17348pt too wide) in paragraph at lines 819--820 \OT1/cmr/bx/n/10 dimer [] ! Undefined control sequence. -l.819 \figuremacro +l.821 \figuremacro {T-time-zoom_abcdef}{Instantaneous kinetic temperatures as... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -86230,13 +85767,13 @@ Missing character: There is no m in font nullfont! ! Missing $ inserted. $ -l.819 \figuremacro{T-time-zoom_ +l.821 \figuremacro{T-time-zoom_ abcdef}{Instantaneous kinetic temperatures as... I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. ! Extra }, or forgotten $. -l.819 \figuremacro{T-time-zoom_abcdef} +l.821 \figuremacro{T-time-zoom_abcdef} {Instantaneous kinetic temperatures as... I've deleted a group-closing symbol because it seems to be spurious, as in `$x}$'. But perhaps the } is legitimate and @@ -86247,7 +85784,7 @@ deleted material, e.g., by typing `I$}'. ! Missing } inserted. } -l.819 ...on energy of 22.5~eV. Impact parameters $ +l.821 ...on energy of 22.5~eV. Impact parameters $ b$ are (a) 2, (b) 3, (c) 0... I've inserted something that you may have forgotten. (See the above.) @@ -86257,15 +85794,15 @@ my insertion and my current dilemma will both disappear. Missing character: There is no b in font nullfont! -LaTeX Warning: Command \r invalid in math mode on input line 819. +LaTeX Warning: Command \r invalid in math mode on input line 821. -LaTeX Warning: Command \r invalid in math mode on input line 819. +LaTeX Warning: Command \r invalid in math mode on input line 821. ! Please use \mathaccent for accents in math mode. \add@accent ...@spacefactor \spacefactor }\accent #1 #2\egroup \spacefactor ... -l.819 ...) 3, (c) 0, (d) 2.5, (e) 2, and (f) 2~\AA +l.821 ...) 3, (c) 0, (d) 2.5, (e) 2, and (f) 2~\AA {}. In cases (a) and (b) d... I'm changing \accent to \mathaccent here; wish me luck. (Accents are not the same in formulas as they are in text.) @@ -86273,7 +85810,7 @@ I'm changing \accent to \mathaccent here; wish me luck. ! Missing { inserted. \edef -l.819 ...) 3, (c) 0, (d) 2.5, (e) 2, and (f) 2~\AA +l.821 ...) 3, (c) 0, (d) 2.5, (e) 2, and (f) 2~\AA {}. In cases (a) and (b) d... A left brace was mandatory here, so I've put one in. You might want to delete and/or insert some corrections @@ -86283,7 +85820,7 @@ so that I will find a matching right brace soon. ! You can't use `\spacefactor' in math mode. \add@accent ...}\accent #1 #2\egroup \spacefactor \accent@spacefactor -l.819 ...) 3, (c) 0, (d) 2.5, (e) 2, and (f) 2~\AA +l.821 ...) 3, (c) 0, (d) 2.5, (e) 2, and (f) 2~\AA {}. In cases (a) and (b) d... Sorry, but I'm not programmed to handle this case; I'll just pretend that you didn't ask for it. @@ -86293,14 +85830,14 @@ return to the right one by typing `I}' or `I$' or `I\par'. ! Missing $ inserted. $ -l.820 +l.822 I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. Missing character: There is no in font cmex10! -Overfull \hbox (1892.87636pt too wide) in paragraph at lines 819--820 +Overfull \hbox (1892.87636pt too wide) in paragraph at lines 821--822 []$[]\OML/cmm/m/it/10 bcdef[]$$are\/cmr/m/n/10 (\OML/cmm/m/it/10 a\/cmr/m/n/10 )2\OML/cmm/m/it/10 ; \/cmr/m/n/10 (\OML/cmm/m/it/10 b\/cmr/m/n/10 )3\OML/cmm/m/ it/10 ; \/cmr/m/n/10 (\OML/cmm/m/it/10 c\/cmr/m/n/10 )0\OML/cmm/m/it/10 ; \/cmr @@ -86310,7 +85847,7 @@ cmm/m/it/10 ; \/cmr/m/n/10 (\OML/cmm/m/it/10 e\/cmr/m/n/10 )2\OML/cmm/m/it/10 ; [] ! Undefined control sequence. -l.821 \figuremacrob +l.823 \figuremacrob {E-time-abcdef}{Instantaneous kinetic energies as a funct... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -86619,17 +86156,17 @@ Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 821--822 +Overfull \hbox (20.0pt too wide) in paragraph at lines 823--824 [] [] -Overfull \hbox (4.29166pt too wide) in paragraph at lines 821--822 +Overfull \hbox (4.29166pt too wide) in paragraph at lines 823--824 \OML/cmm/m/it/10 b$ [] -Overfull \hbox (7.50002pt too wide) in paragraph at lines 821--822 +Overfull \hbox (7.50002pt too wide) in paragraph at lines 823--824 []\/cmr/m/n/10 A [] @@ -86647,8 +86184,7 @@ Missing character: There is no i in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no , in font nullfont! -Missing character: There is no w in font nullfont! -Missing character: There is no e in font nullfont! +Missing character: There is no I in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no d in font nullfont! Missing character: There is no d in font nullfont! @@ -86721,8 +86257,7 @@ Missing character: There is no l in font nullfont! Missing character: There is no a in font nullfont! Missing character: There is no r in font nullfont! Missing character: There is no , in font nullfont! -Missing character: There is no w in font nullfont! -Missing character: There is no e in font nullfont! +Missing character: There is no I in font nullfont! Missing character: There is no l in font nullfont! Missing character: There is no o in font nullfont! Missing character: There is no o in font nullfont! @@ -87467,7 +87002,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.824 \begin{align} +l.826 \begin{align} Your command was ignored. Type I to replace it with another command, @@ -87477,7 +87012,7 @@ Missing character: There is no T in font nullfont! ! Missing $ inserted. $ -l.826 T^ +l.828 T^ k=2 \frac{}{nk_b} I've inserted a begin-math/end-math symbol since I think you left one out. Proceed, with fingers crossed. @@ -87489,7 +87024,7 @@ See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... -l.827 \end{align} +l.829 \end{align} Your command was ignored. Type I to replace it with another command, @@ -87498,7 +87033,7 @@ or to continue without it. ! Missing $ inserted. $ -l.827 \end{align} +l.829 \end{align} I've inserted something that you may have forgotten. (See the above.) @@ -87630,7 +87165,7 @@ Missing character: There is no . in font nullfont! ! Undefined control sequence. ...g: Reference `Eparti' on page \thepage \space undefined\on@line . -l.829 ...termolecular modes (see eqs.~\ref{Eparti} +l.831 ...termolecular modes (see eqs.~\ref{Eparti} ). $T^k$ is plotted in Fig... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -87639,7 +87174,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `Eparti' on page undefined on input line 829. +LaTeX Warning: Reference `Eparti' on page undefined on input line 831. Missing character: There is no ) in font nullfont! Missing character: There is no . in font nullfont! @@ -87663,7 +87198,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ... `T-time-zoom_abcdef' on page \thepage \space undefined\on@line . -l.829 ...lotted in Figure \ref{T-time-zoom_abcdef} +l.831 ...lotted in Figure \ref{T-time-zoom_abcdef} for some selected traject... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -87673,7 +87208,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `T-time-zoom_abcdef' on page undefined on input line -829. +831. Missing character: There is no f in font nullfont! Missing character: There is no o in font nullfont! @@ -87832,7 +87367,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ...rence `E-time-abcdef' on page \thepage \space undefined\on@line . -l.830 ...e presented in Figure \ref{E-time-abcdef} +l.832 ...e presented in Figure \ref{E-time-abcdef} . In Figures \ref{T-time-z... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -87841,7 +87376,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `E-time-abcdef' on page undefined on input line 830. +LaTeX Warning: Reference `E-time-abcdef' on page undefined on input line 832. Missing character: There is no . in font nullfont! Missing character: There is no I in font nullfont! @@ -87856,7 +87391,7 @@ Missing character: There is no s in font nullfont! ! Undefined control sequence. ... `T-time-zoom_abcdef' on page \thepage \space undefined\on@line . -l.830 ...def}. In Figures \ref{T-time-zoom_abcdef} +l.832 ...def}. In Figures \ref{T-time-zoom_abcdef} and \ref{E-time-abcdef}, ... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -87866,7 +87401,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `T-time-zoom_abcdef' on page undefined on input line -830. +832. Missing character: There is no a in font nullfont! Missing character: There is no n in font nullfont! @@ -87874,7 +87409,7 @@ Missing character: There is no d in font nullfont! ! Undefined control sequence. ...rence `E-time-abcdef' on page \thepage \space undefined\on@line . -l.830 ...time-zoom_abcdef} and \ref{E-time-abcdef} +l.832 ...time-zoom_abcdef} and \ref{E-time-abcdef} , simulations (a) and (b) ... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -87883,7 +87418,7 @@ spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Reference `E-time-abcdef' on page undefined on input line 830. +LaTeX Warning: Reference `E-time-abcdef' on page undefined on input line 832. Missing character: There is no , in font nullfont! Missing character: There is no s in font nullfont! @@ -88766,7 +88301,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ... `T-time-zoom_abcdef' on page \thepage \space undefined\on@line . -l.830 ... shown in Figure \ref{T-time-zoom_abcdef} +l.832 ... shown in Figure \ref{T-time-zoom_abcdef} . On the other side, the e... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -88776,7 +88311,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `T-time-zoom_abcdef' on page undefined on input line -830. +832. Missing character: There is no . in font nullfont! Missing character: There is no O in font nullfont! @@ -89040,7 +88575,7 @@ Missing character: There is no e in font nullfont! ! Undefined control sequence. ... `T-time-zoom_abcdef' on page \thepage \space undefined\on@line . -l.830 ...played in Figure \ref{T-time-zoom_abcdef} +l.832 ...played in Figure \ref{T-time-zoom_abcdef} . The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -89050,7 +88585,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Reference `T-time-zoom_abcdef' on page undefined on input line -830. +832. Missing character: There is no . in font nullfont! Missing character: There is no A in font nullfont! @@ -89511,92 +89046,92 @@ Missing character: There is no o in font nullfont! Missing character: There is no n in font nullfont! Missing character: There is no . in font nullfont! -Overfull \hbox (20.0pt too wide) in paragraph at lines 823--832 +Overfull \hbox (20.0pt too wide) in paragraph at lines 825--834 [] [] -Overfull \hbox (15.47568pt too wide) in paragraph at lines 823--832 +Overfull \hbox (15.47568pt too wide) in paragraph at lines 825--834 [] \/cmr/m/n/10 = [] -Overfull \hbox (30.52718pt too wide) in paragraph at lines 823--832 +Overfull \hbox (30.52718pt too wide) in paragraph at lines 825--834 \/cmr/m/n/10 2[]$ [] -Overfull \hbox (9.2227pt too wide) in paragraph at lines 823--832 +Overfull \hbox (9.2227pt too wide) in paragraph at lines 825--834 \OML/cmm/m/it/10 k[]$ [] -Overfull \hbox (6.00235pt too wide) in paragraph at lines 823--832 +Overfull \hbox (6.00235pt too wide) in paragraph at lines 825--834 \OML/cmm/m/it/10 n$ [] -Overfull \hbox (12.87848pt too wide) in paragraph at lines 823--832 +Overfull \hbox (12.87848pt too wide) in paragraph at lines 825--834 \OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 823--832 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 825--834 [] [] -Overfull \hbox (12.15282pt too wide) in paragraph at lines 823--832 +Overfull \hbox (12.15282pt too wide) in paragraph at lines 825--834 \OML/cmm/m/it/10 T[]$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 823--832 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 825--834 [] [] -Overfull \hbox (30.84413pt too wide) in paragraph at lines 823--832 +Overfull \hbox (30.84413pt too wide) in paragraph at lines 825--834 \OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (30.84413pt too wide) in paragraph at lines 823--832 +Overfull \hbox (30.84413pt too wide) in paragraph at lines 825--834 \OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (26.39777pt too wide) in paragraph at lines 823--832 +Overfull \hbox (26.39777pt too wide) in paragraph at lines 825--834 \OML/cmm/m/it/10 E[]$ [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 823--832 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 825--834 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 823--832 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 825--834 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 823--832 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 825--834 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 823--832 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 825--834 [] [] -Overfull \hbox (10.86105pt too wide) in paragraph at lines 823--832 +Overfull \hbox (10.86105pt too wide) in paragraph at lines 825--834 [] [] ! 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Otherwise just continue, and I'll forget about whatever was undefined. -LaTeX Warning: Citation `Chen2014' on page undefined on input line 845. +LaTeX Warning: Citation `Chen2014' on page undefined on input line 847. Missing character: There is no , in font nullfont! \citation{Gatchell2016knockout} ! Undefined control sequence. ...: Citation `\@citeb ' on page \thepage \space undefined\on@line . -l.845 ...ons \cite{Chen2014, Gatchell2016knockout} +l.847 ...ons \cite{Chen2014, Gatchell2016knockout} . These authors showed tha... The control sequence at the end of the top line of your error message was never \def'ed. If you have @@ -92300,7 +91835,7 @@ and I'll forget about whatever was undefined. LaTeX Warning: Citation `Gatchell2016knockout' on page undefined on input line - 845. + 847. Missing character: There is no ] in font nullfont! Missing character: There is no . in font nullfont! @@ -92767,17 +92302,17 @@ Missing character: There is no e in font nullfont! 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If you have @@ -93103,12 +92638,12 @@ Missing character: There is no e in font nullfont! Missing character: There is no s in font nullfont! Missing character: There is no / in font nullfont! ! Extra \fi. -l.857 \fi +l.859 \fi I'm ignoring this; it doesn't match any \if. -Overfull \hbox (20.0pt too wide) in paragraph at lines 854--858 +Overfull \hbox (20.0pt too wide) in paragraph at lines 856--860 [] [] @@ -93120,11 +92655,11 @@ Overfull \hbox (20.0pt too wide) in paragraph at lines 854--858 Here is how much of TeX's memory you used: - 99 strings out of 492649 - 1390 string characters out of 6129622 - 154212 words of memory out of 5000000 - 4076 multiletter control sequences out of 15000+600000 + 98 strings out of 492616 + 1373 string characters out of 6129481 + 156143 words of memory out of 5000000 + 4112 multiletter control sequences out of 15000+600000 4653 words of font info for 17 fonts, out of 8000000 for 9000 1141 hyphenation exceptions out of 8191 - 19i,9n,26p,2014b,196s stack positions out of 5000i,500n,10000p,200000b,80000s + 18i,9n,26p,2014b,196s stack positions out of 5000i,500n,10000p,200000b,80000s ! ==> Fatal error occurred, no output PDF file produced! diff --git a/thesis/4/collision.tex b/thesis/4/collision.tex index 4abca4b..82a7131 100644 --- a/thesis/4/collision.tex +++ b/thesis/4/collision.tex @@ -30,12 +30,12 @@ The stability of cluster can be investigated from dissociation experiments. Clus For instance, the sodium cluster ions and lithium cluster cation were dissociated with a pulsed UV laser source.\cite{Brechignac1989, Brechignac1994} Gaseous hydrated trivalent metal ions were dissociated using blackbody infrared radiative dissociation (BIRD).\cite{Wong2004, Bush2008} The collision between cluster and high or low energetic particles at different pressure also have been investigated. -Collisions between the high energetic projectile ions (such as 3 keV Ar$^+$, 22.5 keV He$^{2+}$) and neutral targets were investigated by Gatchell and Holm.\cite{Holm2010, Gatchell2014, Gatchell2017} +Collisions between the high energetic projectile ions (such as 3 keV Ar$^+$, 22.5 keV He$^{2+}$) and neutral targets were investigated by Gatchell and A. Holm.\cite{Holm2010, M. Gatchell2014, Gatchell2017} Collisions between clusters and projectile have been also explored at low collision energy, which allows for the derivation of dissociation energies and the thermal evaporation and stability of clusters. \cite{Boering1992, Wells2005, Zamith2019thermal} By colliding a molecule, or a molecular aggregate, with a non-reactive rare gas atom (neon, argon) or a small molecule such as H$_2$O or N$_2$, it is possible to monitor the parent ions and collision products by use, for instance, of tandem mass spectrometry (MS/MS).\cite{Ma1997, Chowdhury2009} The resulting mass spectra provide a wealth of information about the structure of the parent and product ions from which one can infer, for instance, dissociation mechanisms \cite{Nelson1994, Molina2015} or bond and hydration enthalpies \cite{Carl2007}. -The overall process of collisional activation followed by dissociation/fragmentation is commonly referred to as the collision‐induced dissociation (CID) that is also named collisionally activated dissociation (CAD). CID is a mass spectrometry technique to induce dissociation/fragmentation of selected ions in the gas phase, which is one of standard methods for the determination of dissociation/fragmentation pathways. \cite{Sleno2004ion, Wells2005} +The overall process of collisional activation followed by dissociation/fragmentation is commonly referred to as the collision-induced dissociation (CID) that is also named collisionally activated dissociation (CAD). CID is a mass spectrometry technique to induce dissociation/fragmentation of selected ions in the gas phase, which is one of standard methods for the determination of dissociation/fragmentation pathways. \cite{Sleno2004ion, Wells2005} The CID technique consists of accelerating a given ion into a collision gas thereby the ion getting energy and inducing fragmentation. The produced ionic fragments are then mass analyzed, yielding essentially a mass spectrum.\cite{Cody1982} The CID technique has been applied in different context. Higher-energy C-trap dissociation is a CID technique specific to the orbitrap mass spectrometer in which dissociation/fragmentation occurs outside the trap \cite{Olsen2007higher, Hart2011} @@ -48,7 +48,7 @@ CID has been applied to a variety of systems, in particular hydrated atomic ions Theoretical and experimental studies devoted to fragmentation of hydrated molecular aggregates are scarce, \cite{Li1992, Bobbert2002, Liu2006, Bakker2008, Markush2016, Castrovilli2017} although CID has been applied to water clusters containing an atomic ion \cite{Carl2013, Hofstetter2013, Coates2018} and on charged water clusters \cite{Dawson1982, Bakker2008, Mcquinn2009, Zamith2012}. This is a real lack as understanding hydration of molecules and biomolecules is of paramount importance to get insights into their structure, stability, dynamics and reactivity in aqueous medium. In that respect, CID investigations could play an important role in understanding those properties in a -environment free from long-range solvent effects but also for different hydration degrees or protonation states. This can be evidenced by the experimental study of Liu \textit{et al.} on the fragmentation of the singly-charged adenosine 5'-monophosphate (AMP$^-$) +environment free from long-range solvent effects but also for different hydration degrees or protonation states. This can be evidenced by the experimental study of B. Liu \textit{et al.} on the fragmentation of the singly-charged adenosine 5'-monophosphate (AMP$^-$) which shows two different fragmentation channel depending on the solvation state of AMP$^-$.\cite{Liu2006} However, to the best of our knowledge, no modelling was performed to complement these experiments except for a few static calculations.\cite{Carl2013, Hofstetter2013, Coates2018}. %colliding with a high or low energetic particles at high or low pressure,\cite{Kambara1977, Kruckeberg1999, Spasov2000, Holm2010, Gatchell2014, Gatchell2017, Zamith2019thermal} and so on has been explored in experiment. %magnetic field and electric field are usually used in the experiment setup for the dissociation of clusters. @@ -57,7 +57,7 @@ which shows two different fragmentation channel depending on the solvation state %I can not find literature which describe only electric field or magnetic field can lead to dissociation of clusters. You know some ?} -Threshold collision-induced dissociation (TCID) method has also been used, for instance to study the fragmentation patterns and to measure the dissociation energies of clusters.\cite{Spasov2000, Armentrout2008} Zamith \textit{et al.} did a CID study of the mass-selected protonated uracil water clusters with water molecules and noble gases, respectively.\cite{Braud2019} +Threshold collision-induced dissociation (TCID) method has also been used, for instance to study the fragmentation patterns and to measure the dissociation energies of clusters.\cite{Spasov2000, Armentrout2008} S. Zamith \textit{et al.} did a CID study of the mass-selected protonated uracil water clusters with water molecules and noble gases, respectively.\cite{Braud2019} In addition, they also reported the TCID study of pyrene cluster cations. \cite{Zamith2020threshold} For these two projects, the single collision event is the predominant process. In this chapter, MD simulations based on a quantum chemical formalism are able to model such complex dissociation mechanism to provide an atomic-scale description for these collisions to explain and complete these experiments. @@ -84,7 +84,7 @@ In this method, ion guides are not used. Therefore, it needs to simulate the ful %\subsection{Experimental setup} \subsection{Experimental Setup} \label{EXPsetup} -The experimental setup of Laboratoire Collisions Agr{\'e}gats R{\'e}activi{\'e} (LCAR) by Zamith {\textit et al.} for the collision of protonated uracil water clusters or pyrene dimer cation with noble gas atoms is set up as follows: +The experimental setup of Laboratoire Collisions Agr{\'e}gats R{\'e}activi{\'e} (LCAR) by S. Zamith {\textit et al.} for the collision of protonated uracil water clusters or pyrene dimer cation with noble gas atoms is set up as follows: \figuremacrob{experiment-setup}{Schematic view of the experimental setup. (a) Cluster gas aggregation source. (b) Thermalization chamber. (c) First Wiley–McLaren acceleration stage. (d) Massfilter. (e) Energy focusing. (f) Deceleration. (g) Collision cell. (h) Second Wiley–McLaren acceleration stage. (i) Reflectron. (j) Micro-channel plate detector.} %%%%%%%%%% @@ -120,7 +120,7 @@ The preparation for the collisional trajectories for the collision of protonated The argon atom is initially positioned at x=10, y=$b$ and z=0~\AA{}, with $b$ being the impact parameter. At each center of mass collision energy $E_{col}$, a series of 300 collision trajectories were conducted (the center of mass of the aggregate was kept at position (0, 0, 0)) for each of the 13 $b$ values which are evenly distributed (interval being 0.5 \AA) between 0 and R+0.5 \AA. R refers to the radius of Py$_2^+$. 600 collision trajectories were performed per isomer of protonated uracil water clusters. Trajectory calculations have been performed with a time step of 0.5~fs and a total duration of 15 ~ps and 3~ps for the collision of argon with protonated uracil water clusters and Py$_2^+$, respectively. -For the collision of Py$_2^+$ with argon, we have checked that for high collision energies such as 20 and 25 eV, a time step of 0.1 fs does not change significantly our numerical results, which will be shown in section \ref{sec:MDanalysis}. +For the collision of Py$_2^+$ with argon, I have checked that for high collision energies such as 20 and 25 eV, a time step of 0.1 fs does not change significantly our numerical results, which will be shown in section \ref{sec:MDanalysis}. It should be noted that the quaternion was used for rotation process in the generation of initial inputs. %In some cases it may be advisable to use the rigid-body approximation. @@ -154,14 +154,14 @@ Mean values are computed using the same approach, followed by a division by $\pi \subsection{Introduction} -Motivated by the recent CID experiments conducted by Braud \textit{et al.} consisting in (H$_2$O)$_{1-15}$UH$^+$ clusters colliding with an impacting atom or molecule M (M = H$_2$O, D$_2$O, neon, and argon) at a constant center of mass collision energy of 7.2~eV,\cite{Braud2019} the dynamical simulations of the collision between the protonated uracil water clusters (H$_2$O)$_{1-7, 11, 12}$UH$^+$ and an argon atom were performed. +Motivated by the recent CID experiments conducted by I. Braud \textit{et al.} consisting in (H$_2$O)$_{1-15}$UH$^+$ clusters colliding with an impacting atom or molecule M (M = H$_2$O, D$_2$O, neon, and argon) at a constant center of mass collision energy of 7.2~eV,\cite{Braud2019} the dynamical simulations of the collision between the protonated uracil water clusters (H$_2$O)$_{1-7, 11, 12}$UH$^+$ and an argon atom were performed. %First, it appears important to understand the interaction of DNA or RNA basis with water seeing %their relevance in living organisms. They can also be subject to radiation damages which is still a medical challenge and thus %needs to be further investigated. In that context, a number of studies have been conducted on molecules deriving from uracil %or on uracil with only a few water molecules. \cite{Rasmussen2010,Imhoff2007,Abdoul2000,Champeaux2010,Delaunay2014, %Bacchus2009,Kossoski2015} \cite{Maclot2011, Domaracka2012, Markush2016, Castrovilli2017}. Second, a very recent The low collision energy (7.2~eV) only leads to intermolecular bond breaking, without any electronic excitation, rather than intramolecular bond breaking. The branching ratios for different charged fragments were determined in experiment, which allows to deduce the fragmentation cross section for all -(H$_2$O)$_{1-15}$UH$^+$ species and the location of the excess proton after collision: on a uracil containing cluster or on a pure water cluster. This allows to determine the proportion of neutral uracil loss (corresponding to cases where the excess proton is located on pure water clusters) as a function of the number $n$ of water molecules. A sharp increase of neutral uracil loss was observed for $n$ = 5-6 (2.8\% and 25.0\% for n = 4 and 7, respectively). +(H$_2$O)$_{1-15}$UH$^+$ species and the location of the excess proton after collision: on a uracil containing cluster or on a pure water cluster. This allows to determine the proportion of neutral uracil loss (corresponding to cases where the excess proton is located on pure water clusters) as a function of the number $n$ of water molecules. A sharp increase of neutral uracil loss was observed for $n$ = 5-6 (2.8\% and 25.0\% for $n$ = 4 and 7, respectively). % Those experiment were complemented by theoretical calculations that aim at characterizing the lowest-energy isomers of (H$_2$O)$_{n}$UH$^+$ ($n$ = 1-7, 11, 12) clusters (see section \ref{structureUH}), which %They show that (i) For $n$ = 1-2, the uracil is protonated; (ii) For $n$ = 3-4, the excess proton is still on the uracil but has a tendency to be displaced towards adjacent water molecules; (iii) When $n$ is larger than 4, the excess proton is transferred to the water molecules. @@ -302,7 +302,7 @@ From Figure~\ref{proporEachFrag-7a12a-zoom}, it is clear that for both aggregate (H$_2$O)$_{10}$UH$^+$ and (H$_2$O)$_{11}$UH$^+$, and the increase of proportion of (H$_2$O)$_{6}$UH$^+$, (H$_2$O)$_{7}$UH$^+$ and (H$_2$O)$_{8}$UH$^+$ indicate sequential dissociation after collision is occurring. It is worth noting that, in contrast to 7a, the proportions of the main fragments of 12a do not tend to be a constant at the end of the simulations. This implies that, for this large aggregate, structural rearrangements are more likely to occur prior to complete dissociation. Proportions of the main fragments of clusters 7d and 12c shown in Figure \ref{proporEachFrag-7d12c-zoom} display similar behavior as for 7a and 12a. -As a first conclusion, Figure~\ref{proporEachFrag-7a12a-zoom} suggests that clusters with 7 water molecules experience a direct dissociation mechanism as was hypothesised by Braud \textit{et al.}.\cite{Braud2019} A similar conclusion can be drawn for smaller cluster sizes as supported by Figures \ref{proporEachFrag-1a2a}-\ref{proporEachFrag-5a6a-zoom}. In contrast, cluster with 11 (see Figure \ref{proporEachFrag-11a-zoom}) and 12 water molecules shows a behavior compatible with a certain amount of statistical dissociation, namely a long-time evolution that allows structural rearrangements. These important observations can now be refined by looking at more detailed properties. +As a first conclusion, Figure~\ref{proporEachFrag-7a12a-zoom} suggests that clusters with 7 water molecules experience a direct dissociation mechanism as was hypothesised by I. Braud \textit{et al.}.\cite{Braud2019} A similar conclusion can be drawn for smaller cluster sizes as supported by Figures \ref{proporEachFrag-1a2a}-\ref{proporEachFrag-5a6a-zoom}. In contrast, cluster with 11 (see Figure \ref{proporEachFrag-11a-zoom}) and 12 water molecules shows a behavior compatible with a certain amount of statistical dissociation, namely a long-time evolution that allows structural rearrangements. These important observations can now be refined by looking at more detailed properties. \figuremacrob{proporEachFrag-1a2a}{Time-dependent proportions of the main fragments obtained from the dissociation of the lowest-energy isomers of (H$_2$O)$_1$UH$^+$ (left) and (H$_2$O)$_{2}$UH$^+$ (right).} \\ @@ -321,7 +321,7 @@ As a first conclusion, Figure~\ref{proporEachFrag-7a12a-zoom} suggests that clus In order to get more insights in the fragmentation, molecular dynamics trajectories were analysed in terms of proportion of neutral uracil loss ($P_{NUL}$) defined in section \ref{convergence} and total fragmentation cross sections ($\sigma_{frag}$) defined in section~\ref{trajecanylysis}. These two properties are also accessible from experiments. Another property extracted from the MD simulations, but not accessible from experiment, -is the proportion of protonated uracil ($P_{PU}$) which is equal to the ratio of the number of simulations leading to a protonated uracil molecule over the number of simulations leading to a fragment containing the uracil and the excess proton. In order to correlate the outcome of the collision and the structure of the aggregate undergoing the collision, all considered low-energy isomers are characterized by there relative energies ($E_{rel.}$) and the location of the excess proton (LEP). For the latter, three distinct configurations were considered: The excess proton is bounded to the uracil molecule (noted U-H); The excess proton is bounded to a water molecule that is adjacent to an oxygen atom of the uracil molecule (noted W-H-U); The excess proton is bounded to a water molecule that is separated by at least one other water molecule from the uracil molecule (noted W-H). All these data are gathered in Table~\ref{tab:full} and we first discuss the behavior of the small species (H$_2$O)$_{1-7}$UH$^+$. +is the proportion of protonated uracil ($P_{PU}$) which is equal to the ratio of the number of simulations leading to a protonated uracil molecule over the number of simulations leading to a fragment containing the uracil and the excess proton. In order to correlate the outcome of the collision and the structure of the aggregate undergoing the collision, all considered low-energy isomers are characterized by there relative energies ($E_{rel.}$) and the location of the excess proton (LEP). For the latter, three distinct configurations were considered: The excess proton is bounded to the uracil molecule (noted U-H); The excess proton is bounded to a water molecule that is adjacent to an oxygen atom of the uracil molecule (noted W-H-U); The excess proton is bounded to a water molecule that is separated by at least one other water molecule from the uracil molecule (noted W-H). All these data are gathered in Table~\ref{tab:full} and will first discuss the behavior of the small species (H$_2$O)$_{1-7}$UH$^+$. \begin{table*} \begin{center} @@ -375,7 +375,7 @@ $\sigma_{{frag}_{exp}}$ are the experimental values for $P_{NUL}$ and $\sigma_{f \end{table*} Various information can be inferred from these properties. Firstly, one observes a general increase of $\sigma_{frag}$ as a function of cluster size with values ranging from 25.9~\AA$^2$~for isomer 1b to 60.2~\AA$^2$~for isomer 12a. Interestingly, only slight variations of $\sigma_{frag}$ are observed for different isomers of the same aggregate. In contrast, $P_{NUL}$ is much more sensitive to the nature of the considered isomers, in particular when these isomers display different LEP values. For instance, $P_{NUL}$ is 46.6 ~\% for 5a (W-H) while it is only 0.1~\% for 5d (U-H). More interestingly, there seems to exist a strong correlation between $P_{NUL}$ and LEP. -Indeed, $P_{NUL}$ values below 1.0~\% are characterized by an excess proton initially bounded to uracil (U-H type). This suggests that when uracil is protonated, probability for deprotonation after collision is very low and thus $P_{NUL}$ is close to 0\%. $P_{NUL}$ values between 9.7 and 29.4~\% are obtained from W-H-U configurations while larger $P_{NUL}$ values, above 31.1~\%, arise from W-H configurations in clusters (H$_2$O)$_{5-7}$UH$^+$. This demonstrates that, from the excess proton point of view, the outcome of the collision is highly sensitive to the nature of the isomer undergoing the collision as hypothesised by Braud \textit{ al.} \cite{Braud2019} This important finding can be of help to determine which isomer, or set of isomers, is likely to undergo collision by comparing experimental and theoretical $P_{NUL}$ as this is not necessarily the lowest-energy isomer as discussed below. +Indeed, $P_{NUL}$ values below 1.0~\% are characterized by an excess proton initially bounded to uracil (U-H type). This suggests that when uracil is protonated, probability for deprotonation after collision is very low and thus $P_{NUL}$ is close to 0\%. $P_{NUL}$ values between 9.7 and 29.4~\% are obtained from W-H-U configurations while larger $P_{NUL}$ values, above 31.1~\%, arise from W-H configurations in clusters (H$_2$O)$_{5-7}$UH$^+$. This demonstrates that, from the excess proton point of view, the outcome of the collision is highly sensitive to the nature of the isomer undergoing the collision as hypothesised by I. Braud \textit{ et al.} \cite{Braud2019} This important finding can be of help to determine which isomer, or set of isomers, is likely to undergo collision by comparing experimental and theoretical $P_{NUL}$ as this is not necessarily the lowest-energy isomer as discussed below. For (H$_2$O)$_{1-2}$UH$^+$, the theoretical and experimental $P_{NUL}$ values, close to zero, are in good agreement regardless of the considered isomer. For (H$_2$O)$_3$UH$^+$, the experimental $P_{NUL}$ is 1.7~\% which is well reproduced by both isomers 3a and 3b although 3b is the one closer to the experimental value, 0.0~\% against 5.7~\% for 3a. This was expected as they are very close in energy, only 0.3 kcal.mol$^{-1}$ difference, and in structure, as displayed in Figure~\ref{fig-1a-3b}, both being of U-H type structure. Consequently, in the experiment, each one of them could be at the origin of the experimental signal. (H$_2$O)$_4$UH$^+$ behaves differently. The two low-energy isomers, 4a and 4b, display very different $P_{NUL}$ values, 29.4 and 2.6~\%, respectively. The experimental value is 2.8~\% which suggests that 4b, although slightly higher in energy by 0.9 kcal.mol$^{-1}$, is the isomer prevailing during the collision process. The difference in behavior can be explained by the U-H configuration of 4b, in which the excess proton is bounded to the uracil, whereas in 4a, it is bounded to a water molecule adjacent to uracil (see Figure~\ref{fig-4a-5d}). The case of (H$_2$O)$_5$UH$^+$ is more complex as this is the first species displaying the three types of LEP configuration among its four lowest-energy isomers as can be seen on Figure~\ref{fig-4a-5d}. This implies very different $P_{NUL}$ values: 46.6~\% for 5a, 28.5 and 27.1~\% for 5b and 5c, respectively, while it is only 0.1~\% for 5d. The experimental $P_{NUL}$ value for (H$_2$O)$_5$UH$^+$ is still relatively low, 7.5~\%, which suggests that a U-H type structure prevails during the collision process. Although 5d is 2.4~kcal.mol$^{-1}$ @@ -406,8 +406,8 @@ small aggregates such as (H$_2$O)$_{5-7}$UH$^+$ ((H$_2$O)$_{1-4}$UH$^+$ do not d \figuremacro{fig-7a-7d}{Selected low-energy configurations of (H$_2$O)$_{7}$UH$^+$. Relative energies at the MP2/Def2TZVP level are in kcal.mol$^{-1}$.} The clusters discussed above are characterized by complex potential energy surfaces characterized by several low-energy isomers, with relative energies that can be lower than 1~kcal.mol$^{-1}$, and which get more complex as the number of water molecules -increases. Consequently, the exact energetic ordering between the low-energy isomers can not be precisely known as this is below chemical accuracy and we thus can not claim here to have found the lowest-energy structure of each aggregate, or the isomer undergoing the collision. Nevertheless, what we show is that $P_{NUL}$ is mainly determined by the initial position -of the proton in the isomer undergoing the collision. Consequently, for the collision energy and the range of cluster size we have considered, the structure of the aggregate undergoing the collision plays a key role in determining the dissociation process and collision +increases. Consequently, the exact energetic ordering between the low-energy isomers can not be precisely known as this is below chemical accuracy and thus can not claim here to have found the lowest-energy structure of each aggregate, or the isomer undergoing the collision. Nevertheless, what I show is that $P_{NUL}$ is mainly determined by the initial position +of the proton in the isomer undergoing the collision. Consequently, for the collision energy and the range of cluster size I have considered, the structure of the aggregate undergoing the collision plays a key role in determining the dissociation process and collision outcomes much more than energetics. This is consistent with the analysis of the time-dependent proportion of fragments which suggests a direct dissociation mechanism. This is further highlighted on Figure~\ref{neutralUloss-Ne-Ar}, which presents the experimental $P_{NUL}$ for collision with Ar and Ne, respectively as a function of $n$ and the corresponding theoretical values obtained from the lowest-energy isomers as well as from the isomers for which $P_{NUL}$ matches best to the experimental data. As can be seen, a very good agreement can be obtained with the experimental data by considering a specific set of isomers. Interestingly, if a similar plot is drawn for $\sigma_{frag}$ considering the same isomers (see Figure~\ref{cross-section-Ne-Ar}), a good agreement with the experimental data and much better than $\sigma_{geo}$ (calculated from formula \ref{cross-section-geo})is also obtained with the two sets of isomers which confirms the weaker dependence upon isomer of $\sigma_{frag}$. @@ -420,7 +420,7 @@ Theory 1 (green line) is obtained from the isomers which $P_{NUL}$ matches best \subsection{Behaviour at Larger Sizes, the Cases of (H$_2$O)$_{11, 12}$UH$^+$} \label{large} -In the experiments conducted by Braud \textit{et al.},\cite{Braud2019} $P_{NUL}$ starts to decrease at $n$=8. This decrease is not consistent with the above argument of a direct dissociation mechanism and larger species more likely characterized by W-H and W-H-U type structures. This apparent discrepancy motivated us to extend the present study to a larger cluster, namely (H$_2$O)$_{11, 12}$UH$^+$. For (H$_2$O)$_{12}$UH$^+$, the only available experimental data is for collisions with Ne instead of Ar, although for the same center of +In the experiments conducted by I. Braud \textit{et al.},\cite{Braud2019} $P_{NUL}$ starts to decrease at $n$=8. This decrease is not consistent with the above argument of a direct dissociation mechanism and larger species more likely characterized by W-H and W-H-U type structures. This apparent discrepancy motivated us to extend the present study to a larger cluster, namely (H$_2$O)$_{11, 12}$UH$^+$. For (H$_2$O)$_{12}$UH$^+$, the only available experimental data is for collisions with Ne instead of Ar, although for the same center of mass collision energy. As shown in Figure~\ref{neutralUloss-Ne-Ar}, experimental $P_{NUL}$ values for Ne or Ar, although not equal, display similar trend. In the following, I thus discuss the experimental data of (H$_2$O)$_{12}$UH$^+$ colliding with Ne. For cluster (H$_2$O)$_{1-7, 11}$UH$^+$, keep discussing the experimental data from colliding with Ar. @@ -436,7 +436,7 @@ assuming that the dissociation mechanism in (H$_2$O)$_{12}$UH$^+$ involves some of structural rearrangement that softens the impact of the isomer undergoing the collision. Indeed, as (H$_2$O)$_{12}$UH$^+$ has more degrees of freedom, it can more easily accommodate the kinetic energy transferred by the colliding atom prior to dissociation which thus takes place on a longer time scale. This excess of internal energy thus fosters structural rearrangements, in particular proton transfers toward the uracil, explaining the smaller $P_{NUL}$ value for (H$_2$O)$_{12}$UH$^+$. This is in full agreement with the conclusions obtained in section~\ref{time} -from Figures~\ref{proporEachFrag-11a-zoom},\ref{proporEachFrag-7a12a-zoom} and \ref{proporEachFrag-7d12c-zoom}. To further support this conclusion, we conducted 200 MD simulations in the micro-canonical ensemble in which the whole kinetic energy of Ar was randomly distributed in all the vibrational modes of isomer 12c by drawing initial velocities in a 1185~K Boltzmann +from Figures~\ref{proporEachFrag-11a-zoom},\ref{proporEachFrag-7a12a-zoom} and \ref{proporEachFrag-7d12c-zoom}. To further support this conclusion, I conducted 200 MD simulations in the micro-canonical ensemble in which the whole kinetic energy of Ar was randomly distributed in all the vibrational modes of isomer 12c by drawing initial velocities in a 1185~K Boltzmann distribution. Among them, 166 simulations display dissociation with one or two water molecules dissociating from the main cluster. No neutral uracil loss is observed. To conclude, although the present simulations are too short to assert that (H$_2$O)$_{12}$UH$^+$ undergoes a statistical dissociation mechanism, they clearly show that a direct mechanism is not sufficient to account for the theoretical and experimental results. Consequently, structural rearrangements are very likely to occur prior to dissociation and the experimental results for $P_{NUL}$ and $\sigma_{frag}$ values can not result from a single (H$_2$O)$_{12}$UH$^+$ isomer. @@ -530,7 +530,7 @@ level can provide a wealth of information about collision-induced mechanism in m PAH clusters have been investigated in several scientific fields. In combustion science, the role of PAH clusters in combustion processes is still under debate, in particular they might or not be the intermediate systems in the growth of soot particles. \cite{Chung2011, Saggese2015, Eaves2015, Mao2017, Wang2018} -In atmospheric and environmental science, PAHs are known as the pollutants, which is harmful to human health. For instance, the carcinogenic PAHs associated with particulate matter in air pollution has showed clear evidence of genotoxic effects, such as DNA adducts, chromosome aberrations. \cite{Kyrtopoulos2001, Farmer2003} +In atmospheric and environmental science, PAHs are known as the pollutants, which is harmful to human health. For instance, the carcinogenic PAHs associated with particulate matter in air pollution has showed clear evidence of genotoxic effects, such as DNA adduct, chromosome aberrations. \cite{Kyrtopoulos2001, Farmer2003} In new energy resources field, for the understanding of the properties of organic crystal or the design of new organic solar cell devices, PAH stacks are investigated as the prototypes.\cite{Aumaitre2019} In astrophysics, PAHs species are believed to be ubiquitous and abundant in the interstellar medium because of their compact and stable structure. \cite{Tielens2008} The PAH clusters are important contributors to the diffuse interstellar bands and UV-visible absorption bands. PAH clusters have been proposed to be the origin of a series of infrared emission bands, which are ubiquitous in the Universe. \cite{Leger1984,Allamandola1985} The broadening of these bands in regions protected from the star's UV flux suggests the following scenario: PAHs are trapped in clusters in UV-protected regions and photo-evaporated by star's UV photons in the so-called photodissociated region. \cite{Rapacioli2005, Berne2008} For all these topics, it is necessary to make a better understanding of the fundamental properties of PAH clusters. The crucial quantities are the stability, molecular growth processes, dissociation energies and their evolution with PAH charge, species, cluster size. @@ -544,14 +544,14 @@ The range of collision energies considered experimentally is quite large, rangin The quantitative data from experiments of PAH clusters are still rather limited, which motivates the modeling studies of them. In the calculation of PAH clusters, the size of the systems limits the use of {\it ab initio} wave function methods to the investigation of properties of the smallest clusters, namely dimers \cite{Piacenza2005, Birer2015}, whereas larger clusters can be addressed either at the DFT level or with more semi-empirical schemes \cite{Zhao2008truhlar, Rapacioli2009corr, Mao2017, Bowal2019}. Many of these studies, focused on structural properties, evidence a stacking growth process in agreement with experimental results. In addition, IR properties were also reported at the DFT level \cite{Ricca2013}. Most of the theoretical studies involve neutral clusters, mostly due to the fact that treating charge resonance process in ions is a challenging task for DFT based methods \cite{Grafenstein2009}. The singly charged PAH clusters are more stable than their neutral counterparts due to charge resonance stabilization.\cite{Rapacioli2009} Cationic PAH clusters are expected to be abundant in the photo-dissociation regions because the ionization energy of the PAH cluster is lower than that of the isolated PAH, which leads to the efficient formation of cationic PAH clusters. In addition, the ionized PAH clusters are easier to control, so it is more important to study them. It should be mentioned the recent studies computing ionisation potentials \cite{Joblin2017} as well as structural \cite{Dontot2019} and spectral (electronic \cite{Dontot2016} and vibrational \cite{Dontot2020}) properties of cations, performed with an original model combining DFTB \cite{Porezag1995, Seifert1996, Elstner1998, Spiegelman2020} with a configuration interaction scheme\cite{Rapacioli2011}. -With respect to these studies, very few is known about the dynamical aspects of PAH clusters carrying internal energy. High energy collisions of PAH clusters with energetic ions have been simulated by Gatchel {\textit et al.} \cite{Gatchell2016, Gatchell2016knockout} at the semi-empirical and DFTB levels. -Recently experiments at lower collision energies were performed by Zamith \textit{et al.} from LCAR \cite{Zamith2020threshold} (the principle of this experiment and the experimental setup were shown in sections \ref{principleTCID} and \ref{EXPsetup}), which were analysed by treating statistically the dissociation after collision energy deposition. Namely, the dissociation rate of pyrene clusters has been computed using phase space theory (PST)\cite{Zamith2019thermal}. A fair agreement with experimental results was obtained concerning the collision energy dependence of the dissociation cross section. However, the employed model failed at reproducing in details the shape of the peaks in the time-of-flight (TOF) spectra. In this section, it is aimed at extending the description of such low energy collision processes (less than several tens of eV) combining a dynamical simulations to describe the fast processes in addition to the statistical theory to address dissociation at longer timescales. With this approach, (i) good agreement between simulated and experimental mass spectra will be shown, thus validating the model, (ii) dissociation cross sections as a function of the collision energy is derived, (iii) the kinetic energy partition between dissociative and non-dissociative modes will be discussed and (iv) the energy transfer efficiency between intra and intermolecular modes will also be discussed. +With respect to these studies, very few is known about the dynamical aspects of PAH clusters carrying internal energy. High energy collisions of PAH clusters with energetic ions have been simulated by M. Gatchel {\textit et al.} \cite{Gatchell2016, Gatchell2016knockout} at the semi-empirical and DFTB levels. +Recently experiments at lower collision energies were performed by S. Zamith \textit{et al.} \cite{Zamith2020threshold} (the principle of this experiment and the experimental setup were shown in sections \ref{principleTCID} and \ref{EXPsetup}), which were analysed by treating statistically the dissociation after collision energy deposition. Namely, the dissociation rate of pyrene clusters has been computed using phase space theory (PST)\cite{Zamith2019thermal}. A fair agreement with experimental results was obtained concerning the collision energy dependence of the dissociation cross section. However, the employed model failed at reproducing in details the shape of the peaks in the time-of-flight (TOF) spectra. In this section, it is aimed at extending the description of such low energy collision processes (less than several tens of eV) combining a dynamical simulations to describe the fast processes in addition to the statistical theory to address dissociation at longer timescales. With this approach, (i) good agreement between simulated and experimental mass spectra will be shown, thus validating the model, (ii) dissociation cross sections as a function of the collision energy is derived, (iii) the kinetic energy partition between dissociative and non-dissociative modes will be discussed and (iv) the energy transfer efficiency between intra and intermolecular modes will also be discussed. % \ref{sec:compapp}, \subsection{Calculation of Energies} -In the analysis, we will discuss the kinetic energy contributors, applying the following decomposition of the total kinetic energy $E^k_{tot}$ of the dimer: +In the analysis, I will discuss the kinetic energy contributors, applying the following decomposition of the total kinetic energy $E^k_{tot}$ of the dimer: \begin{align} \label{Eparti} E^k_{tot}&=E^k_{Ar} + E^k_{td} + E^k_{Py^1} + E^k_{Py^2} + E^k_{Re} \nonumber \\ @@ -603,12 +603,12 @@ $\Vec{\omega}$ is the angular velocity. $\Vec{r}_{i}^n$ and $\Vec{r}_{_{CM}}(Py^n)$ denote the coordinates of atom $i$ and center of mass of dimer of monomer $n$, respectively. $\Vec{r}_{i}$ and $\Vec{r}_{_{CM}}(Py_2)$ and denote the coordinates of atom $i$ and center of mass of dimer, respectively. -From the endpoint of the simulation, we can also compute the total energy transferred towards internal rovibrational modes of the pyrene dimer as: +From the endpoint of the simulation, the total energy transferred towards internal rovibrational modes of the pyrene dimer cal also be computed as: \begin{equation} \Delta E_{int}^{Py_2} = E^{k,0}_{Ar} - E^k_{Ar} - E^k_{td} \end{equation} where $E^{k,0}_{Ar}$ is the initial argon kinetic energy whereas $E^k_{Ar}$ and $E^k_{td}$ correspond to kinetic energies at the end of the MD simulation. -In the case of dissociated dimers at the end of the simulations, we can also deduce the energy deposited in the rovibrational modes of the monomers as: +In the case of dissociated dimers at the end of the simulations, the energy deposited in the rovibrational modes of the monomers can be deduced as: \begin{equation} \Delta E_{int}^{Py^1+Py^2} = E^{k,0}_{Ar} - E^k_{Ar} - E^k_{td} - E^k_{Re} \end{equation} @@ -618,21 +618,21 @@ In the case of dissociated dimers at the end of the simulations, we can also ded The experimental TOFMS are reproduced by simulating the ion trajectories through the experimental setup in the presence of the electric fields. These are calculated by solving numerically the Laplace equation. Equations of motion are integrated using the fourth order Runge-Kutta method with adaptive step size. The occurrence of collision or dissociation is decided at each time step of the ion trajectory based on the collision and dissociation probabilities. -In the work of Zamith {\textit et al.}, \cite{Zamith2020threshold} the energy transfer was treated upon collision by using the Line of Center model (LOC) \cite{Levine1987}. In the LOC model, the transferred energy is the kinetic energy along the line of centers. Evaporation rates were then estimated using PST, in which only statistical dissociation to be possible after energy deposition in the cluster by collision was conside. Although this approach, which will be referred to as PST in the following, has been proved to be able to satisfactorily reproduce CID cross section experiments,\cite{Zamith2020threshold} it fails to reproduce in details the shape and position of the fragment peaks in the TOFMS, as will be shown in section \ref{sec:MS}. +In the work of S. Zamith {\textit et al.}, \cite{Zamith2020threshold} the energy transfer was treated upon collision by using the Line of Center model (LOC) \cite{Levine1987}. In the LOC model, the transferred energy is the kinetic energy along the line of centers. Evaporation rates were then estimated using PST, in which only statistical dissociation to be possible after energy deposition in the cluster by collision was conside. Although this approach, which will be referred to as PST in the following, has been proved to be able to satisfactorily reproduce CID cross section experiments,\cite{Zamith2020threshold} it fails to reproduce in details the shape and position of the fragment peaks in the TOFMS, as will be shown in section \ref{sec:MS}. In order to better reproduce the position and peak shapes, the MD and PST methods were combined. The outputs of the MD simulations were used to treat the collisions in the ion trajectories. At each time step the probability for a collision is evaluated. The principle of MD+PST is displayed in Figure \ref{MDPST}. \figuremacrob{MDPST}{Principle of MD+PST.} -One MD trajectory (with proper weighting of the $b$ values) was randomly picked from all outputs of MD simulations at a given collision energy. Then two cases have to be considered. First, if the dissociation occurred during the picked MD calculation (short time dissociation), then we use the MD final velocities of the fragments to further calculate the ion trajectories. On the other hand, if the pyrene dimer is still intact at the end of the picked MD calculation, then we update the dimer velocity and use the collision energy transfer $\Delta E_{int}^{Py_2}$ deduced from the MD calculation to increase the internal energy of the cluster. The dissociation rate resulting from this new internal energy is then evaluated using PST. +One MD trajectory (with proper weighting of the $b$ values) was randomly picked from all outputs of MD simulations at a given collision energy. Then two cases have to be considered. First, if the dissociation occurred during the picked MD calculation (short time dissociation), then the MD final velocities of the fragments are used to further calculate the ion trajectories. On the other hand, if the pyrene dimer is still intact at the end of the picked MD calculation, then the dimer velocity is updated and use the collision energy transfer $\Delta E_{int}^{Py_2}$ deduced from the MD calculation to increase the internal energy of the cluster. The dissociation rate resulting from this new internal energy is then evaluated using PST. In the latter case, if dissociation occurs (long time dissociation), the relative velocities of the fragment are evaluated using the PST outcome. The whole process of MD+PST is performed many times for different trajectories to ensure the reliability of the final obtained data. For each time, the TOFMS of Py$^+$ or Py$_2^+$ is updated. %Then we can obtain the update TOFMS histogram of the monomer cation Py$^+$ from the short and long time dissociation. -Here we emphasize that, due to the short time scale of the MD calculations (3 ps), only direct dissociation can be captured by the MD simulations. Therefore, one has to evaluate the probability of dissociation at longer time scales after the energy deposition by collision. This is done here by considering that at longer time scales, dissociation occurs statistically and is treated by using PST. +Here I emphasize that, due to the short time scale of the MD calculations (3 ps), only direct dissociation can be captured by the MD simulations. Therefore, one has to evaluate the probability of dissociation at longer time scales after the energy deposition by collision. This is done here by considering that at longer time scales, dissociation occurs statistically and is treated by using PST. \subsection{\label{sec:results}Results and Discussion} -In the following, we will discuss the dissociation at short, experimental and infinite timescales. The first two ones correspond to dissociation occurring during the MD simulation only or with the MD+PST model. The dissociation at infinite time accounts for all MD trajectories where the amount of energy transferred to the internal dimer rovibrational modes $\Delta E_{int}^{Py_2}$ is larger than the dissociation energy of 1.08~eV (value from references \cite{Dontot2019, Zamith2020threshold}). It can be regarded as the dissociation occurring after an infinite time neglecting any cooling processes, such as thermal collisions or photon emissions. +In the following, I will discuss the dissociation at short, experimental and infinite timescales. The first two ones correspond to dissociation occurring during the MD simulation only or with the MD+PST model. The dissociation at infinite time accounts for all MD trajectories where the amount of energy transferred to the internal dimer rovibrational modes $\Delta E_{int}^{Py_2}$ is larger than the dissociation energy of 1.08~eV (value from references \cite{Dontot2019, Zamith2020threshold}). It can be regarded as the dissociation occurring after an infinite time neglecting any cooling processes, such as thermal collisions or photon emissions. \subsubsection{\label{sec:MS}TOFMS Comparison} @@ -649,7 +649,7 @@ In Figure~\ref{expTOF}(b), the experimental result is compared to the PST and MD \textbf{Description of selected trajectories} -A first qualitative description of the collision processes can be obtained from the analysis of some arbitrarily selected MD trajectories. Figure \ref{collisions} (top and bottom) reports some snapshots extracted from two trajectories with the same collision energy (17.5~eV) and impact parameter (3.5~\AA). Only the top one leads to the Py$_2^+$ dissociation. During the results collection, we extract the final snapshot for each trajectory and consider that the dimer is dissociated if the distance between the two monomers molecular mass centers is larger than 10~\AA. +A first qualitative description of the collision processes can be obtained from the analysis of some arbitrarily selected MD trajectories. Figure \ref{collisions} (top and bottom) reports some snapshots extracted from two trajectories with the same collision energy (17.5~eV) and impact parameter (3.5~\AA). Only the top one leads to the Py$_2^+$ dissociation. During the results collection, the final snapshot for each trajectory is extracted and the dimer is dissociated is considered if the distance between the two monomers molecular mass centers is larger than 10~\AA. Figures \ref{collisions}-1/1* represent the system after its preliminary thermalization, when the argon atom introduced in the simulation with its initial velocity. Figures \ref{collisions}-2/2* and 3/3* represent the beginning and end of the collision. From these points, the two trajectories show different behaviors. For the top trajectory in Figure \ref{collisions}, snapshot 5 corresponds to the step where the two pyrene monomers start to go away from each other. After this, the intermolecular distance continues to increase further in snapshot 6. For the bottom trajectory in Figure \ref{collisions}, Figures \ref{collisions}-5* and 6* correspond to the middle and ending snapshots of the simulation, respectively. The snapshots 4*,~5* and 6* show the process of energy redistribution within the clusters. In particular, the soft modes associated to global deformation of the molecular planes appear to be excited. @@ -669,10 +669,10 @@ All these effects are intrinsically taken into account in the MD simulations on \figuremacro{distriPerc-Etf-175eV-d-bin03}{Distribution of transferred energy in rovibrational modes $\Delta E_{int}^{Py_2}$ for trajectories leading to dissociation at the end of MD (center of mass collision energy of 17.5~eV). The dashed line shows the distribution of transferred energy used in the LOC model.} -Finally, we note that the pyrene monomers remained intact (no fragmentation) up to collision energies of 25~eV. +Finally, I note that the pyrene monomers remained intact (no fragmentation) up to collision energies of 25~eV. The snapshots of a fragmentation trajectory at collision energy of 27.5~eV are shown in Figure \ref{fragmentation}. It can be seen that the pyrene molecule impacted by the argon undergoes an opening of an aromatic cycle and the loss of two hydrogen atoms, leaving as a H$_2$ molecule. -As the study of monomer's fragmentation is beyond the scope of the present paper, we will focus on trajectories with collision energies below this fragmentation threshold energy in the following. +As the study of monomer's fragmentation is beyond the scope of the present paper, I will focus on trajectories with collision energies below this fragmentation threshold energy in the following. \figuremacrob{fragmentation}{Snapshots for molecular dynamics trajectory with impact parameter of 0.5~\AA{} and a collision energy of 27.5 eV leading to intramolecular fragmentation.} @@ -688,7 +688,7 @@ The purple curve corresponds to dissociation at infinite timescales. Figure \ref It can be seen that, for low collision energies, the MD and MD+PST cross sections are very close, indicating that most of the dissociations occur on the short timescales. On the opposite, at high collision energies, a non-negligible fraction of the dimers, which are not dissociated at the end of the MD simulation, carry enough energy to evaporate on the experimental timescales. At the experimental center of mass collision energy of 17.5~eV, the MD+PST cross section (about 70~\AA$^2$) is slightly above the pure MD dissociation ratio, which indicates that the dissociation at long timescales represents a small fraction of the dissociated pyrene dimers as already seen from the TOF spectra analysis (see Figure \ref{expTOF}). -We have also plotted in Figure~\ref{cross-section} the model cross section $\sigma_\infty$ that successfully reproduced the threshold collision-induced dissociation experimental results \cite{Zamith2020threshold}. This model cross section is obtained by considering that the collision energy transfer is given by the LOC model and the expression for the cross section is given by: +I have also plotted in Figure~\ref{cross-section} the model cross section $\sigma_\infty$ that successfully reproduced the threshold collision-induced dissociation experimental results \cite{Zamith2020threshold}. This model cross section is obtained by considering that the collision energy transfer is given by the LOC model and the expression for the cross section is given by: \begin{equation} \sigma_{LOC}(E_{col}) = \sigma_0 (E_{col} - D)/(E_{col}). \end{equation} @@ -705,7 +705,7 @@ The dissociation cross sections for MD timescales with time step being 0.1 fs at The mean value obtained for the transferred energy after removing the translation kinetic energy of the dimer, namely $\Delta E_{int}^{Py_2}$, is plotted in Figure \ref{transferredE-Ar-300} as a function of the collision energy. Although this quantity evolves almost linearly with the collision energy, the curves are different when one considers only the trajectories leading to dissociation or non-dissociation. For trajectories where the dimer does not dissociate, $\Delta E_{int-ud}^{Py_2}$ remains small for all collision energies below 20~eV and shows a very slight increase for collision energies larger than 20~eV. For trajectories leading to dissociation, $E_{int-d}^{Py_2}$ grows almost linearly, but above 10-15~eV most of the absorbed energy is actually used to heat the individual monomers (the green curve) whereas the energy given in the dissociative mode (difference between the blue and green curves) remains almost constant. -We note that, despite the trends of the mean energy values derived from all simulations or restricted to the undissociated cases are interesting, their absolute values have small meaning as they depend on the arbitrarily chosen $b_{max}$ value, {\it i.e.} increasing $b_{max}$ would result in more undissociated trajectories with less and less energy transfer. On the opposite, absolute values of mean energies for the dissociation trajectories are relevant, as increasing the $b_{max}$ value would not result in new dissociation trajectories. +I note that, despite the trends of the mean energy values derived from all simulations or restricted to the undissociated cases are interesting, their absolute values have small meaning as they depend on the arbitrarily chosen $b_{max}$ value, {\it i.e.} increasing $b_{max}$ would result in more undissociated trajectories with less and less energy transfer. On the opposite, absolute values of mean energies for the dissociation trajectories are relevant, as increasing the $b_{max}$ value would not result in new dissociation trajectories. For MD simulations with time step being 0.1 fs at collision energy of 20 and 25 ~eV, the corresponding energies in Figure~\ref{transferredE-Ar-300} are close to the ones of time step being 0.5 fs, which indicates a time step of 0.1 fs used in the MD simulation does not change significantly the corresponding deposition of the total transferred energy. @@ -822,7 +822,7 @@ This is actually in line with the fact that the part of the absorbed collision e \figuremacrob{E-time-abcdef}{Instantaneous kinetic energies as a function of time for intra and intermolecular modes of the pyrene dimer at a collision energy of 22.5 eV. Impact parameters $b$ are (a) 2, (b) 3, (c) 0, (d) 2.5, (e) 2, and (f) 2 \AA{}. In cases (a) and (b), dissociation takes place whereas in the other cases the dimer remains undissociated at the end of the MD simulation.} -In this section, we address how the energy is shared inside the dimer after the collision. In particular, we look at the efficiency of energy transfer between the intramolecular modes of each unit and the intermolecular modes. The amount of deposited energy as well as its partition between the intramolecular modes of each molecule and the intermolecular modes is strongly dependent on the collision condition: the impact parameter, the orientation of the dimer, whether a head on collision occurs with one of the dimer atoms (and its nature, carbon or hydrogen). This results in very different evolutions of the subsequent energy flows for which precise values concerning timescales can hardly be derived. Nevertheless, the analysis of the trajectories allows to identify some characteristic behaviors. In order to estimate the thermalization process efficiency, the instantaneous intra and intermolecular kinetic temperatures are evaluated using the following formula: +In this section, I address how the energy is shared inside the dimer after the collision. In particular, I look at the efficiency of energy transfer between the intramolecular modes of each unit and the intermolecular modes. The amount of deposited energy as well as its partition between the intramolecular modes of each molecule and the intermolecular modes is strongly dependent on the collision condition: the impact parameter, the orientation of the dimer, whether a head on collision occurs with one of the dimer atoms (and its nature, carbon or hydrogen). This results in very different evolutions of the subsequent energy flows for which precise values concerning timescales can hardly be derived. Nevertheless, the analysis of the trajectories allows to identify some characteristic behaviors. In order to estimate the thermalization process efficiency, the instantaneous intra and intermolecular kinetic temperatures are evaluated using the following formula: \begin{align} \label{kineticT} T^k=2 \frac{}{nk_b} diff --git a/thesis/5/general_conclusion.aux b/thesis/5/general_conclusion.aux index d7adb96..48ebe3b 100644 --- a/thesis/5/general_conclusion.aux +++ b/thesis/5/general_conclusion.aux @@ -1,14 +1,14 @@ \relax \providecommand\hyper@newdestlabel[2]{} \FN@pp@footnotehinttrue -\@writefile{toc}{\contentsline {chapter}{\numberline {5}General Conclusions and Perspectives}{159}{chapter.5}\protected@file@percent } +\@writefile{toc}{\contentsline {chapter}{\numberline {5}General Conclusions and Perspectives}{157}{chapter.5}\protected@file@percent } \@writefile{lof}{\addvspace {10\p@ }} \@writefile{lot}{\addvspace {10\p@ }} -\@writefile{toc}{\contentsline {section}{\numberline {5.1}General Conclusions}{159}{section.5.1}\protected@file@percent } -\@writefile{toc}{\contentsline {section}{\numberline {5.2}Perspectives}{162}{section.5.2}\protected@file@percent } +\@writefile{toc}{\contentsline {section}{\numberline {5.1}General Conclusions}{157}{section.5.1}\protected@file@percent } +\@writefile{toc}{\contentsline {section}{\numberline {5.2}Perspectives}{160}{section.5.2}\protected@file@percent } \FN@pp@footnotehinttrue \@setckpt{5/general_conclusion}{ -\setcounter{page}{163} +\setcounter{page}{161} \setcounter{equation}{0} \setcounter{enumi}{5} \setcounter{enumii}{0} diff --git a/thesis/6_backmatter/declaration.aux b/thesis/6_backmatter/declaration.aux index c6a72c2..725f57c 100644 --- a/thesis/6_backmatter/declaration.aux +++ b/thesis/6_backmatter/declaration.aux @@ -1,7 +1,7 @@ \relax \providecommand\hyper@newdestlabel[2]{} \@setckpt{6_backmatter/declaration}{ -\setcounter{page}{180} +\setcounter{page}{178} \setcounter{equation}{0} \setcounter{enumi}{5} \setcounter{enumii}{0} @@ -22,7 +22,7 @@ \setcounter{ContinuedFloat}{0} \setcounter{pp@next@reset}{1} \setcounter{@fnserial}{0} -\setcounter{NAT@ctr}{484} +\setcounter{NAT@ctr}{483} \setcounter{Item}{5} \setcounter{Hfootnote}{0} \setcounter{bookmark@seq@number}{65} diff --git a/thesis/6_backmatter/references.bib b/thesis/6_backmatter/references.bib index 41917d5..0edd903 100644 --- a/thesis/6_backmatter/references.bib +++ b/thesis/6_backmatter/references.bib @@ -13,7 +13,7 @@ publisher={ACS Publications}} @article{Kazimirski2003, - title={Search for low energy structures of water clusters (H2O) n, n= 20- 22, 48, 123, and 293}, + title={Search for low energy structures of water clusters (H$_2$O)$_n$, $n$= 20- 22, 48, 123, and 293}, author={Kazimirski, Jan K and Buch, Victoria}, journal={J. Phys. Chem. A}, volume={107}, @@ -33,7 +33,7 @@ publisher={ACS Publications}} @article{Lee2004, - title={Insights into the Structures, Energetics, and Vibrations of Monovalent Cation-(Water) 1-6 Clusters}, + title={Insights into the structures, energetics, and vibrations of monovalent cation-(water) 1-6 clusters}, author={Lee, Han Myoung and Tarakeshwar, P and Park, Jungwon and Ko{\l}aski, Maciej Roman and Yoon, Yeo Jin and Yi, Hai-Bo and Kim, Woo Youn and Kim, Kwang S}, journal={J. Phys. Chem. A}, volume={108}, @@ -83,8 +83,8 @@ publisher={Wiley Online Library}} @article{MCTDH, -title = {The Multiconfiguration Time-Dependent Hartree (MCTDH) Method: A Highly Efficient Algorithm for Propagating Wavepackets}, -journal = {Physics Reports}, +title = {The multiconfiguration time-dependent hartree (MCTDH) method: a highly efficient algorithm for propagating wavepackets}, +journal = {Phys. Rep.}, volume = {324}, number = {1}, pages = {1-105}, @@ -125,7 +125,7 @@ author = {M.H. Beck and A. Jäckle and G.A. Worth and H.-D. Meyer} @article{Montillaud2014, title={Absolute evaporation rates of non-rotating neutral polycyclic aromatic hydrocarbon clusters}, author={Montillaud, Julien and Joblin, Christine}, - journal={Astronomy \& Astrophysics}, + journal={Astron. Astrophys.}, volume={567}, pages={A45}, year={2014}, @@ -134,7 +134,7 @@ author = {M.H. Beck and A. Jäckle and G.A. Worth and H.-D. Meyer} @article{Rapacioli2006, title={Formation and destruction of polycyclic aromatic hydrocarbon clusters in the interstellar medium}, author={Rapacioli, M and Calvo, F and Joblin, C and Parneix, P and Toublanc, D and Spiegelman, F}, - journal={Astronomy \& Astrophysics}, + journal={Astron. Astrophys.}, volume={460}, number={2}, pages={519--531}, @@ -144,7 +144,7 @@ author = {M.H. Beck and A. Jäckle and G.A. Worth and H.-D. Meyer} @article{Darghouth2018, title={Davydov-type excitonic effects on the absorption spectra of parallel-stacked and herringbone aggregates of pentacene: Time-dependent density-functional theory and time-dependent density-functional tight binding}, author={Darghouth, Ala Aldin MHM and Correa, Gabriela Calinao and Juillard, Sacha and Casida, Mark E and Humeniuk, Alexander and Mitri{\'c}, Roland}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={149}, number={13}, pages={134111}, @@ -164,7 +164,7 @@ author = {M.H. Beck and A. Jäckle and G.A. Worth and H.-D. Meyer} @article{Scholz2013, title={Quantifying charge transfer energies at donor--acceptor interfaces in small-molecule solar cells with constrained DFTB and spectroscopic methods}, author={Scholz, Reinhard and Luschtinetz, Regina and Seifert, Gotthard and J{\"a}geler-Hoheisel, Till and K{\"o}rner, Christian and Leo, Karl and Rapacioli, Mathias}, - journal={Journal of physics: Condensed matter}, + journal={J. Condens. Matter Phys.}, volume={25}, number={47}, pages={473201}, @@ -174,7 +174,7 @@ author = {M.H. Beck and A. Jäckle and G.A. Worth and H.-D. Meyer} @article{Violi2007, title={Soot primary particle formation from multiscale coarse-grained molecular dynamics simulation}, author={Violi, Angela and Izvekov, Sergei}, - journal={Proceedings of the Combustion Institute}, + journal={Proc. Combust. Inst.}, volume={31}, number={1}, pages={529--537}, @@ -200,7 +200,7 @@ author = {M.H. Beck and A. Jäckle and G.A. Worth and H.-D. Meyer} @article{Puget1989, title={A new component of the interstellar matter: Small grains and large aromatic molecules}, author={Puget, JL and L{\'e}ger, A}, - journal={Annual review of astronomy and astrophysics}, + journal={Annu. Rev. Astron. Astrophys.}, volume={27}, number={1}, pages={161--198}, @@ -210,7 +210,7 @@ author = {M.H. Beck and A. Jäckle and G.A. Worth and H.-D. Meyer} @article{Kahan2010, title={Hydroxyl radical reactivity at the air-ice interface}, author={Kahan, TF and Zhao, R and Donaldson, DJ}, - journal={Atmospheric Chemistry and Physics}, + journal={Atmos. Chem. Phys.}, volume={10}, number={2}, pages={843--854}, @@ -220,7 +220,7 @@ author = {M.H. Beck and A. Jäckle and G.A. Worth and H.-D. Meyer} @article{Sunden2018, title={Stabilities of protonated water-ammonia clusters}, author={Sund{\'e}n, AEK and St{\o}chkel, K and Hvelplund, P and Br{\o}ndsted Nielsen, S and Dynefors, B and Hansen, K}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={148}, number={18}, pages={184306}, @@ -230,7 +230,7 @@ author = {M.H. Beck and A. Jäckle and G.A. Worth and H.-D. Meyer} @article{Kulmala1995, title={Aerosol formation in diffusive boundary layer: Binary homogeneous nucleation of ammonia and water vapours}, author={Kulmala, M and Vehkam{\"a}ki, H and Vesala, T and Barrett, JC and Clement, CF}, - journal={Journal of aerosol science}, + journal={J. Aerosol Sci.}, volume={26}, number={4}, pages={547--558}, @@ -238,9 +238,9 @@ author = {M.H. Beck and A. Jäckle and G.A. Worth and H.-D. Meyer} publisher={Elsevier}} @article{Payzant1973, - title={Gas Phase Solvation of the Ammonium Ion by NH3 and H2O and Stabilities of Mixed Clusters NH4+ (NH3) n (H2O) w}, + title={Gas phase solvation of the ammonium ion by NH$_3$ and H$_2$O and stabilities of mixed clusters nh$_4^+$(nh$_3$)$_n$(H$_2$O)$_w$}, author={Payzant, JD and Cunningham, AJ and Kebarle, P}, - journal={Canadian Journal of Chemistry}, + journal={Can. J. Chem.}, volume={51}, number={19}, pages={3242--3249}, @@ -250,7 +250,7 @@ author = {M.H. Beck and A. Jäckle and G.A. Worth and H.-D. Meyer} @article{Amiaud2007, title={Interaction of atomic and molecular deuterium with a nonporous amorphous water ice surface between 8 and 30 K}, author={Amiaud, L and Dulieu, F and Fillion, J-H and Momeni, A and Lemaire, JL}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={127}, number={14}, pages={144709}, @@ -260,7 +260,7 @@ author = {M.H. Beck and A. Jäckle and G.A. Worth and H.-D. Meyer} @article{Klan2001, title={Photodegradation of halobenzenes in water ice}, author={Kl{\'a}n, Petr and Del Favero, David and Ansorgov{\'a}, Alena and Kl{\'a}nov{\'a}, Jana and Holoubek, Ivan}, - journal={Environmental Science and Pollution Research}, + journal={Environ. Sci. Pollut. Res.}, volume={8}, number={3}, pages={195--200}, @@ -270,7 +270,7 @@ author = {M.H. Beck and A. Jäckle and G.A. Worth and H.-D. Meyer} @article{Minissale2019, title={Experimental study of the penetration of oxygen and deuterium atoms into porous water ice}, author={Minissale, M and Nguyen, T and Dulieu, F}, - journal={Astronomy \& Astrophysics}, + journal={Astron. Astrophys.}, volume={622}, pages={A148}, year={2019}, @@ -279,7 +279,7 @@ author = {M.H. Beck and A. Jäckle and G.A. Worth and H.-D. Meyer} @article{Hock2009, title={Calorimetric observation of the melting of free water nanoparticles at cryogenic temperatures}, author={Hock, C and Schmidt, M and Kuhnen, R and Bartels, C and Ma, L and Haberland, H and Issendorff, B v}, - journal={Physical review letters}, + journal={Phys. Rev. Lett.}, volume={103}, number={7}, pages={073401}, @@ -305,7 +305,7 @@ author = {M.H. Beck and A. Jäckle and G.A. Worth and H.-D. Meyer} @Article{Perez2012, author = {P\'{e}rez, Crist\'{o}bal and Muckle, Matt T. and Zaleski, Daniel P. and Seifert, Nathan A. and Temelso, Berhane and Shields, George C. and Kisiel, Zbigniew and Pate, Brooks H.}, - title = {Structures of Cage, Prism, and Book Isomers of Water Hexamer from Broadband Rotational Spectroscopy}, + title = {Structures of cage, prism, and book isomers of water hexamer from broadband rotational spectroscopy}, journal = {Science}, year = {2012}, date = {May 18, 2012}, @@ -395,7 +395,7 @@ author = {M.H. Beck and A. Jäckle and G.A. Worth and H.-D. Meyer} publisher={ACS Publications}} @article{Sadlej1999, - title={Structure and Energetics of the Weakly Bound NH$_3$ $\cdots$ H$_2$O Complex}, + title={Structure and energetics of the weakly bound NH$_3$ $\cdots$ H$_2$O complex}, author={Sadlej, J and Moszynski, R and Dobrowolski, J Cz and Mazurek, AP}, journal={J. Phys. Chem. A}, volume={103}, @@ -405,7 +405,7 @@ author = {M.H. Beck and A. Jäckle and G.A. Worth and H.-D. Meyer} publisher={ACS Publications}} @article{Donaldson1999, - title={Adsorption of atmospheric gases at the air- water interface. I. NH3}, + title={Adsorption of atmospheric gases at the air- water interface. I. NH$_3$}, author={Donaldson, DJ}, journal={J. Phys. Chem. A}, volume={103}, @@ -425,7 +425,7 @@ author = {M.H. Beck and A. Jäckle and G.A. Worth and H.-D. Meyer} publisher={American Institute of Physics}} @article{Lee1996, - title={Ionization of Bases in Water: Structure and Stability of the NH$_4^+$ $\cdots$ OH$^-$ Ionic Forms in Ammonia-Water Clusters}, + title={Ionization of bases in water: Structure and stability of the NH$_4^+$ $\cdots$ OH$^-$ ionic forms in ammonia-water clusters}, author={Lee, Chengteh and Fitzgerald, George and Planas, Marc and Novoa, Juan J}, journal={J. Phys. Chem.}, volume={100}, @@ -445,7 +445,7 @@ author = {M.H. Beck and A. Jäckle and G.A. Worth and H.-D. Meyer} publisher={Springer}} @article{Bacelo2002, - title={Theoretical study of microscopic solvation of ammonia in water clusters: NH3 (H2O) n, n= 3, 4}, + title={Theoretical study of microscopic solvation of ammonia in water clusters: NH$_3$(H$_2$O)$_n$, $n=$ 3, 4}, author={Bacelo, Daniel E}, journal={J. Phys. Chem. A}, volume={106}, @@ -465,7 +465,7 @@ author = {M.H. Beck and A. Jäckle and G.A. Worth and H.-D. Meyer} publisher={American Institute of Physics}} @article{Hvelplund2010, - title={Stability and Structure of Protonated Clusters of Ammonia and Water, H+ (NH3) m (H2O) n}, + title={Stability and structure of protonated clusters of ammonia and water, H$^+$(NH$_3$)$_m$(H$_2$O)$_n$}, author={Hvelplund, Preben and Kurten, Theo and St{\o}chkel, Kristian and Ryding, Mauritz Johan and Nielsen, Steen Br{\o}ndsted and Uggerud, Einar}, journal={J. Phys. Chem. A}, volume={114}, @@ -485,7 +485,7 @@ author = {M.H. Beck and A. Jäckle and G.A. Worth and H.-D. Meyer} publisher={Springer}} @article{Chang1998, - title={Studying protonated ion hydration by infrared spectroscopy of size-selected NH4+ (H2O) n clusters in a free jet expansion}, + title={Studying protonated ion hydration by infrared spectroscopy of size-selected NH$_4^+$(H$_2$O)$_n$ clusters in a free jet expansion}, author={Chang, Hai-Chou and Wang, Yih-Sheng and Lee, Yuan T and Chang, Huan-Cheng}, journal={Int. J. Mass Spectrom.}, volume={179}, @@ -494,8 +494,8 @@ author = {M.H. Beck and A. Jäckle and G.A. Worth and H.-D. Meyer} publisher={Elsevier}} @article{Jiang1999, - title={Ab initio Studies of NH4+ (H2O) 1-5 and the Influence of Hydrogen-Bonding Nonadditivity on Geometries and Vibrations}, - author={Jiang, JC and Chang, H-C and Lee, YT and Lin, SH}, + title={Ab initio studies of NH$_4^+$(H$_2$O)$_{1-5}$ and the influence of hydrogen-bonding nonadditivity on geometries and vibrations}, + author={Jiang, J C and Chang, H-C and Lee, YT and Lin, SH}, journal={J. Phys. Chem. A}, volume={103}, number={16}, @@ -505,7 +505,7 @@ author = {M.H. Beck and A. Jäckle and G.A. Worth and H.-D. Meyer} @article{Wang1998, author = {Wang, Yih-Sheng and Chang, Hai-Chou and Jiang, Jyh-Chiang and Lin, Sheng H. and Lee, Yuan T. and Chang, Huan-Cheng}, -title = {Structures and Isomeric Transitions of NH$_4^+$(H$_2$O)$_{3-6}$: From Single to Double Rings}, +title = {Structures and isomeric transitions of NH$_4^+$(H$_2$O)$_{3-6}$: from single to double rings}, journal = {J. Am. Chem. Soc.}, volume = {120}, number = {34}, @@ -523,7 +523,7 @@ year = {1998}} publisher={Elsevier}} @article{Stockman1992, - title={Microwave and tunable far-infrared laser spectroscopy of the ammonia--water dimer}, + title={Microwave and tunable far-infrared laser spectroscopy of the ammonia-water dimer}, author={Stockman, Paul A and Bumgarner, Roger E and Suzuki, Sakae and Blake, Geoffrey A}, journal={J. Chem. Phys.}, volume={96}, @@ -736,7 +736,7 @@ year = {1989}} @article{Chakraborty2020, title={Dynamics of Pyrene-Dimer Association and Ensuing Pyrene-Dimer Dissociation}, author={Chakraborty, Debdutta and Lischka, Hans and Hase, William L}, - journal={The Journal of Physical Chemistry A}, + journal={J. Phys. Chem. A}, volume={124}, number={43}, pages={8907--8917}, @@ -746,7 +746,7 @@ year = {1989}} @article{Zheng2021, title={Dynamical simulation of collision-induced dissociation of pyrene dimer cation}, author={Zheng, Linjie and Zamith, S{\'e}bastien and Rapacioli, Mathias}, - journal={Theoretical Chemistry Accounts}, + journal={Theor. Chem. Acc.}, volume={140}, number={2}, pages={1--14}, @@ -756,7 +756,7 @@ year = {1989}} @article{Hada2003, title={A molecular dynamics simulation of cluster dissociation process under cluster ion implantation}, author={Hada, Yasuhiro}, - journal={Physica B: Condensed Matter}, + journal={Phys. Rev. B Condens. Matter}, volume={340}, pages={1036--1040}, year={2003}, @@ -765,7 +765,7 @@ year = {1989}} @article{Tibshirani2005, title={Cluster validation by prediction strength}, author={Tibshirani, Robert and Walther, Guenther}, - journal={Journal of Computational and Graphical Statistics}, + journal={J. Comput. Graph. Stat.}, volume={14}, number={3}, pages={511--528}, @@ -775,7 +775,7 @@ year = {1989}} @article{Milovanovic2019, title={Theoretical and experimental investigation of geometry and stability of small potassium-iodide KnI (n= 2--6) clusters}, author={Milovanovi{\'c}, Branislav and Milovanovi{\'c}, Milan and Veli{\v{c}}kovi{\'c}, Suzana and Veljkovi{\'c}, Filip and Peri{\'c}-Gruji{\'c}, Aleksandra and Jerosimi{\'c}, Stanka}, - journal={International Journal of Quantum Chemistry}, + journal={Int. J. Quantum Chem.}, volume={119}, number={22}, pages={e26009}, @@ -785,7 +785,7 @@ year = {1989}} @article{Korobeishchikov2005, title={Condensation of argon, monosilane and their mixtures in a pulse free jet}, author={Korobeishchikov, NG and Zarvin, AE and Madirbaev, V Zh and Sharafutdinov, RG}, - journal={Plasma chemistry and plasma processing}, + journal={Plasma Chem. Plasma Process.}, volume={25}, number={4}, pages={319--349}, @@ -795,7 +795,7 @@ year = {1989}} @article{Henglein1989, title={Non-metallic silver clusters in aqueous solution: stabilization and chemical reactions}, author={Henglein, Arnim}, - journal={Chemical physics letters}, + journal={Chem. Phys. Lett.}, volume={154}, number={5}, pages={473--476}, @@ -805,7 +805,7 @@ year = {1989}} @article{Castleman2009, title={Clusters, superatoms, and building blocks of new materials}, author={Castleman Jr, AW and Khanna, SN}, - journal={The Journal of Physical Chemistry C}, + journal={J. Phys. Chem. C}, volume={113}, number={7}, pages={2664--2675}, @@ -815,7 +815,7 @@ year = {1989}} @article{Siegel1993, title={Nanophase materials assembled from atom clusters}, author={Siegel, Richard W}, - journal={Materials Science and Engineering: B}, + journal={Mater. Sci. Eng., B}, volume={19}, number={1-2}, pages={37--43}, @@ -831,7 +831,7 @@ year = {1989}} @article{Katakuse1985, title={Mass distributions of copper, silver and gold clusters and electronic shell structure}, author={Katakuse, I and Ichihara, T and Fujita, Y and Matsuo, T and Sakurai, T and Matsuda, H}, - journal={International journal of mass spectrometry and ion processes}, + journal={Int. J. Mass Spectrom. Ion Processes}, volume={67}, number={2}, pages={229--236}, @@ -851,7 +851,7 @@ year = {1989}} @article{Wang2008, title={Self-organized periodicity of protein clusters in growing bacteria}, author={Wang, Hui and Wingreen, Ned S and Mukhopadhyay, Ranjan}, - journal={Physical review letters}, + journal={Phys. Rev. Lett.}, volume={101}, number={21}, pages={218101}, @@ -867,7 +867,7 @@ year = {1989}} @article{Boulon2014, title={Experimental nanocalorimetry of protonated and deprotonated water clusters}, author={Boulon, Julien and Braud, Isabelle and Zamith, S{\'e}bastien and Labastie, Pierre and L’Hermite, Jean-Marc}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={140}, number={16}, pages={164305}, @@ -877,7 +877,7 @@ year = {1989}} @article{Jortner1992, title={Cluster size effects}, author={Jortner, Joshua}, - journal={Zeitschrift f{\"u}r Physik D Atoms, Molecules and Clusters}, + journal={Z. Phys. D}, volume={24}, number={3}, pages={247--275}, @@ -894,7 +894,7 @@ year = {1989}} @article{Alonso2000, title={Electronic and atomic structure, and magnetism of transition-metal clusters}, author={Alonso, JA}, - journal={Chemical reviews}, + journal={Chem. Rev.}, volume={100}, number={2}, pages={637--678}, @@ -904,7 +904,7 @@ year = {1989}} @article{Kruger2000, title={Properties of isomers of the cluster Ni8 from density functional studies}, author={Kr{\"u}ger, Sven and Seem{\"u}ller, Thomas J and W{\"o}rndle, Alexander and R{\"o}sch, Notker}, - journal={International Journal of Quantum Chemistry}, + journal={Int. J. Quantum Chem.}, volume={80}, number={4-5}, pages={567--574}, @@ -940,7 +940,7 @@ year = {1989}} @article{Ayuela1993, title={Theoretical study of NaCl clusters}, author={Ayuela, A and L{\'o}pez, JM and Alonso, JA and Luana, V}, - journal={Zeitschrift f{\"u}r Physik D Atoms, Molecules and Clusters}, + journal={Z. Phys. D}, volume={26}, number={1}, pages={213--215}, @@ -950,7 +950,7 @@ year = {1989}} @article{Hakkinen2002, title={Bonding in Cu, Ag, and Au clusters: relativistic effects, trends, and surprises}, author={H{\"a}kkinen, Hannu and Moseler, Michael and Landman, Uzi}, - journal={Physical review letters}, + journal={Phys. Rev. Lett.}, volume={89}, number={3}, pages={033401}, @@ -960,7 +960,7 @@ year = {1989}} @article{Harris1984, title={Structure of charged argon clusters formed in a free jet expansion}, author={Harris, IA and Kidwell, RS and Northby, JA}, - journal={Physical review letters}, + journal={Phys. Rev. Lett.}, volume={53}, number={25}, pages={2390}, @@ -970,7 +970,7 @@ year = {1989}} @article{Carslaw1997, title={Modeling the composition of liquid stratospheric aerosols}, author={Carslaw, Kenneth S and Peter, Thomas and Clegg, Simon L}, - journal={Reviews of Geophysics}, + journal={Rev. Geophys. }, volume={35}, number={2}, pages={125--154}, @@ -1026,9 +1026,9 @@ year = {1989}} publisher={Nature Publishing Group}} @article{Wang2010, - title={Stepwise hydration of the cyanide anion: A temperatur-controlled photoelectron spectroscopy and ab initio computational study of CN-(H2O) n, n = 2-5}, + title={Stepwise hydration of the cyanide anion: A temperatur-controlled photoelectron spectroscopy and ab initio computational study of CN-(H$_2$O)$_n$, n = 2-5}, author={Wang, Xue-Bin and Kowalski, Karol and Wang, Lai-Sheng and Xantheas, Sotiris S}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={132}, number={12}, pages={124306}, @@ -1048,7 +1048,7 @@ year = {1989}} @article{Torrent2011, title={Anharmonicity and the Eigen-Zundel dilemma in the IR spectrum of the protonated 21 water cluster}, author={Torrent-Sucarrat, Miquel and Anglada, Josep M}, - journal={Journal of chemical theory and computation}, + journal={J. Chem. Theory Comput.}, volume={7}, number={2}, pages={467--472}, @@ -1064,7 +1064,7 @@ year = {1989}} @article{Kuo2003, title={Short H-bonds and spontaneous self-dissociation in (H2O)20: Effects of H-bond Topology}, author={Kuo, Jer-Lai and Ciobanu, Cristian V and Ojam{\"a}e, Lars and Shavitt, Isaiah and Singer, Sherwin J}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={118}, number={8}, pages={3583--3588}, @@ -1074,7 +1074,7 @@ year = {1989}} @article{Maheshwary2001, title={Structure and stability of water clusters (H2O)n, n= 8-20: An ab initio investigation}, author={Maheshwary, Shruti and Patel, Nitin and Sathyamurthy, Narayanasami and Kulkarni, Anant D and Gadre, Shridhar R}, - journal={The Journal of Physical Chemistry A}, + journal={J. Phys. Chem. A}, volume={105}, number={46}, pages={10525--10537}, @@ -1084,7 +1084,7 @@ year = {1989}} @article{Lee2000, title={Structures, energies, vibrational spectra, and electronic properties of water monomer to decamer}, author={Lee, Han Myoung and Suh, Seung Bum and Lee, Jin Yong and Tarakeshwar, P and Kim, Kwang S}, - journal={The Journal of Chemical Physics}, + journal={J. Chem. Phys.}, volume={112}, number={22}, pages={9759--9772}, @@ -1094,7 +1094,7 @@ year = {1989}} @article{Santra2008, title={On the accuracy of density-functional theory exchange-correlation functionals for H bonds in small water clusters. II. The water hexamer and van der Waals interactions}, author={Santra, Biswajit and Michaelides, Angelos and Fuchs, Martin and Tkatchenko, Alexandre and Filippi, Claudia and Scheffler, Matthias}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={129}, number={19}, pages={194111}, @@ -1104,7 +1104,7 @@ year = {1989}} @article{Hanninen2009, title={Acceptor Tunneling Motion and O-H Stretching Vibration Overtones of the Water Dimer}, author={Hanninen, Vesa and Salmi, Teemu and Halonen, Lauri}, - journal={The Journal of Physical Chemistry A}, + journal={J. Phys. Chem. A}, volume={113}, number={25}, pages={7133--7137}, @@ -1114,7 +1114,7 @@ year = {1989}} @article{Neela2010, title={Hydrogen bonding in water clusters and their ionized counterparts}, author={Neela, Y Indra and Mahadevi, A Subha and Sastry, G Narahari}, - journal={The Journal of Physical Chemistry B}, + journal={J. Phys. Chem. B}, volume={114}, number={51}, pages={17162--17171}, @@ -1124,7 +1124,7 @@ year = {1989}} @article{Ludwig2001, title={Water: From clusters to the bulk}, author={Ludwig, Ralf}, - journal={Angewandte Chemie International Edition}, + journal={Angew. Chem. Int. Ed. }, volume={40}, number={10}, pages={1808--1827}, @@ -1134,7 +1134,7 @@ year = {1989}} @article{Buckingham2008, title={The hydrogen bond}, author={Buckingham, AD and Del Bene, JE and McDowell, SAC}, - journal={Chemical Physics Letters}, + journal={Chem. Phys. Lett.}, volume={463}, number={1-3}, pages={1--10}, @@ -1144,7 +1144,7 @@ year = {1989}} @article{Morrell2010, title={Atmospheric implications for formation of clusters of ammonium and 1-10 water molecules}, author={Morrell, Thomas E and Shields, George C}, - journal={The Journal of Physical Chemistry A}, + journal={J. Phys. Chem. A}, volume={114}, number={12}, pages={4266--4271}, @@ -1154,7 +1154,7 @@ year = {1989}} @article{Vaida2003, title={Hydrated complexes: Relevance to atmospheric chemistry and climate}, author={Vaida, Veronica and Kjaergaard, Henrik G and Feierabend, Karl J}, - journal={International Reviews in Physical Chemistry}, + journal={Int. Rev. Phys. Chem.}, volume={22}, number={1}, pages={203--219}, @@ -1164,7 +1164,7 @@ year = {1989}} @article{Kjaergaard2003, title={Complexes of importance to the absorption of solar radiation}, author={Kjaergaard, Henrik G and Robinson, Timothy W and Howard, Daryl L and Daniel, John S and Headrick, Jill E and Vaida, Veronica}, - journal={The Journal of Physical Chemistry A}, + journal={J. Phys. Chem. A}, volume={107}, number={49}, pages={10680--10686}, @@ -1172,9 +1172,9 @@ year = {1989}} publisher={ACS Publications}} @article{Wales1998, - title={Global minima of water clusters (H2O)n, n $\leqslant$ 21, described by an empirical potential}, + title={Global minima of water clusters (H$_2$O)$_n$, n $\leqslant$ 21, described by an empirical potential}, author={Wales, David J and Hodges, Matthew P}, - journal={Chemical physics letters}, + journal={Chem. Phys. Lett.}, volume={286}, number={1-2}, pages={65--72}, @@ -1193,7 +1193,7 @@ year = {1989}} @article{Brown2017, title={Monitoring water clusters “melt” through vibrational spectroscopy}, author={Brown, Sandra E and Götz, Andreas W and Cheng, Xiaolu and Steele, Ryan P and Mandelshtam, Vladimir A and Paesani, Francesco}, - journal={Journal of the American Chemical Society}, + journal={J. Am. Chem. Soc.}, volume={139}, number={20}, pages={7082--7088}, @@ -1203,7 +1203,7 @@ year = {1989}} @article{Prell2009, title={Structures of thermal, mass-selected water clusters probed with hydrophobic ion tags and infrared photodissociation spectroscopy}, author={Prell, James S and Williams, Evan R}, - journal={Journal of the American Chemical Society}, + journal={J. Am. Chem. Soc.}, volume={131}, number={11}, pages={4110--4119}, @@ -1211,9 +1211,9 @@ year = {1989}} publisher={ACS Publications}} @article{James2005, - title={Global minima for water clusters (H2O)n, n$\leqslant$ 21, described by a five-site empirical potential}, + title={Global minima for water clusters (H$_2$O)$_n$, n$\leqslant$ 21, described by a five-site empirical potential}, author={James, Tim and Wales, David J and Hern{\'a}ndez-Rojas, Javier}, - journal={Chemical Physics Letters}, + journal={Chem. Phys. Lett.}, volume={415}, number={4-6}, pages={302--307}, @@ -1223,7 +1223,7 @@ year = {1989}} @article{Pedulla1998, title={Theoretical study of the n-body interaction energies of the ring, cage and prism forms of (H2O)6}, author={Pedulla, JM and Kim, K and Jordan, KD}, - journal={Chemical physics letters}, + journal={Chem. Phys. Lett.}, volume={291}, number={1-2}, pages={78--84}, @@ -1233,7 +1233,7 @@ year = {1989}} @article{Teeter1984, title={Water structure of a hydrophobic protein at atomic resolution: Pentagon rings of water molecules in crystals of crambin}, author={Teeter, Martha M}, - journal={Proceedings of the National Academy of Sciences}, + journal={Proc. Natl. Acad. Sci.}, volume={81}, number={19}, pages={6014--6018}, @@ -1242,8 +1242,8 @@ year = {1989}} @article{Shields2010, author = {Shields, Robert M. and Temelso, Berhane and Archer, Kaye A. and Morrell, Thomas E. and Shields, George C.}, -title = {Accurate Predictions of Water Cluster Formation, (H2O)n=2-10}, -journal = {The Journal of Physical Chemistry A}, +title = {Accurate predictions of water cluster formation, (H$_2$O)$_{n=2-10}$, +journal = {J. Phys. Chem. 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Theory Comput.}, volume={5}, number={4}, pages={1016--1026}, @@ -1282,7 +1282,7 @@ year = {2010}} @article{Silvestrelli1999, title={Structural, electronic, and bonding properties of liquid water from first principles}, author={Silvestrelli, Pier Luigi and Parrinello, Michele}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={111}, number={8}, pages={3572--3580}, @@ -1292,7 +1292,7 @@ year = {2010}} @article{Silvestrelli2017, title={Hydrogen bonding characterization in water and small molecules}, author={Silvestrelli, Pier Luigi}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={146}, number={24}, pages={244315}, @@ -1302,7 +1302,7 @@ year = {2010}} @article{Yamazoe2019, title={Measurements of ultrafast dissociation in resonant inelastic x-ray scattering of water}, author={Yamazoe, Kosuke and Miyawaki, Jun and Niwa, Hideharu and Nilsson, Anders and Harada, Yoshihisa}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={150}, number={20}, pages={204201}, @@ -1312,7 +1312,7 @@ year = {2010}} @article{Harada2017, title={Probing the OH stretch in different local environments in liquid water}, author={Harada, Y and Miyawaki, J and Niwa, H and Yamazoe, K and Pettersson, Lars GM and Nilsson, Anders}, - journal={The journal of physical chemistry letters}, + journal={J. Phys. Chem. Lett.}, volume={8}, number={22}, pages={5487--5491}, @@ -1322,7 +1322,7 @@ year = {2010}} @article{Pokapanich2009, title={Auger electron spectroscopy as a probe of the solution of aqueous ions}, author={Pokapanich, Wandared and Bergersen, Henrik and Bradeanu, Ioana L and Marinho, Ricardo RT and Lindblad, Andreas and Legendre, Sebastien and Rosso, Aldana and Svensson, Svante and Tchaplyguine, Maxim and Kryzhevoi, Nikolai V and others}, - journal={Journal of the American Chemical Society}, + journal={J. Am. Chem. Soc.}, volume={131}, number={21}, pages={7264--7271}, @@ -1332,7 +1332,7 @@ year = {2010}} @article{Bergmann2007, title={Isotope effects in liquid water probed by x-ray Raman spectroscopy}, author={Bergmann, Uwe and Nordlund, Dennis and Wernet, Ph and Odelius, Michael and Pettersson, Lars GM and Nilsson, Anders}, - journal={Physical Review B}, + journal={Phys. Rev. B}, volume={76}, number={2}, pages={024202}, @@ -1342,7 +1342,7 @@ year = {2010}} @article{Brubach2005, title={Signatures of the hydrogen bonding in the infrared bands of water}, author={Brubach, J-B and Mermet, Al and Filabozzi, A and Gerschel, A and Roy, P}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={122}, number={18}, pages={184509}, @@ -1372,7 +1372,7 @@ year = {2010}} @article{Sun2010, title={The single donator-single acceptor hydrogen bonding structure in water probed by Raman spectroscopy}, author={Sun, Qiang}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={132}, number={5}, pages={054507}, @@ -1382,7 +1382,7 @@ year = {2010}} @article{Ludwig2001, title={Water: From clusters to the bulk}, author={Ludwig, Ralf}, - journal={Angewandte Chemie International Edition}, + journal={Angew. Chem. Int. Ed. }, volume={40}, number={10}, pages={1808--1827}, @@ -1392,7 +1392,7 @@ year = {2010}} @article{Gregory1996, title={Structure of water clusters. The contribution of many-body forces, monomer relaxation, and vibrational zero-point energy}, author={Gregory, Jonathon K and Clary, David C}, - journal={The Journal of Physical Chemistry}, + journal={J. Phys. Chem.}, volume={100}, number={46}, pages={18014--18022}, @@ -1410,7 +1410,7 @@ year = {2010}} @article{Rapacioli2005stacked, title={Stacked clusters of polycyclic aromatic hydrocarbon molecules}, author={Rapacioli, M and Calvo, Florent and Spiegelman, Fernand and Joblin, C and Wales, DJ}, - journal={The Journal of Physical Chemistry A}, + journal={J. Phys. Chem. A}, volume={109}, number={11}, pages={2487--2497}, @@ -1420,7 +1420,7 @@ year = {2010}} @article{Siedschlag2004, title={Small rare-gas clusters in soft x-ray pulses}, author={Siedschlag, Christian and Rost, Jan-Michael}, - journal={Physical review letters}, + journal={Phys. 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A}, volume={118}, number={29}, pages={5464--5473}, @@ -1510,7 +1510,7 @@ year = {2010}} @article{Caleman2007, title={Evaporation from water clusters containing singly charged ions}, author={Caleman, Carl and van der Spoel, David}, - journal={Physical Chemistry Chemical Physics}, + journal={Phys. Chem. Chem. Phys.}, volume={9}, number={37}, pages={5105--5111}, @@ -1520,7 +1520,7 @@ year = {2010}} @article{Zhong2000, title={An ultrafast glimpse of cluster solvation effects on reaction dynamics}, author={Zhong, Q and Castleman, AWa}, - journal={Chemical reviews}, + journal={Chem. Rev.}, volume={100}, number={11}, pages={4039--4058}, @@ -1530,7 +1530,7 @@ year = {2010}} @article{Pinkard2018, title={Molecular clusters: nanoscale building blocks for solid-state materials}, author={Pinkard, Andrew and Champsaur, Anouck M and Roy, Xavier}, - journal={Accounts of chemical research}, + journal={Acc. Chem. Res.}, volume={51}, number={4}, pages={919--929}, @@ -1540,7 +1540,7 @@ year = {2010}} @article{Castleman1978the, title={The properties of ion clusters and their relationship to heteromolecular nucleation}, author={Castleman Jr, AW and Holland, Paul M and Keesee, Robert G}, - journal={The Journal of Chemical Physics}, + journal={J. Chem. Phys.}, volume={68}, number={4}, pages={1760--1767}, @@ -1554,7 +1554,7 @@ year = {2010}} @article{Haag2009, author={N Haag and B Liu and S Br{\o}ndsted Nielsen and H Zettergren and P Hvelplund and B Manil and B A Huber and H A B Johansson and H T Schmidt and H Cederquist}, title = {Collisions with biomolecules embedded in small water clusters}, - journal = {Journal of Physics: Conference Series}, + journal = {J. Phys. Conf. Ser.}, year = 2009, month = {nov}, publisher = {{IOP} Publishing}, @@ -1563,7 +1563,7 @@ year = {2010}} pages = {012053}} @article{Carl2013, - title={Hreshold Collision-Induced Dissociation of Hydrated magnesium: Experimental and Theoretical Investigation of the Binding Energies for Mg$^{2+}$(H$_2$O)$_x$ complexes (x= 2--10)}, + title={Hreshold collision-induced dissociation of hydrated magnesium: experimental and theoretical investigation of the binding energies for Mg$^{2+}$(H$_2$O)$_x$ complexes (x= 2--10)}, author={Carl, Damon R and Armentrout, Peter B}, journal={ChemPhysChem}, volume={14}, @@ -1574,9 +1574,9 @@ year = {2010}} } @article{Bobbert2002, - title={Fragmentation and Reliable Size Distributions of Large Ammonia and Water Clusters}, + title={Fragmentation and reliable size distributions of large ammonia and water clusters}, author={Bobbert, C and Sch{\"u}tte, S and Steinbach, C and Buck, U}, - journal={The European Phys. Rev. A Journal D-Atomic, Molecular, Optical and Plasma Physics}, + journal={Eur. Phys. J. D}, volume={19}, number={2}, pages={183--192}, @@ -1584,7 +1584,7 @@ year = {2010}} publisher={Springer}} @article{Li1992, - title={Toluene--Water Clusters: Ion Fragmentation and Chemistry}, + title={Toluene-water clusters: Ion fragmentation and chemistry}, author={Li, Shijian and Bernstein, Elliot R}, journal={J. Chem. Phys.}, volume={97}, @@ -1793,7 +1793,7 @@ Unique-ID = {{ISI:000240872700020}}, @article{Mcquinn2009, - title={Collision-Induced Dissociation of Protonated Nanodroplets}, + title={Collision-induced dissociation of protonated nanodroplets}, author={McQuinn, Keri and Hof, Fraser and McIndoe, J Scott}, journal={ Int. J. Mass Spectrom.}, volume={279}, @@ -1870,13 +1870,13 @@ Unique-ID = {{ISI:000240872700020}}, Number = {19}, Pages = {3629--3646}, Publisher = {ACS Publications}, - Title = {Thermochemical Investigations of Hydrated Nickel Dication Complexes by Threshold Collision-Induced Dissociation and Theory}, + Title = {Thermochemical investigations of hydrated nickel dication complexes by threshold collision-induced dissociation and theory}, Volume = {121}, Year = {2017}} @article{Hofstetter2013, author = {Hofstetter, Theresa E. and Armentrout, P. B.}, -title = {Threshold Collision-Induced Dissociation and Theoretical Studies of Hydrated Fe(II): Binding Energies and Coulombic Barrier Heights}, +title = {Threshold collision-induced dissociation and theoretical studies of hydrated Fe(II): binding energies and coulombic barrier heights}, journal = {J. Phys. Chem. A}, volume = {117}, number = {6}, @@ -1889,7 +1889,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Chowdhury2009, title={Identification of cross-linked peptides after click-based enrichment using sequential collision-induced dissociation and electron transfer dissociation tandem mass spectrometry}, author={Chowdhury, Saiful M and Du, Xiuxia and Tolic, Nikola and Wu, Si and Moore, Ronald J and Mayer, M Uljana and Smith, Richard D and Adkins, Joshua N}, - journal={Analytical chemistry}, + journal={Anal. Chem.}, volume={81}, number={13}, pages={5524--5532}, @@ -1899,7 +1899,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Ma1997, title={Characterization of flavone and flavonol aglycones by collision-induced dissociation tandem mass spectrometry}, author={Ma, YL and Li, QM and Van den Heuvel, H and Claeys, M}, - journal={Rapid communications in mass spectrometry}, + journal={Rapid Commun. Mass }, volume={11}, number={12}, pages={1357--1364}, @@ -1908,7 +1908,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @incollection{Hayes1990, Author = {Hayes, Roger N and Gross, Michael L}, - Booktitle = {Methods in Enzymology}, + Booktitle = {Methods Enzymol.}, Pages = {237--263}, Publisher = {Elsevier}, Title = {[10] Collision-induced dissociation}, @@ -1922,7 +1922,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Braud2017, title={A gas aggregation source for the production of heterogeneous molecular clusters}, author={Braud, Isabelle and Zamith, S{\'e}bastien and L’Hermite, J-M}, - journal={Review of Scientific Instruments}, + journal={Rev. Sci. Instrum.}, volume={88}, number={4}, pages={043102}, @@ -1932,7 +1932,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Chirot2006new, title={New device to study unimolecular cluster nucleation}, author={Chirot, Fabien and Zamith, S{\'e}bastien and Labastie, Pierre and L’Hermite, J-M}, - journal={Review of scientific instruments}, + journal={Rev. Sci. Instrum.}, volume={77}, number={6}, pages={063108}, @@ -1942,7 +1942,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Armentrout2007, title={Statistical modeling of sequential collision-induced dissociation thresholds}, author={Armentrout, PB}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={126}, number={23}, pages={234302}, @@ -1952,7 +1952,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Rodgers1998, title={Statistical modeling of competitive threshold collision-induced dissociation}, author={Rodgers, MT and Armentrout, PB}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={109}, number={5}, pages={1787--1800}, @@ -1962,7 +1962,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Armentrout2008, title={Statistical rate theory and kinetic energy-resolved ion chemistry: theory and applications}, author={Armentrout, PB and Ervin, Kent M and Rodgers, MT}, - journal={The Journal of Physical Chemistry A}, + journal={J. Phys. Chem. A}, volume={112}, number={41}, pages={10071--10085}, @@ -1972,7 +1972,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Braud2019, title={Size-dependent proton localization in hydrated uracil clusters: A joint experimental and theoretical study}, author={Braud, Isabelle and Zamith, S{\'e}bastien and Cuny, J{\'e}r{\^o}me and Zheng, Linjie and L’Hermite, Jean-Marc}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={150}, number={1}, pages={014303}, @@ -1982,7 +1982,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Laskin2005, title={Activation of large lons in FT-ICR mass spectrometry}, author={Laskin, Julia and Futrell, Jean H}, - journal={Mass spectrometry reviews}, + journal={Mass Spectrom. Rev.}, volume={24}, number={2}, pages={135--167}, @@ -1992,7 +1992,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Hart2011, title={Detection and characterization of low abundance glycopeptides via higher-energy C-trap dissociation and orbitrap mass analysis}, author={Hart-Smith, Gene and Raftery, Mark J}, - journal={Journal of the American Society for Mass Spectrometry}, + journal={J. Am. Soc. Mass Spectrom.}, volume={23}, number={1}, pages={124--140}, @@ -2002,7 +2002,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Olsen2007higher, title={Higher-energy C-trap dissociation for peptide modification analysis}, author={Olsen, Jesper V and Macek, Boris and Lange, Oliver and Makarov, Alexander and Horning, Stevan and Mann, Matthias}, - journal={Nature methods}, + journal={Nat. Methods.}, volume={4}, number={9}, pages={709--712}, @@ -2012,7 +2012,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Cody1982, title={Collision-induced dissociation with Fourier transform mass spectrometry}, author={Cody, RB and Burnier, RC and Freiser, BS}, - journal={Analytical chemistry}, + journal={Anal. Chem.}, volume={54}, number={1}, pages={96--101}, @@ -2022,7 +2022,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Gauthier1991, title={Sustained off-resonance irradiation for collision-activated dissociation involving Fourier transform mass spectrometry. Collision-activated dissociation technique that emulates infrared multiphoton dissociation}, author={Gauthier, JW and Trautman, TR and Jacobson, DB}, - journal={Analytica Chimica Acta}, + journal={Anal. Chim. Acta}, volume={246}, number={1}, pages={211--225}, @@ -2032,7 +2032,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Sleno2004ion, title={Ion activation methods for tandem mass spectrometry}, author={Sleno, Lekha and Volmer, Dietrich A}, - journal={Journal of mass spectrometry}, + journal={J. Mass Spectrom.}, volume={39}, number={10}, pages={1091--1112}, @@ -2042,7 +2042,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Boering1992, title={Low energy collision induced dissociation: phase-shifting excitation control of ion kinetic energy in ion cyclotron resonance spectrometry}, author={Boering, Kristie A and Rolfe, Joseph and Brauman, John I}, - journal={International journal of mass spectrometry and ion processes}, + journal={Int. J. Mass Spectrom. Ion Processes}, volume={117}, pages={357--386}, year={1992}, @@ -2051,7 +2051,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Wells2005, title={Collision-induced dissociation (CID) of peptides and proteins}, author={Wells, J Mitchell and McLuckey, Scott A}, - journal={Methods in enzymology}, + journal={Methods Enzymol.}, volume={402}, pages={148--185}, year={2005}, @@ -2060,7 +2060,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Bush2008, title={Reactivity and infrared spectroscopy of gaseous hydrated trivalent metal ions}, author={Bush, Matthew F and Saykally, Richard J and Williams, Evan R}, - journal={Journal of the American Chemical Society}, + journal={J. Am. Chem. Soc.}, volume={130}, number={28}, pages={9122--9128}, @@ -2068,9 +2068,9 @@ eprint = {https://doi.org/10.1021/jp3044829}} publisher={ACS Publications}} @article{Wong2004, - title={Blackbody infrared radiative dissociation at low temperature: Hydration of X2+ (H2O) n, for X= Mg, Ca}, + title={Blackbody infrared radiative dissociation at low temperature: Hydration of X$^{2+}$(H$_2$O)$_n$, for X= Mg, Ca}, author={Wong, Richard L and Paech, Kolja and Williams, Evan R}, - journal={International Journal of Mass Spectrometry}, + journal={International J. Mass Spectrom.}, volume={232}, number={1}, pages={59--66}, @@ -2080,7 +2080,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Brechignac1994, title={Dissociation pathways and binding energies of lithium clusters from evaporation experiments}, author={Br{\'e}chignac, C and Busch, H and Cahuzac, Ph and Leygnier, J}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={101}, number={8}, pages={6992--7002}, @@ -2090,7 +2090,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Brechignac1989, title={Dynamics of unimolecular dissociation of sodium cluster ions}, author={Br{\'e}chignac, C and Cahuzac, Ph and Leygnier, J and Weiner, J}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={90}, number={3}, pages={1492--1498}, @@ -2100,7 +2100,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Kruckeberg1999, title={Multiple-collision induced dissociation of trapped silver clusters Ag n+(2 $\leqslant$ n $\leqslant$ 25)}, author={Kr{\"u}ckeberg, S and Dietrich, G and L{\"u}tzenkirchen, K and Schweikhard, L and Walther, C and Ziegler, J}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={110}, number={15}, pages={7216--7227}, @@ -2119,7 +2119,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Spasov2000, title={Threshold collision-induced dissociation of anionic copper clusters and copper cluster monocarbonyls}, author={Spasov, Vassil A and Lee, Taeck-Hong and Ervin, Kent M}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={112}, number={4}, pages={1713--1720}, @@ -2129,7 +2129,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Kambara1977, title={Collision-induced dissociation of water cluster ions at high pressure}, author={Kambara, H and Kanomata, I}, - journal={International Journal of Mass Spectrometry and Ion Physics}, + journal={Int. J. Mass Spectrom.}, volume={25}, number={2}, pages={129--136}, @@ -2139,7 +2139,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Zha2013, title={High-pressure measurements of hydrogen phase IV using synchrotron infrared spectroscopy}, author={Zha, Chang-sheng and Liu, Zhenxian and Ahart, Muhtar and Boehler, Reinhard and Hemley, Russell J}, - journal={Physical review letters}, + journal={Phys. Rev. Lett.}, volume={110}, number={21}, pages={217402}, @@ -2149,7 +2149,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Howie2012, title={Mixed molecular and atomic phase of dense hydrogen}, author={Howie, Ross T and Guillaume, Christophe L and Scheler, Thomas and Goncharov, Alexander F and Gregoryanz, Eugene}, - journal={Physical Review Letters}, + journal={Phys. Rev. Lett.}, volume={108}, number={12}, pages={125501}, @@ -2169,7 +2169,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Azadi2014, title={Dissociation of high-pressure solid molecular hydrogen: A quantum Monte Carlo and anharmonic vibrational study}, author={Azadi, Sam and Monserrat, Bartomeu and Foulkes, WMC and Needs, RJ}, - journal={Physical review letters}, + journal={Phys. Rev. Lett.}, volume={112}, number={16}, pages={165501}, @@ -2179,7 +2179,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{li2018high, title={High-pressure dissociation of selenium and tellurium}, author={Li, Xin and Huang, Xiaoli and Wang, Xin and Liu, Mingkun and Wu, Gang and Huang, Yanping and He, Xin and Li, Fangfei and Zhou, Qiang and Liu, Bingbing and others}, - journal={Physical Chemistry Chemical Physics}, + journal={Phys. Chem. Chem. Phys.}, volume={20}, number={9}, pages={6116--6120}, @@ -2199,7 +2199,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Gao2010, title={Dissociation of methane under high pressure}, author={Gao, Guoying and Oganov, Artem R and Ma, Yanming and Wang, Hui and Li, Peifang and Li, Yinwei and Iitaka, Toshiaki and Zou, Guangtian}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={133}, number={14}, pages={144508}, @@ -2220,19 +2220,19 @@ eprint = {https://doi.org/10.1021/jp3044829}} publisher={APS}} @article{Zundel1968, - title={Energieb{\"a}nder der tunnelnden {\"U}berschu{\ss}-Protonen in fl{\"u}ssigen S{\"a}uren. Eine IR-spektroskopische Untersuchung der Natur der Gruppierungen H5O2+}, + title={Energieb{\"a}nder der tunnelnden {\"U}berschu{\ss}-Protonen in fl{\"u}ssigen S{\"a}uren. Eine IR-spektroskopische Untersuchung der Natur der Gruppierungen H$_5$O$_2^+$}, author={G. Zundel and H. Metzger}, - journal={Zeitschrift f{\"u}r Physikalische Chemie}, + journal={Proc. Z. Phys. Chem.}, year={1968}, volume={58}, - pages={225 - 245}, + pages={225-245}, number={5\_6}, publisher={De Gruyter Oldenbourg}} @article{Homayoon2018, title={Chemical dynamics simulations of CID of peptide ions: comparisons between TIK (H+) 2 and TLK (H+) 2 fragmentation dynamics, and with thermal simulations}, author={Homayoon, Zahra and Macaluso, Veronica and Martin-Somer, Ana and Muniz, Maria Carolina Nicola Barbosa and Borges, Itamar and Hase, William L and Spezia, Riccardo}, - journal={Physical Chemistry Chemical Physics}, + journal={Phys. Chem. Chem. Phys.}, volume={20}, number={5}, pages={3614--3629}, @@ -2242,7 +2242,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Spezia2009, title={Protonated urea collision-induced dissociation. Comparison of experiments and chemical dynamics simulations}, author={Spezia, Riccardo and Salpin, Jean-Yves and Gaigeot, Marie-Pierre and Hase, William L and Song, Kihyung}, - journal={The Journal of Physical Chemistry A}, + journal={J. Phys. Chem. A}, volume={113}, number={50}, pages={13853--13862}, @@ -2254,14 +2254,14 @@ eprint = {https://doi.org/10.1021/jp3044829}} publisher = {{IOP} Publishing}, Pages = {012005}, Title = {Ion interaction with biomolecular systems and the effect of the environment}, - journal = {Journal of Physics: Conference Series}, + journal = {J. Phys. Conf. Ser.}, Volume = {373}, Year = {2012}} @article{Wolken2000, title={Proton affinity of uracil. A computational study of protonation sites}, author={Wolken, Jill K and Ture{\v{c}}ek, Franti{\v{s}}ek}, - journal={Journal of the American Society for Mass Spectrometry}, + journal={J. Am. Soc. Mass Spectrom.}, volume={11}, number={12}, pages={1065--1071}, @@ -2271,7 +2271,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Cheng1998, title={Water clusters: fascinating hydrogen-bonding networks, solvation shell structures, and proton motion}, author={Cheng, Hai-Ping}, - journal={The Journal of Physical Chemistry A}, + journal={J. Phys. Chem. A}, volume={102}, number={31}, pages={6201--6204}, @@ -2281,7 +2281,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Magnera1991, title={The first twenty-eight gas-phase proton hydration energies}, author={Magnera, Thomas F and David, Donald E and Michl, Josef}, - journal={Chemical physics letters}, + journal={Chem. Phys. Lett.}, volume={182}, number={3-4}, pages={363--370}, @@ -2301,7 +2301,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Wincel2009, title={Microhydration of protonated nucleic acid bases and protonated nucleosides in the gas phase}, author={Wincel, Henryk}, - journal={Journal of the American Society for Mass Spectrometry}, + journal={J. Am. Soc. Mass Spectrom.}, volume={20}, number={10}, pages={1900--1905}, @@ -2311,7 +2311,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Hansen2009, title={Activation energies for evaporation from protonated and deprotonated water clusters from mass spectra}, author={Hansen, K and Andersson, PU and Uggerud, E}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={131}, number={12}, pages={124303}, @@ -2327,7 +2327,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Zamith2012, title={Fragmentation cross sections of protonated water clusters}, author={Zamith, S{\'e}bastien and Labastie, Pierre and l'Hermite, Jean-Marc}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={136}, number={21}, pages={214301}, @@ -2337,7 +2337,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Dalleska1993, title={Stepwise solvation enthalpies of protonated water clusters: Collision-induced dissociation as an alternative to equilibrium studies}, author={Dalleska, NF and Honma, Kenji and Armentrout, PB}, - journal={Journal of the American Chemical Society}, + journal={J. Am. Chem. Soc.}, volume={115}, number={25}, pages={12125--12131}, @@ -2356,7 +2356,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Bacchus2015, title={Nanohydration of uracil: emergence of three-dimensional structures and proton-induced charge transfer}, author={Bacchus-Montabonel, Marie-Christine and Calvo, Florent}, - journal={Physical Chemistry Chemical Physics}, + journal={Phys. Chem. Chem. Phys.}, volume={17}, number={15}, pages={9629--9633}, @@ -2366,7 +2366,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Danilov2006, title={Modeling of the 'hydration shell' of uracil and thymine in small water clusters by DFT and MP2 methods}, author={Danilov, Victor I and van Mourik, Tanja and Poltev, Valery I}, - journal={Chemical physics letters}, + journal={Chem. Phys. Lett.}, volume={429}, number={1-3}, pages={255--260}, @@ -2376,7 +2376,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Gaigeot2001, title={Geometrical and Vibrational Properties of Nucleic Acid Constituents Interacting with Explicit Water Molecules as Analyzed by Density Functional Theory Calculations. 1. Uracil + n$_w$H$_2$O (n$_w$= 1, ..., 7)}, author={Gaigeot, Marie-Pierre and Ghomi, Mahmoud}, - journal={The Journal of Physical Chemistry B}, + journal={J. Phys. Chem. B}, volume={105}, number={21}, pages={5007--5017}, @@ -2386,7 +2386,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Gadre2000, title={Electrostatics for exploring hydration patterns of molecules. 3. Uracil}, author={Gadre, Shridhar R and Babu, K and Rendell, Alistair P}, - journal={The Journal of Physical Chemistry A}, + journal={J. Phys. Chem. A}, volume={104}, number={39}, pages={8976--8982}, @@ -2396,7 +2396,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Shishkin2000, title={Modeling of the hydration shell of uracil and thymine}, author={Shishkin, Oleg V and Gorb, Leonid and Leszczynski, Jerzy}, - journal={International Journal of Molecular Sciences}, + journal={Int. J. Mol. Sci.}, volume={1}, number={2}, pages={17--27}, @@ -2409,7 +2409,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} Number = {48}, Pages = {12393--12400}, Publisher = {ACS Publications}, - Title = {Tautomerism of Uracil Probed via Infrared Spectroscopy of Singly Hydrated Protonated Uracil}, + Title = {Tautomerism of uracil probed via infrared spectroscopy of singly hydrated protonated uracil}, Volume = {112}, Year = {2008}} @@ -2419,7 +2419,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} Number = {30}, Pages = {19807--19814}, Publisher = {Royal Society of Chemistry}, - Title = {Fragmentation of Pure and Hydrated Clusters of 5Br-Uracil by Low Energy Carbon Ions: Observation of Hydrated Fragments}, + Title = {Fragmentation of pure and hydrated clusters of 5br-uracil by low energy carbon ions: observation of hydrated fragments}, Volume = {19}, Year = {2017}} @@ -2429,13 +2429,13 @@ eprint = {https://doi.org/10.1021/jp3044829}} Number = {25}, Pages = {16721--16729}, Publisher = {Royal Society of Chemistry}, - Title = {The Role of the Environment in the Ion Induced Fragmentation of Uracil}, + Title = {The role of the environment in the ion induced fragmentation of Uracil}, Volume = {18}, Year = {2016}} @inproceedings{Domaracka2012, Author = {Domaracka, Alicja and Capron, Michael and Maclot, Sylvain and Chesnel, Jean-Yves and M{\'e}ry, Alain and Poully, Jean-Christophe and Rangama, Jimmy and Adoui, Lamri and Rousseau, Patrick and Huber, Bernd A}, - Booktitle = {Journal of Physics: Conference Series}, + Booktitle = {J. Phys. Conf. Ser.}, Number = {1}, Organization = {IOP Publishing}, Pages = {012005}, @@ -2450,7 +2450,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} Number = {5}, Pages = {930--936}, Publisher = {Wiley Online Library}, - Title = {Ion-Induced Fragmentation of Amino Acids: Effect of the Environment}, + Title = {Ion-induced fragmentation of amino acids: effect of the environment}, Volume = {12}, Year = {2011}} @@ -2476,7 +2476,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Alizadeh2013, title={Radiation damage to DNA: The indirect effect of low-energy electrons}, author={Alizadeh, Elahe and Sanz, Ana G and Garcia, Gustavo and Sanche, Leon}, - journal={The journal of physical chemistry letters}, + journal={J. Phys. Chem. Lett.}, volume={4}, number={5}, pages={820--825}, @@ -2486,7 +2486,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Siefermann2011, title={The hydrated electron: a seemingly familiar chemical and biological transient}, author={Siefermann, Katrin R and Abel, Bernd}, - journal={Angewandte Chemie International Edition}, + journal={Angew. Chem. Int. Ed. }, volume={50}, number={23}, pages={5264--5272}, @@ -2496,7 +2496,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Smyth2011, title={Excess electron localization in solvated DNA bases}, author={Smyth, Maeve and Kohanoff, Jorge}, - journal={Physical review letters}, + journal={Phys. Rev. Lett.}, volume={106}, number={23}, pages={238108}, @@ -2505,11 +2505,11 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Rasmussen2010, Author = {Rasmussen, Andrew M and Lind, Maria C and Kim, Sunghwan and Schaefer III, Henry F}, - Journal = {Journal of chemical theory and computation}, + Journal = {J. Chem. Theory Comput.}, Number = {3}, Pages = {930--939}, Publisher = {ACS Publications}, - Title = {Hydration of the Lowest Triplet States of the DNA/RNA Pyrimidines}, + Title = {Hydration of the lowest triplet states of the DNA/RNA pyrimidines}, Volume = {6}, Year = {2010}} @@ -2525,7 +2525,7 @@ eprint = {https://doi.org/10.1021/jp3044829}} @article{Pedersen2014, Author = {Pedersen, Sara {\O}vad and Byskov, Camilla Skinnerup and Turecek, Frantisek and Nielsen, Steen Br{\o}ndsted}, - Journal = {The Journal of Physical Chemistry A}, + Journal = {J. Phys. Chem. A}, Number = {24}, Pages = {4256--4265}, Publisher = {ACS Publications}, @@ -2546,7 +2546,7 @@ note ={PMID: 32696649}, URL = {https://doi.org/10.1021/acs.jpcb.0c04167}} @article{Simon2019, - title={Contribution of the Density-Functional-Based Tight-Binding Scheme to the Description of Water Clusters: Methods, Applications and Extension to Bulk Systems}, + title={Contribution of the density-functional-based tight-binding scheme to the description of water clusters: methods, applications and extension to bulk systems}, author={Simon, Aude and Rapacioli, Mathias and Michoulier, Eric and Zheng, Linjie and Korchagina, Kseniia and Cuny, J{\'e}r{\^o}me}, journal={Mol. Simul.}, volume={45}, @@ -2567,7 +2567,7 @@ URL = {https://doi.org/10.1021/acs.jpcb.0c04167}} @article{Korchagina2016, author = {Korchagina, Kseniia A. and Simon, Aude and Rapacioli, Mathias and Spiegelman, Fernand and Cuny, Jérôme}, -title = {Structural Characterization of Sulfur-Containing Water Clusters Using a Density-Functional Based Tight-Binding Approach}, +title = {Structural characterization of sulfur-containing water clusters using a density-functional based tight-binding approach}, journal = {J. Phys. Chem. A}, volume = {120}, number = {45}, @@ -2596,7 +2596,7 @@ year = {2016}} @article{Sugita2000, title={Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape}, author={Sugita, Yuji and Okamoto, Yuko}, - journal={Chemical Physics Letters}, + journal={Chem. Phys. Lett.}, volume={329}, number={3-4}, pages={261--270}, @@ -2609,7 +2609,7 @@ year = {2016}} Number = {9}, Pages = {1057--1065}, Publisher = {Royal Society of Chemistry}, - Title = {Accurate Coulomb-Fitting Basis Sets for H to Rn}, + Title = {Accurate Coulomb-fitting basis sets for H to Rn}, Volume = {8}, Year = {2006}} @@ -2619,7 +2619,7 @@ year = {2016}} Number = {18}, Pages = {3297--3305}, Publisher = {The Royal Society of Chemistry}, - Title = {Balanced Basis Sets of Split Valence, Triple Zeta Valence and Quadruple Zeta Valence Quality for H to Rn: Design and Assessment of Accuracy}, + Title = {Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: design and assessment of accuracy}, Volume = {7}, Year = {2005}} @@ -2649,7 +2649,7 @@ year = {2016}} @article{Rapacioli2018atomic, title={Atomic hydrogen interactions with gas-phase coronene cations: hydrogenation versus fragmentation}, author={Rapacioli, Mathias and Cazaux, St{\'e}phanie and Foley, Nolan and Simon, Aude and Hoekstra, Ronnie and Schlath{\"o}lter, Thomas}, - journal={Physical Chemistry Chemical Physics}, + journal={Phys. Chem. Chem. Phys.}, volume={20}, number={35}, pages={22427--22438}, @@ -2700,7 +2700,7 @@ year = {2016}} @article{Cui2001, title={A QM/MM implementation of the self-consistent charge density functional tight binding (SCC-DFTB) method}, author={Cui, Qiang and Elstner, Marcus and Kaxiras, Efthimios and Frauenheim, Thomas and Karplus, Martin}, - journal={The Journal of Physical Chemistry B}, + journal={J. Phys. Chem. B}, volume={105}, number={2}, pages={569--585}, @@ -2708,9 +2708,9 @@ year = {2016}} publisher={ACS Publications}} @article{Iftner2014, - title={A density functional tight binding/force field approach to the interaction of molecules with rare gas clusters: Application to (C6H6)+/0Ar n clusters}, + title={A density functional tight binding/force field approach to the interaction of molecules with rare gas clusters: Application to (C$_6$H$_6$)$^{+/0}$Ar$_n$ clusters}, author={Iftner, Christophe and Simon, Aude and Korchagina, Kseniia and Rapacioli, Mathias and Spiegelman, Fernand}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={140}, number={3}, pages={034301}, @@ -2726,7 +2726,7 @@ year = {2016}} @article{Gatchell2016knockout, title={Knockout driven reactions in complex molecules and their clusters}, author={Gatchell, Michael and Zettergren, Henning}, - journal={Journal of Physics B: Atomic, Molecular and Optical Physics}, + journal={J. Phys. B}, volume={49}, number={16}, pages={162001}, @@ -2742,7 +2742,7 @@ year = {2016}} @article{Spiegelman2020, title={Density-functional tight-binding: basic concepts and applications to molecules and clusters}, author={Spiegelman, Fernand and Tarrat, Nathalie and Cuny, J{\'e}r{\^o}me and Dontot, Leo and Posenitskiy, Evgeny and Mart{\'\i}, Carles and Simon, Aude and Rapacioli, Mathias}, - journal={Advances in physics: X}, + journal={Adv. Phys. -X}, volume={5}, number={1}, pages={1710252}, @@ -2764,7 +2764,7 @@ year = {2016}} @article{Dontot2016, title={An extended DFTB-CI model for charge-transfer excited states in cationic molecular clusters: model studies versus ab initio calculations in small PAH clusters}, author={Dontot, L{\'e}o and Suaud, Nicolas and Rapacioli, Mathias and Spiegelman, Fernand}, - journal={Physical Chemistry Chemical Physics}, + journal={Phys. Chem. Chem. Phys.}, volume={18}, number={5}, pages={3545--3557}, @@ -2774,7 +2774,7 @@ year = {2016}} @article{Dontot2019, title={Structures and energetics of neutral and cationic pyrene clusters}, author={Dontot, L{\'e}o and Spiegelman, Fernand and Rapacioli, Mathias}, - journal={The Journal of Physical Chemistry A}, + journal={J. Phys. Chem. A}, volume={123}, number={44}, pages={9531--9543}, @@ -2784,7 +2784,7 @@ year = {2016}} @article{Grafenstein2009, title={The self-interaction error and the description of non-dynamic electron correlation in density functional theory}, author={Gr{\"a}fenstein, J{\"u}rgen and Cremer, Dieter}, - journal={Theoretical Chemistry Accounts}, + journal={Theor. Chem. Acc.}, volume={123}, number={3}, pages={171--182}, @@ -2792,9 +2792,10 @@ year = {2016}} publisher={Springer}} @article{Ricca2013, - title={The Infrared Spectroscopy of Neutral Polycyclic Aromatic Hydrocarbon Clusters}, + title={The infrared spectroscopy of neutral polycyclic aromatic hydrocarbon clusters}, author={Ricca, Alessandra and Bauschlicher Jr, Charles W and Allamandola, Louis J}, - journal={The Astrophysical Journal}, + journal={Astrophys. J. +}, volume={776}, number={1}, pages={31}, @@ -2817,7 +2818,7 @@ year = {2016}} Date-Modified = {2019-07-24 05:49:59 +0000}, Journal = {J. Phys. Chem. C}, Pages = {4061-4067}, - Title = {A Prototype for Graphene Material Simulation; Structures and Interaction Potentials of Coronene Dimers}, + Title = {A Prototype for graphene material simulation; structures and interaction potentials of coronene dimers}, Type = {doi:10.1021/jp710918f}, Url = {http://pubs.acs.org/doi/abs/10.1021/jp710918f}, Volume = {112}, @@ -2827,7 +2828,7 @@ year = {2016}} @article{Piacenza2005, title={Van der Waals complexes of polar aromatic molecules: Unexpected structures for dimers of azulene}, author={Piacenza, Manuel and Grimme, Stefan}, - journal={Journal of the American Chemical Society}, + journal={J. Am. Chem. Soc.}, volume={127}, number={42}, pages={14841--14848}, @@ -2837,7 +2838,7 @@ year = {2016}} @article{Birer2015, title={Dimer formation of perylene: An ultracold spectroscopic and computational study}, author={Birer, {\"O} and Yurtsever, E}, - journal={Journal of Molecular Structure}, + journal={J. Mol. Struct.}, volume={1097}, pages={29--36}, year={2015}, @@ -2846,7 +2847,7 @@ year = {2016}} @article{Yurtsever2010, title={Stacking of triphenylene: characterization of the potential energy surface}, author={Yurtsever, Ersin}, - journal={Theoretical Chemistry Accounts}, + journal={Theor. Chem. Acc.}, volume={127}, number={3}, pages={133--139}, @@ -2856,7 +2857,7 @@ year = {2016}} @article{Zamith2020threshold, title={Threshold collision induced dissociation of pyrene cluster cations}, author={Zamith, S{\'e}bastien and L’hermite, Jean-Marc and Dontot, L{\'e}o and Zheng, Linjie and Rapacioli, Mathias and Spiegelman, Fernand and Joblin, Christine}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={153}, number={5}, pages={054311}, @@ -2866,7 +2867,8 @@ year = {2016}} @article{Chen2018, title={Formation of covalently bonded polycyclic aromatic hydrocarbons in the interstellar medium}, author={Chen, Tao}, - journal={The Astrophysical Journal}, + journal={Astrophys. J. +}, volume={866}, number={2}, pages={113}, @@ -2876,7 +2878,8 @@ year = {2016}} @article{Zhen2018, title={Laboratory photochemistry of pyrene clusters: An efficient way to form large PAHs}, author={Zhen, Junfeng and Chen, Tao and Tielens, Alexander GGM}, - journal={The Astrophysical Journal}, + journal={Astrophys. J. +}, volume={863}, number={2}, pages={128}, @@ -2886,7 +2889,7 @@ year = {2016}} @article{Delaunay2015, title={Molecular growth inside of polycyclic aromatic hydrocarbon clusters induced by ion collisions}, author={Delaunay, Rudy and Gatchell, Michael and Rousseau, Patrick and Domaracka, Alicja and Maclot, Sylvain and Wang, Yang and Stockett, Mark H and Chen, Tao and Adoui, Lamri and Alcam{\'\i}, Manuel and others}, - journal={The journal of physical chemistry letters}, + journal={J. Phys. Chem. Lett.}, volume={6}, number={9}, pages={1536--1542}, @@ -2895,8 +2898,8 @@ year = {2016}} @article{Holm2010, title={Ions colliding with cold polycyclic aromatic hydrocarbon clusters}, - author={Holm, Anne IS and Zettergren, Henning and Johansson, Henrik AB and Seitz, Fabian and Rosen, Stefan and Schmidt, Henning T and {\L}awicki, A and Rangama, Jimmy and Rousseau, Patrick and Capron, Micha{\"e}l and others}, - journal={Physical review letters}, + author={Holm, Anne I S and Zettergren, Henning and Johansson, Henrik AB and Seitz, Fabian and Rosen, Stefan and Schmidt, Henning T and {\L}awicki, A and Rangama, Jimmy and Rousseau, Patrick and Capron, Micha{\"e}l and others}, + journal={Phys. Rev. Lett.}, volume={105}, number={21}, pages={213401}, @@ -2906,7 +2909,7 @@ year = {2016}} @article{Gatchell2015, title={Failure of hydrogenation in protecting polycyclic aromatic hydrocarbons from fragmentation}, author={Gatchell, Michael and Stockett, Mark H and de Ruette, Nathalie and Chen, Tao and Giacomozzi, Linda and Nascimento, Rodrigo F and Wolf, Michael and Anderson, Emma K and Delaunay, Rudy and Vizcaino, Violaine and others}, - journal={Physical Review A}, + journal={Phys. Rev. A}, volume={92}, number={5}, pages={050702}, @@ -2916,7 +2919,7 @@ year = {2016}} @article{Lemmens2019, title={Far-IR and UV spectral signatures of controlled complexation and microhydration of the polycyclic aromatic hydrocarbon acenaphthene}, author={Lemmens, Alexander K and Gruet, S{\'e}bastien and Steber, Amanda L and Antony, Jens and Grimme, Stefan and Schnell, Melanie and Rijs, Anouk M}, - journal={Physical Chemistry Chemical Physics}, + journal={Phys. Chem. Chem. Phys.}, volume={21}, number={7}, pages={3414--3422}, @@ -2926,7 +2929,8 @@ year = {2016}} @article{Roser2015, title={Polycyclic aromatic hydrocarbon clusters as sources of interstellar infrared emission}, author={Roser, JE and Ricca, A}, - journal={The Astrophysical Journal}, + journal={Astrophys. J. +}, volume={801}, number={2}, pages={108}, @@ -2936,7 +2940,7 @@ year = {2016}} @article{Joblin2017, title={Size effect in the ionization energy of PAH clusters}, author={Joblin, Christine and Dontot, L{\'e}o and Garcia, GA and Spiegelman, Fernand and Rapacioli, Mathias and Nahon, Laurent and Parneix, Pascal and Pino, T and Br{\'e}chignac, P}, - journal={The journal of physical chemistry letters}, + journal={J. Phys. Chem. Lett.}, volume={8}, number={15}, pages={3697--3702}, @@ -2946,7 +2950,7 @@ year = {2016}} @article{Schmidt2006, title={Coronene cluster experiments: Stability and thermodynamics}, author={Schmidt, Martin and Masson, Albert and Br{\'e}chignac, Catherine}, - journal={International Journal of Mass Spectrometry}, + journal={International J. Mass Spectrom.}, volume={252}, number={2}, pages={173--179}, @@ -2956,7 +2960,7 @@ year = {2016}} @article{Eschenbach1998, title={Fate and stability of nonextractable residues of [14C] PAH in contaminated soils under environmental stress conditions}, author={Eschenbach, Annette and Wienberg, Reinhard and Mahro, Bernd}, - journal={Environmental science \& technology}, + journal={Environ. Sci. Technol.}, volume={32}, number={17}, pages={2585--2590}, @@ -2964,9 +2968,9 @@ year = {2016}} publisher={ACS Publications}} @article{Lei2019, - title={Electron Diffraction of Pyrene Nanoclusters Embedded in Superfluid Helium Droplets}, + title={Electron diffraction of pyrene nanoclusters embedded in superfluid helium droplets}, author={Lei, Lei and Yao, Yuzhong and Zhang, Jie and Tronrud, Dale and Kong, Wei and Zhang, Chengzhu and Xue, Lan and Dontot, L{\'e}o and Rapacioli, Mathias}, - journal={The journal of physical chemistry letters}, + journal={J. Phys. Chem. Lett.}, volume={11}, number={3}, pages={724--729}, @@ -2976,7 +2980,7 @@ year = {2016}} @article{Goulart2017, title={The structure of coronene cluster ions inferred from H 2 uptake in the gas phase}, author={Goulart, Marcelo and Kuhn, Martin and Rasul, Bilal and Postler, Johannes and Gatchell, Michael and Zettergren, Henning and Scheier, Paul and Echt, Olof}, - journal={Physical Chemistry Chemical Physics}, + journal={Phys. Chem. Chem. Phys.}, volume={19}, number={41}, pages={27968--27973}, @@ -2986,7 +2990,7 @@ year = {2016}} @article{Kyrtopoulos2001, title={Biomarkers of genotoxicity of urban air pollution: overview and descriptive data from a molecular epidemiology study on populations exposed to moderate-to-low levels of polycyclic aromatic hydrocarbons: the AULIS project}, author={Kyrtopoulos, SA and Georgiadis, Panagiotis and Autrup, H and Demopoulos, N and Farmer, P and Haugen, A and Katsouyanni, K and Lambert, B and Ovrebo, S and Sram, R and others}, - journal={Mutation Research/Genetic Toxicology and Environmental Mutagenesis}, + journal={Mutat. Res. Genet. Toxicol. Environ.}, volume={496}, number={1-2}, pages={207--228}, @@ -2996,7 +3000,7 @@ year = {2016}} @article{Farmer2003, title={Molecular epidemiology studies of carcinogenic environmental pollutants: effects of polycyclic aromatic hydrocarbons (PAHs) in environmental pollution on exogenous and oxidative DNA damage}, author={Farmer, Peter B and Singh, Rajinder and Kaur, Balvinder and Sram, Radim J and Binkova, Blanka and Kalina, Ivan and Popov, Todor A and Garte, Seymour and Taioli, Emanuela and Gabelova, Alena and others}, - journal={Mutation Research/Reviews in Mutation Research}, + journal={Mutat. Res.-Rev. Mutat. Res.}, volume={544}, number={2-3}, pages={397--402}, @@ -3006,7 +3010,7 @@ year = {2016}} @article{Aumaitre2019, title={Polycyclic aromatic hydrocarbons as potential building blocks for organic solar cells}, author={Aumaitre, Cyril and Morin, Jean-Fran{\c{c}}ois}, - journal={The Chemical Record}, + journal={Chem. Rec.}, volume={19}, number={6}, pages={1142--1154}, @@ -3014,9 +3018,9 @@ year = {2016}} publisher={Wiley Online Library}} @article{Berne2008, - title={Extended Red Emission and the evolution of carbonaceous nanograins in NGC 7023}, + title={Extended red emission and the evolution of carbonaceous nanograins in NGC 7023}, author={Bern{\'e}, O and Joblin, C and Rapacioli, M and Thomas, J and Cuillandre, J-C and Deville, Y}, - journal={Astronomy \& Astrophysics}, + journal={Astron. Astrophys.}, volume={479}, number={3}, pages={L41--L44}, @@ -3026,7 +3030,7 @@ year = {2016}} @article{Berne2007, title={Analysis of the emission of very small dust particles from Spitzer spectro-imagery data using blind signal separation methods}, author={Berne, Olivier and Joblin, C and Deville, Y and Smith, JD and Rapacioli, M and Bernard, JP and Thomas, J and Reach, W and Abergel, A}, - journal={Astronomy \& Astrophysics}, + journal={Astron. Astrophys.}, volume={469}, number={2}, pages={575--586}, @@ -3036,7 +3040,7 @@ year = {2016}} @article{Rapacioli2005, title={Spectroscopy of polycyclic aromatic hydrocarbons and very small grains in photodissociation regions}, author={Rapacioli, M and Joblin, C and Boissel, P}, - journal={Astronomy \& Astrophysics}, + journal={Astron. Astrophys.}, volume={429}, number={1}, pages={193--204}, @@ -3046,7 +3050,8 @@ year = {2016}} @article{Allamandola1985, title={Polycyclic aromatic hydrocarbons and the unidentified infrared emission bands-Auto exhaust along the Milky Way}, author={Allamandola, L J and Tielens, A G G M and Barker, JRz}, - journal={The Astrophysical Journal}, + journal={Astrophys. J. +}, volume={290}, pages={L25--L28}, year={1985}} @@ -3075,7 +3080,7 @@ year = {2016}} @article{Chung2011, title={Peri-condensed aromatics with aliphatic chains as key intermediates for the nucleation of aromatic hydrocarbons}, author={Chung, Seung-Hyun and Violi, Angela}, - journal={Proceedings of the Combustion Institute}, + journal={Proc. Combust. Inst.}, volume={33}, number={1}, pages={693--700}, @@ -3085,7 +3090,7 @@ year = {2016}} @article{Saggese2015, title={Kinetic modeling of particle size distribution of soot in a premixed burner-stabilized stagnation ethylene flame}, author={Saggese, Chiara and Ferrario, Sara and Camacho, Joaquin and Cuoci, Alberto and Frassoldati, Alessio and Ranzi, Eliseo and Wang, Hai and Faravelli, Tiziano}, - journal={Combustion and Flame}, + journal={Combust. Flame}, volume={162}, number={9}, pages={3356--3369}, @@ -3104,7 +3109,7 @@ s @article{Eaves2015, title={The importance of reversibility in modeling soot nucleation and condensation processes}, author={Eaves, NA and Dworkin, SB and Thomson, MJ}, - journal={Proceedings of the Combustion Institute}, + journal={Proc. Combust. Inst.}, volume={35}, number={2}, pages={1787--1794}, @@ -3124,7 +3129,7 @@ s @article{Zamith2019thermal, title={Thermal evaporation of pyrene clusters}, author={Zamith, S{\'e}bastien and Ji, Ming-Chao and l’Hermite, Jean-Marc and Joblin, Christine and Dontot, L{\'e}o and Rapacioli, Mathias and Spiegelman, Fernand}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={151}, number={19}, pages={194303}, @@ -3134,7 +3139,7 @@ s @article{Joblin2017, title={Size effect in the ionization energy of PAH clusters}, author={Joblin, Christine and Dontot, L{\'e}o and Garcia, GA and Spiegelman, Fernand and Rapacioli, Mathias and Nahon, Laurent and Parneix, Pascal and Pino, T and Br{\'e}chignac, P}, - journal={The journal of physical chemistry letters}, + journal={J. Phys. Chem. Lett.}, volume={8}, number={15}, pages={3697--3702}, @@ -3144,7 +3149,7 @@ s @article{Gatchell2017, title={Ion-induced molecular growth in clusters of small hydrocarbon chains}, author={Gatchell, Michael and Delaunay, Rudy and D'Angelo, Giovanna and Mika, Arkadiusz and Kulyk, Kostiantyn and Domaracka, Alicja and Rousseau, Patrick and Zettergren, Henning and Huber, Bernd A and Cederquist, Henrik}, - journal={Physical Chemistry Chemical Physics}, + journal={Phys. Chem. Chem. Phys.}, volume={19}, number={30}, pages={19665--19672}, @@ -3170,7 +3175,7 @@ s publisher={Oxford University Press on Demand}} @article{Klippenstein1992, - title={Variational Optimizations in the Rice--Ramsperger--Kassel--Marcus Theory Calculations for Unimolecular Dissociations with No Reverse Barrier}, + title={Variational optimizations in the rice--ramsperger--kassel--marcus theory calculations for unimolecular dissociations with no reverse barrier}, author={Klippenstein, Stephen J}, journal={J. Chem. Phys.}, volume={96}, @@ -3180,7 +3185,7 @@ s publisher={American Institute of Physics}} @article{Bera2018, - title={Collision Induced Dissociation of Positive Ions of Dimethylnitramine, a Model System for Nitramine Energetic Molecules}, + title={Collision induced dissociation of positive ions of dimethylnitramine, a model system for nitramine energetic molecules}, author={Bera, Anupam and Concina, Bruno and Schindler, Baptiste and Renois, Gina Predelus and Karras, Gabriel and Compagnon, Isabelle and Bhattacharya, Atanu and L{\'e}pine, Franck}, journal={ Int. J. Mass Spectrom.}, volume={431}, @@ -3189,17 +3194,17 @@ s publisher={Elsevier}} @article{Shuck2014, -title={Mass Spectrometric Methods for the Analysis of Nucleoside–Protein Cross-Links: Application to Oxopropenyl-Deoxyadenosine}, +title={Mass spectrometric methods for the analysis of nucleoside–protein cross-links: application to oxopropenyl-deoxyadenosine}, volume={27}, ISSN={0893-228X}, url={https://dx.doi.org/10.1021/tx400384e}, DOI={10.1021/tx400384e}, number={1}, journal={Chem. Res. Toxicol.}, publisher={Chemical Research in Toxicology}, author={Shuck, Sarah C. and Rose, Kristie L. and Marnett, Lawrence J.}, year={2014}, -pages={136–146}} +pages={136-146}} @article{Nguyen2011, Author = {Viet Hung Nguyen and Afonso, Carlos and Tabet, Jean-Claude}, -Title = {{Concomitant EDD and EID of DNA Evidenced by MSn and Double Resonance Experiments}}, +Title = {{Concomitant EDD and EID of DNA evidenced by MSn and double resonance experiments}}, Journal = {{Int. J. Mass Spectrom.}}, Year = {{2011}}, Volume = {{301}}, @@ -3215,8 +3220,7 @@ Unique-ID = {{ISI:000290190000027}},} @article{Carl2007, Author = {Carl, Damon R. and Moision, Robert M. and Armentrout, P. B.}, -Title = {{Binding Energies for the Inner Hydration Shells of Ca$^{2+}$: An Experimental - and Theoretical Investigation of Ca$^{2+}$(H$_2$O)$_x$ Complexes (x=5-9)}}, +Title = {{Binding energies for the inner hydration shells of Ca$^{2+}$: An experimental and theoretical investigation of Ca$^{2+}$(H$_2$O)$_x$ complexes (x=5-9)}}, Journal = { Int. J. Mass Spectrom.}, Year = {{2007}}, Volume = {{265}}, @@ -3229,7 +3233,7 @@ EISSN = {{1873-2798}}, Unique-ID = {{ISI:000248936500027}},} @article{Molina2015, - title={Elucidating Collision Induced Dissociation Products and Reaction Mechanisms of Protonated Uracil by Coupling Chemical Dynamics Simulations with Tandem Mass Spectrometry Experiments}, + title={Elucidating collision induced dissociation products and reaction mechanisms of protonated uracil by coupling chemical dynamics simulations with tandem mass spectrometry experiments}, author={Molina, Estefan{\'\i}a Rossich and Ortiz, Daniel and Salpin, Jean-Yves and Spezia, Riccardo}, journal={J. Mass Spectrom.}, volume={50}, @@ -3244,7 +3248,7 @@ Unique-ID = {{ISI:000248936500027}},} Number = {5}, Pages = {339--349}, Publisher = {Springer}, - Title = {Collision-Induced Dissociation of Uracil and Its Derivatives}, + Title = {Collision-induced dissociation of uracil and its derivatives}, Volume = {5}, Year = {1994}} @@ -3260,7 +3264,7 @@ Unique-ID = {{ISI:000248936500027}},} publisher={Annual Reviews}} @article{Goebbert2006, - title={Collision-Induced Dissociation Studies of Protonated Ether-(H$_2$O)$_n$ (n= 1--3) Clusters}, + title={Collision-induced dissociation studies of protonated ether-(H$_2$O)$_n$ (n= 1--3) clusters}, author={Goebbert, Daniel J and Chen, Hao and Wenthold, Paul G}, journal={J. Mass Spectrom.}, volume={41}, @@ -3270,7 +3274,7 @@ Unique-ID = {{ISI:000248936500027}},} publisher={Wiley Online Library}} @article{Wei1991, - title={Metastable Unimolecular and Collision-Induced Dissociation of Hydrogen-Bonded Clusters: Evidence for Intracluster Molecular Rearrangement and the Structure of Solvated Protonated Complexes}, + title={Metastable unimolecular and collision-induced dissociation of hydrogen-bonded clusters: evidence for intracluster molecular rearrangement and the structure of solvated protonated complexes}, author={Wei, S and Tzeng, WB and Keesee, RG and Castleman Jr, AW}, journal={J. Am. Chem. Soc.}, volume={113}, @@ -3292,7 +3296,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Liu2006, title={Collision-induced dissociation of hydrated adenosine monophosphate nucleotide ions: Protection of the ion in water nanoclusters}, author={Liu, B and Nielsen, S Br{\o}ndsted and Hvelplund, P and Zettergren, H and Cederquist, H and Manil, B and Huber, BA}, - journal={Physical review letters}, + journal={Phys. Rev. Lett.}, volume={97}, number={13}, pages={133401}, @@ -3305,14 +3309,14 @@ Unique-ID = {{ISI:000248936500027}},} Number = {2}, Pages = {802--818}, Publisher = {Royal Society of Chemistry}, - Title = {Binding Energies of Hydrated Cobalt (II) by Collision-Induced Dissociation and Theoretical Studies: Evidence for a New Critical Size}, + Title = {Binding energies of hydrated cobalt (ii) by collision-induced dissociation and theoretical studies: evidence for a new critical size}, Volume = {20}, Year = {2018}} @article{Dawson1982, title={The collision-induced dissociation of protonated water clusters studied using a triple quadrupole}, author={Dawson, PH}, - journal={International Journal of Mass Spectrometry and Ion Physics}, + journal={Int. J. Mass Spectrom.}, volume={43}, number={2-3}, pages={195--209}, @@ -3322,7 +3326,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Buck2000, title={Infrared spectroscopy of size-selected water and methanol clusters}, author={Buck, Udo and Huisken, Friedrich}, - journal={Chemical Reviews}, + journal={Chem. Rev.}, volume={100}, number={11}, pages={3863--3890}, @@ -3338,7 +3342,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Berden1996, title={High resolution UV spectroscopy of phenol and the hydrogen bonded phenol-water cluster}, author={Berden, Giel and Meerts, W Leo and Schmitt, Michael and Kleinermanns, Karl}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={104}, number={3}, pages={972--982}, @@ -3346,9 +3350,9 @@ Unique-ID = {{ISI:000248936500027}},} publisher={American Institute of Physics}} @article{Rozenberg2009, - title={Matrix Isolation Infrared Spectrum of the Sulfuric Acid- Monohydrate Complex: New Assignments and Resolution of the “Missing H-Bonded $\nu$ (OH) Band” Issue}, + title={Matrix isolation infrared spectrum of the sulfuric acid- monohydrate complex: new assignments and resolution of the “missing h-bonded $\nu$ (oh) band” issue}, author={Rozenberg, M and Loewenschuss, A}, - journal={The Journal of Physical Chemistry A}, + journal={J. Phys. Chem. A}, volume={113}, number={17}, pages={4963--4971}, @@ -3356,9 +3360,9 @@ Unique-ID = {{ISI:000248936500027}},} publisher={ACS Publications}} @article{Huneycutt2003, - title={Infrared cavity ringdown spectroscopy of acid--water clusters: HCl--H 2 O, DCl--D 2 O, and DCl--(D 2 O) 2}, + title={Infrared cavity ringdown spectroscopy of acid--water clusters: HCl--H$_2$O, DCl--D$_2$O, and DCl--(D$_2$O)$_2$}, author={Huneycutt, Alex J and Stickland, Ross J and Hellberg, Fredrik and Saykally, Richard J}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={118}, number={3}, pages={1221--1229}, @@ -3368,7 +3372,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Latimer1920, title={Polarity and ionization from the standpoint of the Lewis theory of valence.}, author={Latimer, Wendell M and Rodebush, Worth H}, - journal={Journal of the American Chemical Society}, + journal={J. Am. Chem. Soc.}, volume={42}, number={7}, pages={1419--1433}, @@ -3391,7 +3395,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Hartt2008, title={Hydration of OCS with one to four water molecules in atmospheric and laboratory conditions}, author={Hartt, Gregory M and Shields, George C and Kirschner, Karl N}, - journal={The Journal of Physical Chemistry A}, + journal={J. Phys. Chem. A}, volume={112}, number={19}, pages={4490--4495}, @@ -3401,7 +3405,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Vaida2000, title={Physicochemical properties of hydrated complexes in the Earth's atmosphere}, author={Vaida, Veronica and Headrick, Jill E}, - journal={The Journal of Physical Chemistry A}, + journal={J. Phys. Chem. A}, volume={104}, number={23}, pages={5401--5412}, @@ -3409,9 +3413,9 @@ Unique-ID = {{ISI:000248936500027}},} publisher={ACS Publications}} @article{Mccurdy2002, - title={Nitric Acid- Water Complexes: Theoretical Calculations and Comparison to Experiment}, + title={Nitric acid- water complexes: Theoretical calculations and comparison to experiment}, author={McCurdy, Patrick R and Hess, Wayne P and Xantheas, Sotiris S}, - journal={The Journal of Physical Chemistry A}, + journal={J. Phys. Chem. A}, volume={106}, number={33}, pages={7628--7635}, @@ -3419,9 +3423,9 @@ Unique-ID = {{ISI:000248936500027}},} publisher={ACS Publications}} @article{Aloisio2000, - title={Radical- Water complexes in earth's atmosphere}, + title={Radical-water complexes in earth's atmosphere}, author={Aloisio, Simone and Francisco, Joseph S}, - journal={Accounts of Chemical Research}, + journal={Acc. Chem. Res.}, volume={33}, number={12}, pages={825--830}, @@ -3431,7 +3435,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Vaida2011, title={Perspective: Water cluster mediated atmospheric chemistry}, author={Vaida, Veronica}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={135}, number={2}, pages={020901}, @@ -3464,7 +3468,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Rapacioli2011, title={Modeling charge resonance in cationic molecular clusters: combining DFT-tight binding with configuration interaction}, author={Rapacioli, Mathias and Spiegelman, Fernand and Scemama, Anthony and Mirtschink, Andr{\'e}}, - journal={Journal of chemical theory and computation}, + journal={J. Chem. Theory Comput.}, volume={7}, number={1}, pages={44--55}, @@ -3474,7 +3478,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Kanamori2018, title={Exploring a potential energy surface by machine learning for characterizing atomic transport}, author={Kanamori, Kenta and Toyoura, Kazuaki and Honda, Junya and Hattori, Kazuki and Seko, Atsuto and Karasuyama, Masayuki and Shitara, Kazuki and Shiga, Motoki and Kuwabara, Akihide and Takeuchi, Ichiro}, - journal={Physical Review B}, + journal={Phys. Rev. B}, volume={97}, number={12}, pages={125124}, @@ -3484,7 +3488,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Iannuzzi2003, title={Efficient exploration of reactive potential energy surfaces using Car-Parrinello molecular dynamics}, author={Iannuzzi, Marcella and Laio, Alessandro and Parrinello, Michele}, - journal={Physical Review Letters}, + journal={Phys. Rev. Lett.}, volume={90}, number={23}, pages={238302}, @@ -3494,7 +3498,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Schlegel2003, title={Exploring potential energy surfaces for chemical reactions: an overview of some practical methods}, author={Schlegel, H Bernhard}, - journal={Journal of computational chemistry}, + journal={J. Comput. Chem}, volume={24}, number={12}, pages={1514--1527}, @@ -3520,16 +3524,16 @@ Unique-ID = {{ISI:000248936500027}},} @article{Gao1996, title={Methods and applications of combined quantum mechanical and molecular mechanical potentials}, author={Gao, Jiali}, - journal={Reviews in computational chemistry}, + journal={Rev. Comput. Chem. }, volume={7}, pages={119--186}, year={1996}, publisher={Wiley Online Library}} @article{Singh1986, - title={A combined ab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: Applications to the CH3Cl+ Cl- exchange reaction and gas phase protonation of polyethers}, + title={A combined ab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: Applications to the CH$_3$Cl + Cl$^-$ exchange reaction and gas phase protonation of polyethers}, author={Singh, U Chandra and Kollman, Peter A}, - journal={Journal of Computational Chemistry}, + journal={J. Comput. Chem}, volume={7}, number={6}, pages={718--730}, @@ -3537,9 +3541,9 @@ Unique-ID = {{ISI:000248936500027}},} publisher={Wiley Online Library}} @article{Cremer1993, - title={Exploration of the potential energy surface of C9H9+ by ab initio methods. 1. The barbaralyl cation}, + title={Exploration of the potential energy surface of C$_9$H$_9^+$ by ab initio methods. 1. The barbaralyl cation}, author={Cremer, Dieter and Svensson, Peder and Kraka, Elfi and Ahlberg, Per}, - journal={Journal of the American Chemical Society}, + journal={J. Am. Chem. Soc.}, volume={115}, number={16}, pages={7445--7456}, @@ -3552,7 +3556,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Binder1993, title={Monte Carlo simulation in statistical physics}, author={Binder, Kurt and Heermann, Dieter and Roelofs, Lyle and Mallinckrodt, A John and McKay, Susan}, - journal={Computers in Physics}, + journal={Comput. Phys.}, volume={7}, number={2}, pages={156--157}, @@ -3562,7 +3566,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Baeurle2009, title={Multiscale modeling of polymer materials using field-theoretic methodologies: a survey about recent developments}, author={Baeurle, Stephan A}, - journal={Journal of Mathematical Chemistry}, + journal={J. Math. Chem.}, volume={46}, number={2}, pages={363--426}, @@ -3572,7 +3576,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Rosenbluth1955, title={Monte Carlo calculation of the average extension of molecular chains}, author={Rosenbluth, Marshall N and Rosenbluth, Arianna W}, - journal={The Journal of Chemical Physics}, + journal={J. Chem. Phys.}, volume={23}, number={2}, pages={356--359}, @@ -3614,7 +3618,7 @@ Unique-ID = {{ISI:000248936500027}},} publisher={Oxford university press}} @article{Metropolis1987, - title={The beginning of the Monte Carlo Method}, + title={The beginning of the Monte Carlo method}, author={Metropolis, N}, journal={Los Alamos Science}, volume={15}, @@ -3623,9 +3627,9 @@ Unique-ID = {{ISI:000248936500027}},} publisher={Los Alamos Scientific Laboratory}} @article{Metropolis1949, - title={The Monte Carlo Method}, + title={The Monte Carlo method}, author={Metropolis, Nicholas and Ulam, Stanislaw}, - journal={Journal of the American statistical association}, + journal={J. Am. Stat. Assoc.}, volume={44}, number={247}, pages={335--341}, @@ -3635,7 +3639,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Unger1993, title={Genetic algorithms for protein folding simulations}, author={Unger, Ron and Moult, John}, - journal={Journal of molecular biology}, + journal={J. Mol. Biol., volume={231}, number={1}, pages={75--81}, @@ -3645,7 +3649,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Hartke1993, title={Global geometry optimization of clusters using genetic algorithms}, author={Hartke, Bernd}, - journal={The Journal of Physical Chemistry}, + journal={J. Phys. Chem.}, volume={97}, number={39}, pages={9973--9976}, @@ -3655,7 +3659,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Toledo2014, title={Global optimization using a genetic algorithm with hierarchically structured population}, author={Toledo, Claudio Fabiano Motta and Oliveira, L and Fran{\c{c}}a, Paulo Morelato}, - journal={Journal of Computational and Applied Mathematics}, + journal={J. Comput. Appl. Math.}, volume={261}, pages={341--351}, year={2014}, @@ -3682,7 +3686,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Wales1997, title={Global optimization by basin-hopping and the lowest energy structures of Lennard-Jones clusters containing up to 110 atoms}, author={Wales, David J and Doye, Jonathan PK}, - journal={The Journal of Physical Chemistry A}, + journal={J. Phys. Chem. A}, volume={101}, number={28}, pages={5111--5116}, @@ -3692,7 +3696,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Dougherty1998, title={Equilibrium structural model of liquid water: evidence from heat capacity, spectra, density, and other properties}, author={Dougherty, Ralph C and Howard, Louis N}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={109}, number={17}, pages={7379--7393}, @@ -3702,7 +3706,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Schmidt2012, title={Gas-phase calorimetry of protonated water clusters}, author={Schmidt, M and von Issendorff, B}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={136}, number={16}, pages={164307}, @@ -3712,7 +3716,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Korchagina2017, title={Theoretical investigation of the solid--liquid phase transition in protonated water clusters}, author={Korchagina, Kseniia and Simon, Aude and Rapacioli, Mathias and Spiegelman, Fernand and L’Hermite, Jean-Marc and Braud, Isabelle and Zamith, S{\'e}bastien and Cuny, J{\'e}r{\^o}me}, - journal={Physical Chemistry Chemical Physics}, + journal={Phys. Chem. Chem. Phys.}, volume={19}, number={40}, pages={27288--27298}, @@ -3722,7 +3726,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Rapacioli2018, title={Melting of the Au$_{20}$ gold cluster: Does charge matter?}, author={Rapacioli, Mathias and Tarrat, Nathalie and Spiegelman, Fernand}, - journal={The Journal of Physical Chemistry A}, + journal={J. Phys. Chem. A}, volume={122}, number={16}, pages={4092--4098}, @@ -3742,7 +3746,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Barducci2011, title={Metadynamics}, author={Barducci, Alessandro and Bonomi, Massimiliano and Parrinello, Michele}, - journal={Wiley Interdisciplinary Reviews: Computational Molecular Science}, + journal={Wiley Interdiscip. Rev. Comput. Mol. Sci.}, volume={1}, number={5}, pages={826--843}, @@ -3752,7 +3756,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Iannuzzi2003, title={Efficient exploration of reactive potential energy surfaces using Car-Parrinello molecular dynamics}, author={Iannuzzi, Marcella and Laio, Alessandro and Parrinello, Michele}, - journal={Physical Review Letters}, + journal={Phys. Rev. Lett.}, volume={90}, number={23}, pages={238302}, @@ -3762,7 +3766,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Laio2002, title={Escaping free-energy minima}, author={Laio, Alessandro and Parrinello, Michele}, - journal={Proceedings of the National Academy of Sciences}, + journal={Proc. Natl. Acad. Sci.}, volume={99}, number={20}, pages={12562--12566}, @@ -3776,7 +3780,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Goursot2007, title={Interaction between n-alkane chains: Applicability of the empirically corrected density functional theory for van der Waals complexes}, author={Goursot, Annick and Mineva, Tzonka and Kevorkyants, Ruslan and Talbi, Dahbia}, - journal={Journal of chemical theory and computation}, + journal={J. Chem. Theory Comput.}, volume={3}, number={3}, pages={755--763}, @@ -3786,7 +3790,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Koskinen2009, title={Density-functional tight-binding for beginners}, author={Koskinen, Pekka and M{\"a}kinen, Ville}, - journal={Computational Materials Science}, + journal={Comput. Mater. Sci.}, volume={47}, number={1}, pages={237--253}, @@ -3808,7 +3812,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Neumann2005, title={Energy ranking of molecular crystals using density functional theory calculations and an empirical van der Waals correction}, author={Neumann, Marcus A and Perrin, Marc-Antoine}, - journal={The Journal of Physical Chemistry B}, + journal={J. Phys. Chem. B}, volume={109}, number={32}, pages={15531--15541}, @@ -3818,7 +3822,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Goursot2007, title={Interaction between n-alkane chains: Applicability of the empirically corrected density functional theory for van der Waals complexes}, author={Goursot, Annick and Mineva, Tzonka and Kevorkyants, Ruslan and Talbi, Dahbia}, - journal={Journal of chemical theory and computation}, + journal={J. Chem. Theory Comput.}, volume={3}, number={3}, pages={755--763}, @@ -3828,7 +3832,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Zimmerli2004, title={Dispersion corrections to density functionals for water aromatic interactions}, author={Zimmerli, Urs and Parrinello, Michele and Koumoutsakos, Petros}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={120}, number={6}, pages={2693--2699}, @@ -3838,7 +3842,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Wu2002, title={Empirical correction to density functional theory for van der Waals interactions}, author={Wu, Qin and Yang, Weitao}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={116}, number={2}, pages={515--524}, @@ -3848,7 +3852,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Elstner2001, title={Hydrogen bonding and stacking interactions of nucleic acid base pairs: A density-functional-theory based treatment}, author={Elstner, Marcus and Hobza, Pavel and Frauenheim, Thomas and Suhai, S{\'a}ndor and Kaxiras, Efthimios}, - journal={The Journal of Chemical Physics}, + journal={J. Chem. Phys.}, volume={114}, number={12}, pages={5149--5155}, @@ -3856,9 +3860,9 @@ Unique-ID = {{ISI:000248936500027}},} publisher={American Institute of Physics}} @article{Gianturco1999, - title={Intermolecular forces from density functional theory. III. A multiproperty analysis for the Ar (1 S)-CO (1 $\Sigma$) interaction}, + title={Intermolecular forces from density functional theory. III. A multiproperty analysis for the Ar($^1$S)-CO($^1\Sigma$) interaction}, author={Gianturco, FA and Paesani, F and Laranjeira, MF and Vassilenko, V and Cunha, MA}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={110}, number={16}, pages={7832--7845}, @@ -3868,7 +3872,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Lewis1995, title={Geometry and energetics of DNA basepairs and triplets from first principles quantum molecular relaxations}, author={Lewis, James P and Sankey, Otto F}, - journal={Biophysical journal}, + journal={Biophys. J.}, volume={69}, number={3}, pages={1068--1076}, @@ -3878,7 +3882,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Grimme2004, title={Accurate description of van der Waals complexes by density functional theory including empirical corrections}, author={Grimme, Stefan}, - journal={Journal of computational chemistry}, + journal={J. Comput. Chem}, volume={25}, number={12}, pages={1463--1473}, @@ -3888,7 +3892,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Cances1997, title={A new integral equation formalism for the polarizable continuum model: Theoretical background and applications to isotropic and anisotropic dielectrics}, author={Cances, E and Mennucci, Benedetta and Tomasi, J}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={107}, number={8}, pages={3032--3041}, @@ -3898,7 +3902,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Lu2012, title={Multiwfn: a multifunctional wavefunction analyzer}, author={Lu, Tian and Chen, Feiwu}, - journal={Journal of computational chemistry}, + journal={J. Comput. Chem}, volume={33}, number={5}, pages={580--592}, @@ -3908,7 +3912,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Mayer1983, title={Charge, bond order and valence in the AB initio SCF theory}, author={Mayer, Istvan}, - journal={Chemical Physics Letters}, + journal={Chem. Phys. Lett.}, volume={97}, number={3}, pages={270--274}, @@ -3918,7 +3922,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Kelly2005, title={Accurate partial atomic charges for high-energy molecules using class IV charge models with the MIDI! basis set}, author={Kelly, Casey P and Cramer, Christopher J and Truhlar, Donald G}, - journal={Theoretical Chemistry Accounts}, + journal={Theor. Chem. Acc.}, volume={113}, number={3}, pages={133--151}, @@ -3928,7 +3932,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Kalinowski2004, title={Class IV charge model for the self-consistent charge density-functional tight-binding method}, author={Kalinowski, Jaroslaw A and Lesyng, Bogdan and Thompson, Jason D and Cramer, Christopher J and Truhlar, Donald G}, - journal={The Journal of Physical Chemistry A}, + journal={J. Phys. Chem. A}, volume={108}, number={13}, pages={2545--2549}, @@ -3938,7 +3942,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Rapacioli2009corr, title={Correction for dispersion and Coulombic interactions in molecular clusters with density functional derived methods: Application to polycyclic aromatic hydrocarbon clusters}, author={Rapacioli, Mathias and Spiegelman, Fernand and Talbi, Dahbia and Mineva, Tzonka and Goursot, Annick and Heine, Thomas and Seifert, Gotthard}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={130}, number={24}, pages={244304}, @@ -3948,7 +3952,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Li1998, title={New class IV charge model for extracting accurate partial charges from wave functions}, author={Li, Jiabo and Zhu, Tianhai and Cramer, Christopher J and Truhlar, Donald G}, - journal={The Journal of Physical Chemistry A}, + journal={J. Phys. Chem. A}, volume={102}, number={10}, pages={1820--1831}, @@ -3958,7 +3962,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Besler1990, title={Atomic charges derived from semiempirical methods}, author={Besler, Brent H and Merz Jr, Kenneth M and Kollman, Peter A}, - journal={Journal of computational chemistry}, + journal={J. Comput. Chem}, volume={11}, number={4}, pages={431--439}, @@ -3968,7 +3972,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Singh1984, title={An approach to computing electrostatic charges for molecules}, author={Singh, U Chandra and Kollman, Peter A}, - journal={Journal of computational chemistry}, + journal={J. Comput. Chem}, volume={5}, number={2}, pages={129--145}, @@ -3984,7 +3988,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Bader1985, title={Atoms in molecules}, author={Bader, Richard F. W.}, - journal={Accounts of Chemical Research}, + journal={Acc. Chem. Res.}, volume={18}, number={1}, pages={9--15}, @@ -3994,7 +3998,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Glendening2012, title={Natural bond orbital methods}, author={Glendening, Eric D and Landis, Clark R and Weinhold, Frank}, - journal={Wiley interdisciplinary reviews: computational molecular science}, + journal={Wiley Interdiscip. Rev. Comput. Mol. Sci.}, volume={2}, number={1}, pages={1--42}, @@ -4004,7 +4008,7 @@ Unique-ID = {{ISI:000248936500027}},} @article{Glendening1998, title={Natural resonance theory: II. Natural bond order and valency}, author={Glendening, Eric D and Weinhold, Frank}, - journal={Journal of Computational Chemistry}, + journal={J. Comput. Chem}, volume={19}, number={6}, pages={610--627}, @@ -4012,9 +4016,9 @@ Unique-ID = {{ISI:000248936500027}},} publisher={Wiley Online Library}} @article{Elstne2007, -title = {Density Functional Tight Binding: Contributions from the American Chemical Society Symposium}, +title = {Density functional tight binding: Contributions from the american chemical society symposium}, author={Elstner, Marcus and Frauenheim, T and McKelvey, J and Seifert, G}, -journal = {The Journal of Physical Chemistry A}, +journal = {J. Phys. Chem. A}, volume = {111}, number = {26}, pages = {5607-5608}, @@ -4024,7 +4028,7 @@ doi = {10.1021/jp079512r}} @article{Stillinger1985, title={Computer simulation of local order in condensed phases of silicon}, author={Stillinger, Frank H and Weber, Thomas A}, - journal={Physical review B}, + journal={Phys. Rev. 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Sci.}, volume={106}, number={738}, pages={441--462}, @@ -4122,7 +4126,7 @@ doi = {10.1021/jp079512r}} @article{Hansmann1993, title={Prediction of peptide conformation by multicanonical algorithm: New approach to the multiple-minima problem}, author={Hansmann, Ulrich HE and Okamoto, Yuko}, - journal={Journal of computational chemistry}, + journal={J. Comput. Chem}, volume={14}, number={11}, pages={1333--1338}, @@ -4132,7 +4136,7 @@ doi = {10.1021/jp079512r}} @article{Darve2001, title={Calculating free energies using average force}, author={Darve, Eric and Pohorille, Andrew}, - journal={The Journal of Chemical Physics}, + journal={J. Chem. Phys.}, volume={115}, number={20}, pages={9169--9183}, @@ -4142,7 +4146,7 @@ doi = {10.1021/jp079512r}} @article{Torrie1977, title={Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling}, author={Torrie, Glenn M and Valleau, John P}, - journal={Journal of Computational Physics}, + journal={J. Comput. Phys.}, volume={23}, number={2}, pages={187--199}, @@ -4153,7 +4157,7 @@ doi = {10.1021/jp079512r}} @article{Marchi1999, title={Adiabatic bias molecular dynamics: a method to navigate the conformational space of complex molecular systems}, author={Marchi, Massimo and Ballone, Pietro}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={110}, number={8}, pages={3697--3702}, @@ -4163,7 +4167,7 @@ doi = {10.1021/jp079512r}} @article{Bartels2000, title={Analyzing biased Monte Carlo and molecular dynamics simulations}, author={Bartels, Christian}, - journal={Chemical Physics Letters}, + journal={Chem. Phys. Lett.}, volume={331}, number={5-6}, pages={446--454}, @@ -4174,7 +4178,7 @@ doi = {10.1021/jp079512r}} @article{Sugita1999, title={Replica-exchange molecular dynamics method for protein folding}, author={Sugita, Yuji and Okamoto, Yuko}, - journal={Chemical physics letters}, + journal={Chem. Phys. Lett.}, volume={314}, number={1-2}, pages={141--151}, @@ -4184,7 +4188,7 @@ doi = {10.1021/jp079512r}} @article{Earl2005, title={Parallel tempering: Theory, applications, and new perspectives}, author={Earl, David J and Deem, Michael W}, - journal={Physical Chemistry Chemical Physics}, + journal={Phys. Chem. Chem. Phys.}, volume={7}, number={23}, pages={3910--3916}, @@ -4194,7 +4198,7 @@ doi = {10.1021/jp079512r}} @article{Falcioni1999, title={A biased Monte Carlo scheme for zeolite structure solution}, author={Falcioni, Marco and Deem, Michael W}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={110}, number={3}, pages={1754--1766}, @@ -4204,12 +4208,12 @@ doi = {10.1021/jp079512r}} @article{Hukushima1996, title={Exchange Monte Carlo method and application to spin glass simulations}, author={Hukushima, Koji and Nemoto, Koji}, - journal={Journal of the Physical Society of Japan}, + journal={J. Phys. Soc. Jpn.}, volume={65}, number={6}, pages={1604--1608}, year={1996}, - publisher={The Physical Society of Japan}} + publisher={J. Phys. Soc. Japan.}} @article{Geyer1991, title={Computing science and statistics: Proceedings of the 23rd Symposium on the Interface}, @@ -4221,7 +4225,7 @@ doi = {10.1021/jp079512r}} @article{Swendsen1986, title={Replica Monte Carlo simulation of spin-glasses}, author={Swendsen, Robert H and Wang, Jian-Sheng}, - journal={Physical review letters}, + journal={Phys. Rev. Lett.}, volume={57}, number={21}, pages={2607}, @@ -4249,7 +4253,7 @@ doi = {10.1021/jp079512r}} @article{Ray1981, title={Direct calculation of fluctuation formulae in the microcanonical ensemble}, author={Ray, John R and Graben, HW}, - journal={Molecular Physics}, + journal={Mol. Phys.}, volume={43}, number={6}, pages={1293--1297}, @@ -4259,7 +4263,7 @@ doi = {10.1021/jp079512r}} @article{Ray1999, title={Correct microcanonical ensemble in molecular dynamics}, author={Ray, John R and Zhang, Hongwei}, - journal={Physical Review E}, + journal={Phys. Rev. E}, volume={59}, number={5}, pages={4781-4785}, @@ -4269,7 +4273,7 @@ doi = {10.1021/jp079512r}} @article{Nose1984M, title={A molecular dynamics method for simulations in the canonical ensemble}, author={Nos{\'e}, Sh{\=u}ichi}, - journal={Molecular physics}, + journal={Mol. Phys.}, volume={52}, number={2}, pages={255--268}, @@ -4287,7 +4291,7 @@ doi = {10.1021/jp079512r}} @article{Hoover1985, title={Canonical dynamics: Equilibrium phase-space distributions}, author={Hoover, William G}, - journal={Physical review A}, + journal={Phys. Rev. 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Phys.}, volume={76}, number={1}, pages={637--649}, @@ -4337,7 +4341,7 @@ doi = {10.1021/jp079512r}} @article{Batina1991, title={Unsteady Euler algorithm with unstructured dynamic mesh for complex-aircraft aerodynamic analysis}, author={Batina, John T}, - journal={AIAA journal}, + journal={AIAA J.}, volume={29}, number={3}, pages={327--333}, @@ -4354,7 +4358,7 @@ doi = {10.1021/jp079512r}} @article{Runge1895, title={{\"U}ber die numerische Aufl{\"o}sung von Differentialgleichungen}, author={Runge, Carl}, - journal={Mathematische Annalen}, + journal={Math. Ann}, volume={46}, number={2}, pages={167--178}, @@ -4372,7 +4376,7 @@ doi = {10.1021/jp079512r}} @article{Butcher1996, title={A history of Runge-Kutta methods}, author={Butcher, John Charles}, - journal={Applied numerical mathematics}, + journal={Appl. Numer. Math.}, volume={20}, number={3}, pages={247--260}, @@ -4382,7 +4386,7 @@ doi = {10.1021/jp079512r}} @article{Diethelm2002, title={A predictor-corrector approach for the numerical solution of fractional differential equations}, author={Diethelm, Kai and Ford, Neville J and Freed, Alan D}, - journal={Nonlinear Dynamics}, + journal={Nonlinear Dyn.}, volume={29}, number={1-4}, pages={3--22}, @@ -4414,7 +4418,7 @@ doi = {10.1021/jp079512r}} @article{Wang2003, title={Multilayer formulation of the multiconfiguration time-dependent Hartree theory}, author={Wang, Haobin and Thoss, Michael}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={119}, number={3}, pages={1289--1299}, @@ -4424,7 +4428,7 @@ doi = {10.1021/jp079512r}} @article{Wei1994, title={Discrete variable representations of complicated kinetic energy operators}, author={Wei, Hua and Carrington Jr, Tucker}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={101}, number={2}, pages={1343--1360}, @@ -4434,7 +4438,7 @@ doi = {10.1021/jp079512r}} @article{Beck2000, title={The multiconfiguration time-dependent Hartree (MCTDH) method: a highly efficient algorithm for propagating wavepackets}, author={Beck, Michael H and J{\"a}ckle, Andreas and Worth, Graham A and Meyer, H-D}, - journal={Physics reports}, + journal={Phys. Rep.}, volume={324}, number={1}, pages={1--105}, @@ -4444,7 +4448,7 @@ doi = {10.1021/jp079512r}} @article{Aragon1976, title={Fluorescence correlation spectroscopy as a probe of molecular dynamics}, author={Aragon, SR and Pecora, R}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={64}, number={4}, pages={1791--1803}, @@ -4452,7 +4456,7 @@ doi = {10.1021/jp079512r}} publisher={American Institute of Physics}} @article{Pavone2006, - title={Spectroscopic Properties in the Liquid Phase: Combining High-Level Ab Initio Calculations and Classical Molecular Dynamics}, + title={Spectroscopic properties in the liquid phase: combining high-level ab initio calculations and classical molecular dynamics}, author={Pavone, Michele and Brancato, Giuseppe and Morelli, Giovanni and Barone, Vincenzo}, journal={ChemPhysChem}, volume={7}, @@ -4464,7 +4468,7 @@ doi = {10.1021/jp079512r}} @article{Vuilleumier1999, title={Transport and spectroscopy of the hydrated proton: a molecular dynamics study}, author={Vuilleumier, Rodolphe and Borgis, Daniel}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={111}, number={9}, pages={4251--4266}, @@ -4474,7 +4478,7 @@ doi = {10.1021/jp079512r}} @article{Brancato2006, title={A quantum mechanical/molecular dynamics/mean field study of acrolein in aqueous solution: analysis of H bonding and bulk effects on spectroscopic properties}, author={Brancato, Giuseppe and Rega, Nadia and Barone, Vincenzo}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={125}, number={16}, pages={164515}, @@ -4484,7 +4488,7 @@ doi = {10.1021/jp079512r}} @article{Mondello1997, title={Viscosity calculations of n-alkanes by equilibrium molecular dynamics}, author={Mondello, Maurizio and Grest, Gary S}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={106}, number={22}, pages={9327--9336}, @@ -4494,7 +4498,7 @@ doi = {10.1021/jp079512r}} @article{Zhang2015, title={Reliable viscosity calculation from equilibrium molecular dynamics simulations: A time decomposition method}, author={Zhang, Yong and Otani, Akihito and Maginn, Edward J}, - journal={Journal of chemical theory and computation}, + journal={J. Chem. Theory Comput.}, volume={11}, number={8}, pages={3537--3546}, @@ -4504,7 +4508,7 @@ doi = {10.1021/jp079512r}} @article{Hess2002, title={Determining the shear viscosity of model liquids from molecular dynamics simulations}, author={Hess, Berk}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={116}, number={1}, pages={209--217}, @@ -4514,7 +4518,7 @@ doi = {10.1021/jp079512r}} @article{Yeh2004, title={System-size dependence of diffusion coefficients and viscosities from molecular dynamics simulations with periodic boundary conditions}, author={Yeh, In-Chul and Hummer, Gerhard}, - journal={The Journal of Physical Chemistry B}, + journal={J. Phys. Chem. B}, volume={108}, number={40}, pages={15873--15879}, @@ -4534,7 +4538,7 @@ doi = {10.1021/jp079512r}} @article{Braga2014, title={Nonequilibrium molecular dynamics simulation of diffusion at the liquid-liquid interface}, author={Braga, Carlos and Galindo, Amparo and M{\"u}ller, Erich A}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={141}, number={15}, pages={154101}, @@ -4544,7 +4548,7 @@ doi = {10.1021/jp079512r}} @article{Pranami2015, title={Estimating error in diffusion coefficients derived from molecular dynamics simulations}, author={Pranami, Gaurav and Lamm, Monica H}, - journal={Journal of chemical theory and computation}, + journal={J. Chem. Theory Comput.}, volume={11}, number={10}, pages={4586--4592}, @@ -4563,7 +4567,7 @@ doi = {10.1021/jp079512r}} @article{Coveney2016, title={On the calculation of equilibrium thermodynamic properties from molecular dynamics}, author={Coveney, Peter V and Wan, Shunzhou}, - journal={Physical Chemistry Chemical Physics}, + journal={Phys. Chem. Chem. Phys.}, volume={18}, number={44}, pages={30236--30240}, @@ -4573,7 +4577,7 @@ doi = {10.1021/jp079512r}} @article{Dang1997, title={Molecular dynamics study of water clusters, liquid, and liquid--vapor interface of water with many-body potentials}, author={Dang, Liem X and Chang, Tsun-Mei}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={106}, number={19}, pages={8149--8159}, @@ -4593,7 +4597,7 @@ doi = {10.1021/jp079512r}} @article{Briant1975, title={Molecular dynamics study of the structure and thermodynamic properties of argon microclusters}, author={Briant, CL and Burton, JJ}, - journal={The Journal of Chemical Physics}, + journal={J. Chem. Phys.}, volume={63}, number={5}, pages={2045--2058}, @@ -4603,7 +4607,7 @@ doi = {10.1021/jp079512r}} @article{Ballone1988, title={Equilibrium structures and finite temperature properties of silicon microclusters from ab initio molecular-dynamics calculations}, author={Ballone, Pietro and Andreoni, Wanda and Car, Roberto and Parrinello, Michele}, - journal={Physical review letters}, + journal={Phys. Rev. Lett.}, volume={60}, number={4}, pages={271-274}, @@ -4613,7 +4617,7 @@ doi = {10.1021/jp079512r}} @article{Gutierrez1996, title={Stability of silicon carbide structures: from clusters to solid surfaces}, author={Gutierrez, Rafael and Frauenheim, Thomas and K{\"o}hler, Thomas and Seifert, Gothard}, - journal={Journal of Materials Chemistry}, + journal={J. Mater. Chem. 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Phys.}, volume={27}, number={5}, pages={1208--1209}, @@ -4673,7 +4677,7 @@ doi = {10.1021/jp079512r}} @article{Van1990, title={Computer simulation of molecular dynamics: methodology, applications, and perspectives in chemistry}, author={Van Gunsteren, Wilfred F and Berendsen, Herman JC}, - journal={Angewandte Chemie International Edition in English}, + journal={Angew. Chem. Int. Ed.}, volume={29}, number={9}, pages={992--1023}, @@ -4683,7 +4687,7 @@ doi = {10.1021/jp079512r}} @article{Van2006, title={Biomolecular modeling: goals, problems, perspectives}, author={van Gunsteren, Wilfred F and Bakowies, Dirk and Baron, Riccardo and Chandrasekhar, Indira and Christen, Markus and Daura, Xavier and Gee, Peter and Geerke, Daan P and Gl{\"a}ttli, Alice and H{\"u}nenberger, Philippe H and others}, - journal={Angewandte Chemie International Edition}, + journal={Angew. Chem. Int. Ed. }, volume={45}, number={25}, pages={4064--4092}, @@ -4713,7 +4717,7 @@ doi = {10.1021/jp079512r}} @article{Karplus2002, title={Molecular dynamics simulations of biomolecules}, author={Karplus, Martin and McCammon, J Andrew}, - journal={Nature structural biology}, + journal={Nat. Struct. Biol.}, volume={9}, number={9}, pages={646--652}, @@ -4728,7 +4732,7 @@ doi = {10.1021/jp079512r}} publisher={Elsevier}} @misc{Cicccotti1987, - title={Simulations of Liquids and Solids--Molecular Dynamics and Monte Carlo Methods in statistical Mechanics}, + title={Simulations of liquids and solids--molecular dynamics and monte carlo methods in statistical mechanics}, author={Cicccotti, G and Frenkel, D and McDonald, IR}, year={1987}, publisher={North-Holland, Amsterdam}} @@ -4748,7 +4752,7 @@ doi = {10.1021/jp079512r}} @article{Mulliken1955, title={Electronic population analysis on LCAO--MO molecular wave functions. I}, author={Mulliken, Robert S}, - journal={The Journal of Chemical Physics}, + journal={J. Chem. Phys.}, volume={23}, number={10}, pages={1833--1840}, @@ -4758,7 +4762,7 @@ doi = {10.1021/jp079512r}} @article{Gaus2011, title={DFTB3: extension of the self-consistent-charge density-functional tight-binding method (SCC-DFTB)}, author={Gaus, Michael and Cui, Qiang and Elstner, Marcus}, - journal={Journal of chemical theory and computation}, + journal={J. Chem. Theory Comput.}, volume={7}, number={4}, pages={931--948}, @@ -4768,7 +4772,7 @@ doi = {10.1021/jp079512r}} @article{Oliveira2009, title={Density-functional based tight-binding: an approximate DFT method}, author={Oliveira, Augusto F and Seifert, Gotthard and Heine, Thomas and Duarte, H{\'e}lio A}, - journal={Journal of the Brazilian Chemical Society}, + journal={J. Braz. Chem. Soc., volume={20}, number={7}, pages={1193--1205}, @@ -4779,7 +4783,7 @@ doi = {10.1021/jp079512r}} @article{Seifert1996, title={Calculations of molecules, clusters, and solids with a simplified LCAO-DFT-LDA scheme}, author={Seifert, G and Porezag, D and Frauenheim, Th}, - journal={International journal of quantum chemistry}, + journal={Int. J. Quantum Chem.}, volume={58}, number={2}, pages={185--192}, @@ -4789,7 +4793,7 @@ doi = {10.1021/jp079512r}} @article{Foulkes1989, title={Tight-binding models and density-functional theory}, author={Foulkes, W Matthew C and Haydock, Roger}, - journal={Physical review B}, + journal={Phys. Rev. B}, volume={39}, number={17}, pages={12520}, @@ -4799,7 +4803,7 @@ doi = {10.1021/jp079512r}} @article{Elstner1998, title={Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties}, author={Elstner, Marcus and Porezag, Dirk and Jungnickel, G and Elsner, J and Haugk, M and Frauenheim, Th and Suhai, Sandor and Seifert, Gotthard}, - journal={Physical Review B}, + journal={Phys. Rev. B}, volume={58}, number={11}, pages={7260}, @@ -4809,7 +4813,7 @@ doi = {10.1021/jp079512r}} @article{Porezag1995, title={Construction of tight-binding-like potentials on the basis of density-functional theory: Application to carbon}, author={Porezag, Dirk and Frauenheim, Th and K{\"o}hler, Th and Seifert, Gotthard and Kaschner, R}, - journal={Physical Review B}, + journal={Phys. Rev. B}, volume={51}, number={19}, pages={12947}, @@ -4819,7 +4823,7 @@ doi = {10.1021/jp079512r}} @article{Li2018, title={Localized orbital scaling correction for systematic elimination of delocalization error in density functional approximations}, author={Li, Chen and Zheng, Xiao and Su, Neil Qiang and Yang, Weitao}, - journal={National Science Review}, + journal={Natl. Sci. Rev.}, volume={5}, number={2}, pages={203--215}, @@ -4829,7 +4833,7 @@ doi = {10.1021/jp079512r}} @article{Krukau2006, title={Influence of the exchange screening parameter on the performance of screened hybrid functionals}, author={Krukau, Aliaksandr V and Vydrov, Oleg A and Izmaylov, Artur F and Scuseria, Gustavo E}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={125}, number={22}, pages={224106}, @@ -4839,7 +4843,7 @@ doi = {10.1021/jp079512r}} @article{Henderson2009, title={Can short-range hybrids describe long-range-dependent properties?}, author={Henderson, Thomas M and Izmaylov, Artur F and Scalmani, Giovanni and Scuseria, Gustavo E}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={131}, number={4}, pages={044108}, @@ -4849,7 +4853,7 @@ doi = {10.1021/jp079512r}} @article{Zhao2008, title={The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals}, author={Zhao, Yan and Truhlar, Donald G}, - journal={Theoretical Chemistry Accounts}, + journal={Theor. Chem. Acc.}, volume={120}, number={1-3}, pages={215-241}, @@ -4859,7 +4863,7 @@ doi = {10.1021/jp079512r}} @article{Adamo1999, title={Toward reliable density functional methods without adjustable parameters: The PBE0 model}, author={Adamo, Carlo and Barone, Vincenzo}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={110}, number={13}, pages={6158--6170}, @@ -4869,7 +4873,7 @@ doi = {10.1021/jp079512r}} @article{Stephens1994, title={Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields}, author={Stephens, Philip J and Devlin, Frank J and Chabalowski, Cary F and Frisch, Michael J}, - journal={The Journal of physical chemistry}, + journal={J. Phys. Chem.}, volume={98}, number={45}, pages={11623--11627}, @@ -4879,7 +4883,7 @@ doi = {10.1021/jp079512r}} @article{Becke1988, title={Density-functional exchange-energy approximation with correct asymptotic behavior}, author={Becke, Axel D}, - journal={Physical review A}, + journal={Phys. Rev. A}, volume={38}, number={6}, pages={3098}, @@ -4889,7 +4893,7 @@ doi = {10.1021/jp079512r}} @article{Lee1988, title={Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density}, author={Lee, Chengteh and Yang, Weitao and Parr, Robert G}, - journal={Physical review B}, + journal={Phys. Rev. B}, volume={37}, number={2}, pages={785-789}, @@ -4899,7 +4903,7 @@ doi = {10.1021/jp079512r}} @article{Becke1993, title={Density functional thermochemistry. III. The role of exact exchange}, author={Becke, Axel D}, - journal={The Journal of Chemical Physics}, + journal={J. Chem. Phys.}, volume={98}, pages={5648-5652}, year={1993}, @@ -4909,7 +4913,7 @@ doi = {10.1021/jp079512r}} @article{Becke1993, title={A new mixing of Hartree--Fock and local density-functional theories}, author={Becke, Axel D}, - journal={The Journal of chemical physics}, + journal={J. Chem. Phys.}, volume={98}, number={2}, pages={1372--1377}, @@ -4919,7 +4923,7 @@ doi = {10.1021/jp079512r}} @article{Perdew1996, title={Comparison shopping for a gradient-corrected density functional}, author={Perdew, John P and Burke, Kieron}, - journal={International journal of quantum chemistry}, + journal={Int. J. Quantum Chem.}, volume={57}, number={3}, pages={309--319}, @@ -4929,7 +4933,7 @@ doi = {10.1021/jp079512r}} @article{Herman1969, title={Improved statistical exchange approximation for inhomogeneous many-electron systems}, author={Herman, Frank and Van Dyke, John P and Ortenburger, Irene B}, - journal={Physical Review Letters}, + journal={Phys. Rev. Lett.}, volume={22}, number={16}, pages={807-811}, @@ -4939,7 +4943,7 @@ doi = {10.1021/jp079512r}} @article{Levy1979, title={Universal variational functionals of electron densities, first-order density matrices, and natural spin-orbitals and solution of the v-representability problem}, author={Levy, Mel}, - journal={Proceedings of the National Academy of Sciences}, + journal={Proc. Natl. Acad. Sci.}, volume={76}, number={12}, pages={6062--6065}, @@ -4957,7 +4961,7 @@ doi = {10.1021/jp079512r}} publisher={APS}} @article{Fermi1928, - title={Eine statistische Methode zur Bestimmung einiger Eigenschaften des Atoms und ihre Anwendung auf die Theorie des periodischen Systems der Elemente}, + title={Eine statistische methode zur bestimmung einiger eigenschaften des atoms und ihre anwendung auf die theorie des periodischen systems der elemente}, author={Fermi, Enrico}, journal={Zeitschrift f{\"u}r Physik}, volume={48}, @@ -4969,7 +4973,8 @@ doi = {10.1021/jp079512r}} @article{Thomas1927, title={The calculation of atomic fields}, author={Thomas, Llewellyn H}, - journal={Mathematical Proceedings of the Cambridge Philosophical Society}, + journal={Proc. Camb. Philos. Soc. +}, volume={23}, number={5}, pages={542--548}, @@ -4979,7 +4984,7 @@ doi = {10.1021/jp079512r}} @article{kohn1999nobel, title={Nobel Lecture: Electronic structure of matter—wave functions and density functionals}, author={Kohn, Walter}, - journal={Reviews of Modern Physics}, + journal={Rev. Mod. Phys.}, volume={71}, number={5}, pages={1253}, @@ -5185,7 +5190,7 @@ doi = {10.1021/jp079512r}} @article{Head1994, title={A doubles correction to electronic excited states from configuration interaction in the space of single substitutions}, author={Head-Gordon, Martin and Rico, Rudolph J and Oumi, Manabu and Lee, Timothy J}, - journal={Chemical Physics Letters}, + journal={Chem. Phys. Lett.}, volume={219}, number={1-2}, pages={21--29}, @@ -5201,7 +5206,7 @@ doi = {10.1021/jp079512r}} @article{Cramer2003, title={Essentials of computational chemistry}, author={Cramer, Christopher J and Bickelhaupt, FM}, - journal={ANGEWANDTE CHEMIE-INTERNATIONAL EDITION IN ENGLISH-}, + journal={Angew. Chem. Int. Ed. }, volume={42}, number={4}, pages={381--381}, @@ -5211,7 +5216,7 @@ doi = {10.1021/jp079512r}} @article{Trofimov1995, title={An efficient polarization propagator approach to valence electron excitation spectra}, author={Trofimov, AB and Schirmer, J}, - journal={Journal of Physics B: Atomic, Molecular and Optical Physics}, + journal={J. Phys. B}, volume={28}, number={12}, pages={2299-2324}, @@ -5221,7 +5226,7 @@ doi = {10.1021/jp079512r}} @article{Vcivzek1966, title={On the correlation problem in atomic and molecular systems. Calculation of wavefunction components in Ursell-type expansion using quantum-field theoretical methods}, author={{\v{C}}{\'\i}{\v{z}}ek, Ji{\v{r}}{\'\i}}, - journal={The Journal of Chemical Physics}, + journal={J. Chem. Phys.}, volume={45}, number={11}, pages={4256--4266}, @@ -5232,7 +5237,7 @@ doi = {10.1021/jp079512r}} @article{Pople1976, title={Theoretical models incorporating electron correlation}, author={Pople, John A and Binkley, J Stephen and Seeger, Rolf}, - journal={International Journal of Quantum Chemistry}, + journal={Int. J. Quantum Chem.}, volume={10}, number={S10}, pages={1--19}, @@ -5357,7 +5362,7 @@ publisher={John Wiley \& Sons,Ltd}} @article{Born1927, title={Zur quantentheorie der molekeln}, author={Born, Max and Oppenheimer, Robert}, - journal={Annalen der physik}, + journal={Ann. Phys. }, volume={389}, number={20}, pages={457--484}, @@ -5366,7 +5371,7 @@ publisher={John Wiley \& Sons,Ltd}} } @article{Epstein1966, - title={Ground-State Energy of a Molecule in the Adiabatic Approximation}, + title={Ground-state energy of a molecule in the adiabatic approximation}, author={Epstein, Saul T}, journal={J. Chem. Phys.}, volume={44}, @@ -5390,7 +5395,7 @@ publisher={John Wiley \& Sons,Ltd}} @article{schrodinger1926quantisierung, title={Quantisierung als eigenwertproblem}, author={Schr{\"o}dinger, Erwin}, - journal={Annalen der physik}, + journal={Ann. Phys. }, volume={385}, number={13}, pages={437--490}, @@ -5411,11 +5416,10 @@ publisher={John Wiley \& Sons,Ltd}} Number = {2}, Pages = {185--192}, Publisher = {Wiley Online Library}, - Title = {Calculations of Molecules, Clusters, and Solids with a Simplified LCAO-DFT-LDA Scheme}, + Title = {Calculations of molecules, clusters, and solids with a simplified LCAO-DFT-LDA scheme}, Volume = {58}, Year = {1996}} - @article{dftb1, Author = {Porezag, Dirk and Frauenheim, Th and K{\"o}hler, Th and Seifert, Gotthard and Kaschner, R}, Date-Added = {2019-10-15 11:27:56 +0000}, @@ -5424,7 +5428,7 @@ publisher={John Wiley \& Sons,Ltd}} Number = {19}, Pages = {12947--12958}, Publisher = {APS}, - Title = {Construction of Tight-Binding-Like Potentials on the Basis of Density-Functional Theory: Application to Carbon}, + Title = {Construction of tight-binding-like potentials on the basis of density-functional theory: application to carbon}, Volume = {51}, Year = {1995}} @@ -5445,7 +5449,7 @@ publisher={John Wiley \& Sons,Ltd}} Number = {2011}, Pages = {20120483}, Publisher = {The Royal Society Publishing}, - Title = {Density Functional Tight Binding}, + Title = {Density functional tight binding}, Volume = {372}, Year = {2014}} @@ -5484,14 +5488,14 @@ ISSN = {{0004-640X}}, Unique-ID = {ISI:A1979HW27300006}} @inproceedings{Castleman1978, - title={MOLECULAR-PROPERTIES OF SMALL CLUSTERS AND THEIR RELATIONSHIP TO UNDERSTANDING NUCLEATION PHENOMENA}, + title={Molecular-properties of small clusters and their relationship to understanding nucleation phenomena}, author={CASTLEMAN, A. W and HOLLAND, P. M.}, - booktitle={ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY}, + booktitle={Abstracts of papers of the american chemical society}, volume={175}, number={MAR}, pages={74--74}, year={1978}, - organization={AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036}} + organization={Am. Chem. Soc. 1155 16TH ST, NW, WASHINGTON, DC 20036}} @article{Hoover2014, title={Need to track organic nano-particles across the universe? NASA’s got an app for that}, @@ -5511,7 +5515,8 @@ Unique-ID = {ISI:A1979HW27300006}} @article{Hudgins2005, title={Variations in the peak position of the 6.2 $\mu$m interstellar emission feature: A tracer of N in the interstellar polycyclic aromatic hydrocarbon population}, author={Hudgins, Douglas M and Bauschlicher Jr, Charles W and Allamandola, LJ}, - journal={The Astrophysical Journal}, + journal={Astrophys. J. +}, volume={632}, number={1}, pages={316}, @@ -5528,7 +5533,7 @@ Unique-ID = {ISI:A1979HW27300006}} @article{Rapacioli2019, Author = {Rapacioli, Mathias and Spiegelman, Fernand and Tarrat, Nathalie}, Title = {{Evidencing the relationship between isomer spectra and melting: the 20-and 55-atom silver and gold cluster cases}}, -Journal = {{PHYSICAL CHEMISTRY CHEMICAL PHYSICS}}, +Journal = {{Phys. Chem. Chem. Phys.}}, Year = {{2019}}, Volume = {{21}}, Number = {{45}}, @@ -5541,8 +5546,8 @@ ResearcherID-Numbers = {Rapacioli, mathias/F-7141-2019}} @article{Deng2018, Author = {Deng, Y. H. and Wen, D. D. and Li, Y. and Liu, J. and Peng, P.}, -Title = {{Local atomic structures of amorphous Pd80Si20 alloys and their configuration heredity in the rapid solidification}}, -Journal = {{PHILOSOPHICAL MAGAZINE}}, +Title = {{Local atomic structures of amorphous Pd$_{80}$Si$_{20}$ alloys and their configuration heredity in the rapid solidification}}, +Journal = {{Philos. Mag.}}, Year = {{2018}}, Volume = {{98}}, Number = {{31, A}}, @@ -5556,7 +5561,7 @@ ResearcherID-Numbers = {Yonghe, Deng/F-8623-2019}} @article{Tian2018, Author = {Tian Xiao-Lin and Zhao Yu-Hong and Tian Jin-Zhong and Hou Hua}, Title = {{Effects of interatomic potential on precipitation sequences of medium Al concentration in Ni75AlxV25-x alloys}}, -Journal = {{ACTA PHYSICA SINICA}}, +Journal = {{Acta Phys. Sin.}}, Year = {{2018}}, Volume = {{67}}, Number = {{23}}, @@ -5569,7 +5574,7 @@ Unique-ID = {ISI:000455404700001}} @article{Xu2020, Author = {Xu, Qiaofei and Xu, Baijie and Kong, Hui and He, Peipei and Wang, Jiawei and Kannan, Thirumurthy and Ma, Pengtao and Wang, Jingping and Niu, Jingyang}, Title = {{Synthesis and Characterization of a Crown-Shaped 36-Molybdate Cluster and Application in Catalyzing Knoevenagel Condensation}}, -Journal = {{INORGANIC CHEMISTRY}}, +Journal = {{Inorg. Chem.}}, Year = {{2020}}, Volume = {{59}}, Number = {{15}}, @@ -5596,14 +5601,14 @@ EISSN = {1932-7455}} @article{Fucugauchi1994, title={Chemical effects of (n, $\gamma$) nuclear reaction on (Mo$_6$Cl$_8$)Cl$_4$}, author={Fucugauchi, L and Millan, S and Mondragon, A and Solache-Rios, M}, - journal={Journal of radioanalytical and nuclear chemistry}, + journal={ J. Radioanal. Nucl. Chem.}, volume={178}, number={2}, pages={437--442}, year={1994}} @article{Colton1965, - title={Magnetic Evidence for Trinuclear Clusters in Rhenium (IV) Chloride}, + title={Magnetic evidence for trinuclear clusters in rhenium (IV) chloride}, author={Colton, R and Martin, R. L.}, journal={Nature}, volume={205}, @@ -5625,7 +5630,7 @@ doi = {10.1021/om00028a082}} @article{Dahl1963, title={The crystal structure of dimanganese decacarbonyl Mn$_2$(CO)$_{10}$}, author={Dahl, L. F. and Rundle, R. E.}, - journal={Acta Crystallographica}, + journal={Acta Crystallogr.}, volume={16}, number={5}, pages={419--426}, @@ -5635,7 +5640,7 @@ doi = {10.1021/om00028a082}} @article{Mayer2002, title={Ion rearrangement at the beginning of cluster formation: isomerization pathways and dissociation kinetics for the ionized dimethylamine dimer}, author={Mayer, Paul M}, - journal={International Journal of Mass Spectrometry}, + journal={International J. Mass Spectrom.}, volume={218}, number={1}, pages={1--10}, @@ -5644,8 +5649,8 @@ doi = {10.1021/om00028a082}} @article{Castleman1996, author = {Castleman, A. W. and Bowen, K. H.}, -title = {Clusters:  Structure, Energetics, and Dynamics of Intermediate States of Matter}, -journal = {The Journal of Physical Chemistry}, +title = {Clusters:  Structure, energetics, and dynamics of intermediate states of matter}, +journal = {J. Phys. Chem.}, volume = {100}, number = {31}, pages = {12911-12944}, @@ -5693,7 +5698,7 @@ URL = {https://doi.org/10.1146/annurev.pc.45.100194.003345 @article{Luo2016, author = {Luo, Zhixun and Castleman, A. W. and Khanna, Shiv N.}, -title = {Reactivity of Metal Clusters}, +title = {Reactivity of metal clusters}, journal = {Chem. Rev.}, volume = {116}, number = {23}, @@ -5706,7 +5711,7 @@ URL = {https://doi.org/10.1021/acs.chemrev.6b00230}} @article{Wang2016, author = {Lai-Sheng Wang}, title = {Photoelectron spectroscopy of size-selected boron clusters: from planar structures to borophenes and borospherenes}, -journal = {International Reviews in Physical Chemistry}, +journal = {Int. Rev. Phys. Chem.}, volume = {35}, number = {1}, pages = {69-142}, @@ -5730,8 +5735,8 @@ URL = {https://doi.org/10.1080/0144235X.2012.760836}} @article{Fassler2004, author = {F{\"a}ssler, Thomas F. and Hoffmann, Stephan D.}, -title = {Endohedral Zintl Ions: Intermetalloid Clusters}, -journal = {Angewandte Chemie International Edition}, +title = {Endohedral zintl ions: intermetalloid clusters}, +journal = {Angew. Chem. Int. Ed.}, volume = {43}, number = {46}, pages = {6242-6247}, @@ -5757,8 +5762,8 @@ year = {2004}} @article{Schnepf2002, author = {Schnepf, Andreas and Schnöckel, Hansgeorg}, -title = {Metalloid Aluminum and Gallium Clusters: Element Modifications on the Molecular Scale?}, -journal = {Angewandte Chemie International Edition}, +title = {Metalloid aluminum and gallium clusters: element modifications on the molecular scale?}, +journal = {Angew. Chem. Int. Ed. }, volume = {41}, number = {19}, pages = {3532-3554}, @@ -5768,8 +5773,8 @@ year = {2002}} @article{Yoon2020, Author = {Yoon, Jiho and Lesne, Edouard and Sklarek, Kornelia and Sheckelton, John and Pasco, Chris and Parkin, Stuart S. P. and McQueen, Tyrel M. and Ali, Mazhar N.}, -Title = {{Anomalous thickness-dependent electrical conductivity in van der Waals layered transition metal halide, Nb3Cl8}}, -Journal = {Journal of Physics-Condensed Matter}, +Title = {{Anomalous thickness-dependent electrical conductivity in van der Waals layered transition metal halide, Nb$_3$Cl$_8$}}, +Journal = {J. Phys. Condens. Matter}, Year = {{2020}}, Volume = {{32}}, Number = {{30}}, @@ -5781,8 +5786,8 @@ EISSN = {1361-648X}} @article{Sutton2016, author = {Sutton, Paul W. and Dahl, Lawrence F.}, -title = {The Molecular Structure of Co3(CO)9CCH3. A Tricyclic Organocobalt Complex Containing a Metal-Coordinated Triply Bridging Aliphatic Carbon Atom}, -journal = {Journal of the American Chemical Society}, +title = {The Molecular structure of Co$_3$(CO)$_9$CCH$_3$. A tricyclic organocobalt complex containing a metal-coordinated triply bridging aliphatic carbon atom}, +journal = {J. Am. Chem. Soc.}, volume = {89}, number = {2}, pages = {261-268}, @@ -5809,7 +5814,7 @@ URL = {https://doi.org/10.1021/ja00978a016}, @article{evans1973, title={The meaning and definition of “charge” in molecules}, author={Evans, Robert S and Huheey, James E}, - journal={Chemical Physics Letters}, + journal={Chem. Phys. Lett.}, volume={19}, number={1}, pages={114--116}, diff --git a/thesis/thesis.aux b/thesis/thesis.aux index f1f9bb7..cc98612 100644 --- a/thesis/thesis.aux +++ b/thesis/thesis.aux @@ -79,9 +79,9 @@ \bibcite{Faraday1857}{{32}{}{{}}{{}}} \bibcite{Kulmala2000}{{33}{}{{}}{{}}} \bibcite{Wang2008}{{34}{}{{}}{{}}} -\@writefile{toc}{\contentsline {chapter}{References}{163}{chapter*.82}\protected@file@percent } \bibcite{Depalma2014}{{35}{}{{}}{{}}} \bibcite{Katakuse1985}{{36}{}{{}}{{}}} +\@writefile{toc}{\contentsline {chapter}{References}{161}{chapter*.82}\protected@file@percent } \bibcite{Posthumus2009}{{37}{}{{}}{{}}} \bibcite{Castleman2009}{{38}{}{{}}{{}}} \bibcite{Henglein1989}{{39}{}{{}}{{}}} @@ -467,69 +467,68 @@ \bibcite{Brechignac1994}{{419}{}{{}}{{}}} \bibcite{Wong2004}{{420}{}{{}}{{}}} \bibcite{Bush2008}{{421}{}{{}}{{}}} -\bibcite{Gatchell2014}{{422}{}{{}}{{}}} -\bibcite{Boering1992}{{423}{}{{}}{{}}} -\bibcite{Wells2005}{{424}{}{{}}{{}}} -\bibcite{Ma1997}{{425}{}{{}}{{}}} 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-\bibcite{Warshel1976}{{451}{}{{}}{{}}} -\bibcite{Cui2001}{{452}{}{{}}{{}}} -\bibcite{Iftner2014}{{453}{}{{}}{{}}} -\bibcite{Kukk2015}{{454}{}{{}}{{}}} -\bibcite{Rapacioli2018atomic}{{455}{}{{}}{{}}} -\bibcite{Dontot2019}{{456}{}{{}}{{}}} -\bibcite{Chung2011}{{457}{}{{}}{{}}} -\bibcite{Saggese2015}{{458}{}{{}}{{}}} -\bibcite{Mao2017}{{459}{}{{}}{{}}} -\bibcite{Wang2018}{{460}{}{{}}{{}}} -\bibcite{Kyrtopoulos2001}{{461}{}{{}}{{}}} -\bibcite{Farmer2003}{{462}{}{{}}{{}}} -\bibcite{Aumaitre2019}{{463}{}{{}}{{}}} -\bibcite{Rapacioli2005}{{464}{}{{}}{{}}} -\bibcite{Berne2008}{{465}{}{{}}{{}}} -\bibcite{Eschenbach1998}{{466}{}{{}}{{}}} -\bibcite{Goulart2017}{{467}{}{{}}{{}}} -\bibcite{Lei2019}{{468}{}{{}}{{}}} -\bibcite{Roser2015}{{469}{}{{}}{{}}} -\bibcite{Lemmens2019}{{470}{}{{}}{{}}} -\bibcite{Delaunay2015}{{471}{}{{}}{{}}} -\bibcite{Piacenza2005}{{472}{}{{}}{{}}} -\bibcite{Birer2015}{{473}{}{{}}{{}}} -\bibcite{Zhao2008truhlar}{{474}{}{{}}{{}}} -\bibcite{Bowal2019}{{475}{}{{}}{{}}} -\bibcite{Ricca2013}{{476}{}{{}}{{}}} -\bibcite{Grafenstein2009}{{477}{}{{}}{{}}} -\bibcite{Dontot2016}{{478}{}{{}}{{}}} -\bibcite{Dontot2020}{{479}{}{{}}{{}}} -\bibcite{Rapacioli2011}{{480}{}{{}}{{}}} -\bibcite{Gatchell2016}{{481}{}{{}}{{}}} -\bibcite{Gatchell2016knockout}{{482}{}{{}}{{}}} -\bibcite{Levine1987}{{483}{}{{}}{{}}} -\bibcite{Chen2014}{{484}{}{{}}{{}}} +\bibcite{Boering1992}{{422}{}{{}}{{}}} +\bibcite{Wells2005}{{423}{}{{}}{{}}} +\bibcite{Ma1997}{{424}{}{{}}{{}}} +\bibcite{Chowdhury2009}{{425}{}{{}}{{}}} +\bibcite{Sleno2004ion}{{426}{}{{}}{{}}} +\bibcite{Cody1982}{{427}{}{{}}{{}}} +\bibcite{Olsen2007higher}{{428}{}{{}}{{}}} +\bibcite{Hart2011}{{429}{}{{}}{{}}} +\bibcite{Gauthier1991}{{430}{}{{}}{{}}} +\bibcite{Laskin2005}{{431}{}{{}}{{}}} +\bibcite{Mcquinn2009}{{432}{}{{}}{{}}} +\bibcite{Carl2013}{{433}{}{{}}{{}}} +\bibcite{Hofstetter2013}{{434}{}{{}}{{}}} +\bibcite{Coates2017}{{435}{}{{}}{{}}} +\bibcite{Haag2009}{{436}{}{{}}{{}}} +\bibcite{Li1992}{{437}{}{{}}{{}}} +\bibcite{Bobbert2002}{{438}{}{{}}{{}}} +\bibcite{Spasov2000}{{439}{}{{}}{{}}} +\bibcite{Armentrout2008}{{440}{}{{}}{{}}} +\bibcite{Rodgers1998}{{441}{}{{}}{{}}} +\bibcite{Armentrout2007}{{442}{}{{}}{{}}} +\bibcite{Braud2017}{{443}{}{{}}{{}}} +\bibcite{Chirot2006new}{{444}{}{{}}{{}}} +\bibcite{Frenzel2004}{{445}{}{{}}{{}}} +\bibcite{Spiegelman2020}{{446}{}{{}}{{}}} +\bibcite{Simon2017}{{447}{}{{}}{{}}} +\bibcite{Rapacioli2018}{{448}{}{{}}{{}}} +\bibcite{Simon2018}{{449}{}{{}}{{}}} +\bibcite{Warshel1976}{{450}{}{{}}{{}}} +\bibcite{Cui2001}{{451}{}{{}}{{}}} +\bibcite{Iftner2014}{{452}{}{{}}{{}}} +\bibcite{Kukk2015}{{453}{}{{}}{{}}} +\bibcite{Rapacioli2018atomic}{{454}{}{{}}{{}}} +\bibcite{Dontot2019}{{455}{}{{}}{{}}} +\bibcite{Chung2011}{{456}{}{{}}{{}}} +\bibcite{Saggese2015}{{457}{}{{}}{{}}} +\bibcite{Mao2017}{{458}{}{{}}{{}}} +\bibcite{Wang2018}{{459}{}{{}}{{}}} +\bibcite{Kyrtopoulos2001}{{460}{}{{}}{{}}} +\bibcite{Farmer2003}{{461}{}{{}}{{}}} +\bibcite{Aumaitre2019}{{462}{}{{}}{{}}} +\bibcite{Rapacioli2005}{{463}{}{{}}{{}}} +\bibcite{Berne2008}{{464}{}{{}}{{}}} +\bibcite{Eschenbach1998}{{465}{}{{}}{{}}} +\bibcite{Goulart2017}{{466}{}{{}}{{}}} +\bibcite{Lei2019}{{467}{}{{}}{{}}} +\bibcite{Roser2015}{{468}{}{{}}{{}}} +\bibcite{Lemmens2019}{{469}{}{{}}{{}}} +\bibcite{Delaunay2015}{{470}{}{{}}{{}}} +\bibcite{Piacenza2005}{{471}{}{{}}{{}}} +\bibcite{Birer2015}{{472}{}{{}}{{}}} +\bibcite{Zhao2008truhlar}{{473}{}{{}}{{}}} +\bibcite{Bowal2019}{{474}{}{{}}{{}}} +\bibcite{Ricca2013}{{475}{}{{}}{{}}} +\bibcite{Grafenstein2009}{{476}{}{{}}{{}}} +\bibcite{Dontot2016}{{477}{}{{}}{{}}} +\bibcite{Dontot2020}{{478}{}{{}}{{}}} +\bibcite{Rapacioli2011}{{479}{}{{}}{{}}} +\bibcite{Gatchell2016}{{480}{}{{}}{{}}} +\bibcite{Gatchell2016knockout}{{481}{}{{}}{{}}} +\bibcite{Levine1987}{{482}{}{{}}{{}}} +\bibcite{Chen2014}{{483}{}{{}}{{}}} \FN@pp@footnotehinttrue \@input{6_backmatter/declaration.aux} \providecommand\NAT@force@numbers{}\NAT@force@numbers diff --git a/thesis/thesis.bbl 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Rev.}, {\bf 116}(23):14456--14492, 2016. \newblock PMID: 27960263. @@ -321,8 +310,7 @@ \newblock \href{https://doi.org/10.1080/0144235X.2016.1147816}{{\bf Photoelectron spectroscopy of size-selected boron clusters: from planar structures to borophenes and borospherenes}}. -\newblock {\em International Reviews in Physical Chemistry}, {\bf - 35}(1):69--142, 2016. +\newblock {\em Int. Rev. Phys. Chem.}, {\bf 35}(1):69--142, 2016. \bibitem{Jiang2019} {\sc Shuai Jiang, Xiaoli Zhang, Xiucheng Zheng, and Xiangtao Kong}. @@ -347,9 +335,8 @@ \bibitem{Castleman1996} {\sc A.~W. Castleman and K.~H. Bowen}. \newblock \href{https://doi.org/10.1021/jp961030k}{{\bf Clusters:  Structure, - Energetics, and Dynamics of Intermediate States of Matter}}. -\newblock {\em The Journal of Physical Chemistry}, {\bf 100}(31):12911--12944, - 1996. + energetics, and dynamics of intermediate states of matter}}. +\newblock {\em J. Phys. 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Environ.}, {\bf 496}(1-2):207--228, + 2001. \bibitem{Farmer2003} {\sc Peter~B Farmer, Rajinder Singh, Balvinder Kaur, Radim~J Sram, Blanka @@ -2928,64 +2818,59 @@ \newblock {\bf Molecular epidemiology studies of carcinogenic environmental pollutants: effects of polycyclic aromatic hydrocarbons (PAHs) in environmental pollution on exogenous and oxidative DNA damage}. -\newblock {\em Mutation Research/Reviews in Mutation Research}, {\bf - 544}(2-3):397--402, 2003. +\newblock {\em Mutat. Res.-Rev. Mutat. Res.}, {\bf 544}(2-3):397--402, 2003. \bibitem{Aumaitre2019} {\sc Cyril Aumaitre and Jean-Fran{\c{c}}ois Morin}. \newblock {\bf Polycyclic aromatic hydrocarbons as potential building blocks for organic solar cells}. -\newblock {\em The Chemical Record}, {\bf 19}(6):1142--1154, 2019. +\newblock {\em Chem. Rec.}, {\bf 19}(6):1142--1154, 2019. \bibitem{Rapacioli2005} {\sc M~Rapacioli, C~Joblin, and P~Boissel}. \newblock {\bf Spectroscopy of polycyclic aromatic hydrocarbons and very small grains in photodissociation regions}. -\newblock {\em Astronomy \& Astrophysics}, {\bf 429}(1):193--204, 2005. +\newblock {\em Astron. Astrophys.}, {\bf 429}(1):193--204, 2005. \bibitem{Berne2008} {\sc O~Bern{\'e}, C~Joblin, M~Rapacioli, J~Thomas, J-C Cuillandre, and Y~Deville}. -\newblock {\bf Extended Red Emission and the evolution of carbonaceous +\newblock {\bf Extended red emission and the evolution of carbonaceous nanograins in NGC 7023}. -\newblock {\em Astronomy \& Astrophysics}, {\bf 479}(3):L41--L44, 2008. +\newblock {\em Astron. Astrophys.}, {\bf 479}(3):L41--L44, 2008. \bibitem{Eschenbach1998} {\sc Annette Eschenbach, Reinhard Wienberg, and Bernd Mahro}. \newblock {\bf Fate and stability of nonextractable residues of [14C] PAH in contaminated soils under environmental stress conditions}. -\newblock {\em Environmental science \& technology}, {\bf 32}(17):2585--2590, - 1998. +\newblock {\em Environ. Sci. Technol.}, {\bf 32}(17):2585--2590, 1998. \bibitem{Goulart2017} {\sc Marcelo Goulart, Martin Kuhn, Bilal Rasul, Johannes Postler, Michael Gatchell, Henning Zettergren, Paul Scheier, and Olof Echt}. \newblock {\bf The structure of coronene cluster ions inferred from H 2 uptake in the gas phase}. -\newblock {\em Physical Chemistry Chemical Physics}, {\bf 19}(41):27968--27973, - 2017. +\newblock {\em Phys. Chem. Chem. Phys.}, {\bf 19}(41):27968--27973, 2017. \bibitem{Lei2019} {\sc Lei Lei, Yuzhong Yao, Jie Zhang, Dale Tronrud, Wei Kong, Chengzhu Zhang, Lan Xue, L{\'e}o Dontot, and Mathias Rapacioli}. -\newblock {\bf Electron Diffraction of Pyrene Nanoclusters Embedded in - Superfluid Helium Droplets}. -\newblock {\em The journal of physical chemistry letters}, {\bf - 11}(3):724--729, 2019. +\newblock {\bf Electron diffraction of pyrene nanoclusters embedded in + superfluid helium droplets}. +\newblock {\em J. Phys. Chem. Lett.}, {\bf 11}(3):724--729, 2019. \bibitem{Roser2015} {\sc JE~Roser and A~Ricca}. \newblock {\bf Polycyclic aromatic hydrocarbon clusters as sources of interstellar infrared emission}. -\newblock {\em The Astrophysical Journal}, {\bf 801}(2):108, 2015. +\newblock {\em Astrophys. J.}, {\bf 801}(2):108, 2015. \bibitem{Lemmens2019} {\sc Alexander~K Lemmens, S{\'e}bastien Gruet, Amanda~L Steber, Jens Antony, Stefan Grimme, Melanie Schnell, and Anouk~M Rijs}. \newblock {\bf Far-IR and UV spectral signatures of controlled complexation and microhydration of the polycyclic aromatic hydrocarbon acenaphthene}. -\newblock {\em Physical Chemistry Chemical Physics}, {\bf 21}(7):3414--3422, - 2019. +\newblock {\em Phys. Chem. Chem. Phys.}, {\bf 21}(7):3414--3422, 2019. \bibitem{Delaunay2015} {\sc Rudy Delaunay, Michael Gatchell, Patrick Rousseau, Alicja Domaracka, @@ -2993,27 +2878,25 @@ Alcam{\'\i}, et~al.} \newblock {\bf Molecular growth inside of polycyclic aromatic hydrocarbon clusters induced by ion collisions}. -\newblock {\em The journal of physical chemistry letters}, {\bf - 6}(9):1536--1542, 2015. +\newblock {\em J. Phys. Chem. Lett.}, {\bf 6}(9):1536--1542, 2015. \bibitem{Piacenza2005} {\sc Manuel Piacenza and Stefan Grimme}. \newblock {\bf Van der Waals complexes of polar aromatic molecules: Unexpected structures for dimers of azulene}. -\newblock {\em Journal of the American Chemical Society}, {\bf - 127}(42):14841--14848, 2005. +\newblock {\em J. Am. Chem. Soc.}, {\bf 127}(42):14841--14848, 2005. \bibitem{Birer2015} {\sc {\"O}~Birer and E~Yurtsever}. \newblock {\bf Dimer formation of perylene: An ultracold spectroscopic and computational study}. -\newblock {\em Journal of Molecular Structure}, {\bf 1097}:29--36, 2015. +\newblock {\em J. Mol. Struct.}, {\bf 1097}:29--36, 2015. \bibitem{Zhao2008truhlar} {\sc Y.~Zh{ao} and Donald~G. Truhlar}. \newblock \href{http://pubs.acs.org/doi/abs/10.1021/jp710918f}{{\bf A Prototype - for Graphene Material Simulation; Structures and Interaction Potentials of - Coronene Dimers}}. + for graphene material simulation; structures and interaction potentials of + coronene dimers}}. \newblock {\em J. Phys. Chem. C}, {\bf 112}:4061--4067, 2008. \bibitem{Bowal2019} @@ -3024,23 +2907,22 @@ \bibitem{Ricca2013} {\sc Alessandra Ricca, Charles~W Bauschlicher~Jr, and Louis~J Allamandola}. -\newblock {\bf The Infrared Spectroscopy of Neutral Polycyclic Aromatic - Hydrocarbon Clusters}. -\newblock {\em The Astrophysical Journal}, {\bf 776}(1):31, 2013. +\newblock {\bf The infrared spectroscopy of neutral polycyclic aromatic + hydrocarbon clusters}. +\newblock {\em Astrophys. J.}, {\bf 776}(1):31, 2013. \bibitem{Grafenstein2009} {\sc J{\"u}rgen Gr{\"a}fenstein and Dieter Cremer}. \newblock {\bf The self-interaction error and the description of non-dynamic electron correlation in density functional theory}. -\newblock {\em Theoretical Chemistry Accounts}, {\bf 123}(3):171--182, 2009. +\newblock {\em Theor. Chem. Acc.}, {\bf 123}(3):171--182, 2009. \bibitem{Dontot2016} {\sc L{\'e}o Dontot, Nicolas Suaud, Mathias Rapacioli, and Fernand Spiegelman}. \newblock {\bf An extended DFTB-CI model for charge-transfer excited states in cationic molecular clusters: model studies versus ab initio calculations in small PAH clusters}. -\newblock {\em Physical Chemistry Chemical Physics}, {\bf 18}(5):3545--3557, - 2016. +\newblock {\em Phys. Chem. Chem. Phys.}, {\bf 18}(5):3545--3557, 2016. \bibitem{Dontot2020} {\sc L{\'e}o Dontot, Fernand Spiegelman, S{\'e}bastien Zamith, and Mathias @@ -3054,8 +2936,7 @@ Mirtschink}. \newblock {\bf Modeling charge resonance in cationic molecular clusters: combining DFT-tight binding with configuration interaction}. -\newblock {\em Journal of chemical theory and computation}, {\bf 7}(1):44--55, - 2011. +\newblock {\em J. Chem. Theory Comput.}, {\bf 7}(1):44--55, 2011. \bibitem{Gatchell2016} {\sc Michael Gatchell}. @@ -3067,8 +2948,7 @@ {\sc Michael Gatchell and Henning Zettergren}. \newblock {\bf Knockout driven reactions in complex molecules and their clusters}. -\newblock {\em Journal of Physics B: Atomic, Molecular and Optical Physics}, - {\bf 49}(16):162001, 2016. +\newblock {\em J. Phys. B}, {\bf 49}(16):162001, 2016. \bibitem{Levine1987} {\sc Raphael~D Levine, Richard~Barry Bernstein, et~al.} diff --git a/thesis/thesis.blg b/thesis/thesis.blg index a4dee5a..aeca36f 100644 --- a/thesis/thesis.blg +++ b/thesis/thesis.blg @@ -1,4 +1,4 @@ -This is BibTeX, Version 0.99d (TeX Live 2018) +This is BibTeX, Version 0.99d (TeX Live 2019) Capacity: max_strings=100000, hash_size=100000, hash_prime=85009 The top-level auxiliary file: thesis.aux A level-1 auxiliary file: 0_frontmatter/abstract.aux @@ -9,11 +9,20 @@ A level-1 auxiliary file: 1_GeneIntro/GeneIntro.aux A level-1 auxiliary file: 2_Introduction/introduction.aux A level-1 auxiliary file: 3/structure_stability.aux A level-1 auxiliary file: 4/collision.aux +White space in argument---line 6 of file 4/collision.aux + : \citation{Holm2010,M. + : Gatchell2014,Gatchell2017} +I'm skipping whatever remains of this command A level-1 auxiliary file: 5/general_conclusion.aux The style file: Latex/Classes/PhDbiblio-url2.bst A level-1 auxiliary file: 6_backmatter/declaration.aux -Reallocated field_info (elt_size=4) to 18068 items from 5000. +Reallocated field_info (elt_size=4) to 18041 items from 5000. Database file #1: 6_backmatter/references.bib +I was expecting a `,' or a `}'---line 1252 of file 6_backmatter/references.bib + : + : @article{Bernal1933, +(Error may have been on previous line) +I'm skipping whatever remains of this entry You're missing a field name---line 1451 of file 6_backmatter/references.bib : : %howpublished={\url{https://en.wikipedia.org/wiki/Cluster_(physics)}}} @@ -25,118 +34,132 @@ Repeated entry---line 2436 of file 6_backmatter/references.bib I'm skipping whatever remains of this entry Warning--I'm ignoring Simon2018's extra "publisher" field --line 2669 of file 6_backmatter/references.bib -Repeated entry---line 3134 of file 6_backmatter/references.bib +Repeated entry---line 3139 of file 6_backmatter/references.bib : @article{Joblin2017 : , I'm skipping whatever remains of this entry -Repeated entry---line 3272 of file 6_backmatter/references.bib +Repeated entry---line 3276 of file 6_backmatter/references.bib : @article{Wei1991 : , I'm skipping whatever remains of this entry -Repeated entry---line 3292 of file 6_backmatter/references.bib +Repeated entry---line 3296 of file 6_backmatter/references.bib : @article{Liu2006 : , I'm skipping whatever remains of this entry Reallocated str_pool (elt_size=1) to 130000 items from 65000. -Repeated entry---line 3732 of file 6_backmatter/references.bib +I was expecting a `,' or a `}'---line 3649 of file 6_backmatter/references.bib + : + : @article{Hartke1993, +(Error may have been on previous line) +I'm skipping whatever remains of this entry +Repeated entry---line 3736 of file 6_backmatter/references.bib : @article{Douady2009 : , I'm skipping whatever remains of this entry -Repeated entry---line 3752 of file 6_backmatter/references.bib +Repeated entry---line 3756 of file 6_backmatter/references.bib : @article{Iannuzzi2003 : , I'm skipping whatever remains of this entry -Repeated entry---line 3818 of file 6_backmatter/references.bib +Repeated entry---line 3822 of file 6_backmatter/references.bib : @article{Goursot2007 : , I'm skipping whatever remains of this entry -Repeated entry---line 4044 of file 6_backmatter/references.bib +Repeated entry---line 4048 of file 6_backmatter/references.bib : @book{Kaplan2006 : , I'm skipping whatever remains of this entry -Repeated entry---line 4713 of file 6_backmatter/references.bib +Repeated entry---line 4717 of file 6_backmatter/references.bib : @article{Karplus2002 : , I'm skipping whatever remains of this entry -Repeated entry---line 4742 of file 6_backmatter/references.bib +Repeated entry---line 4746 of file 6_backmatter/references.bib : @book{Allen2017 : , I'm skipping whatever remains of this entry -Repeated entry---line 4909 of file 6_backmatter/references.bib +I was expecting a `,' or a `}'---line 4783 of file 6_backmatter/references.bib + : + : @article{Seifert1996, +(Error may have been on previous line) +I'm skipping whatever remains of this entry +Repeated entry---line 4913 of file 6_backmatter/references.bib : @article{Becke1993 : , I'm skipping whatever remains of this entry -Repeated entry---line 5145 of file 6_backmatter/references.bib +Repeated entry---line 5150 of file 6_backmatter/references.bib : @article{Raghavachari1989 : , I'm skipping whatever remains of this entry -Repeated entry---line 5155 of file 6_backmatter/references.bib +Repeated entry---line 5160 of file 6_backmatter/references.bib : @article{Purvis1982 : , I'm skipping whatever remains of this entry -Repeated entry---line 5185 of file 6_backmatter/references.bib +Repeated entry---line 5190 of file 6_backmatter/references.bib : @article{Head1994 : , I'm skipping whatever remains of this entry -Repeated entry---line 5221 of file 6_backmatter/references.bib +Repeated entry---line 5226 of file 6_backmatter/references.bib : @article{Vcivzek1966 : , I'm skipping whatever remains of this entry -Repeated entry---line 5351 of file 6_backmatter/references.bib +Repeated entry---line 5356 of file 6_backmatter/references.bib : @book{Jensen2017 : , I'm skipping whatever remains of this entry -Repeated entry---line 5431 of file 6_backmatter/references.bib +Repeated entry---line 5435 of file 6_backmatter/references.bib : @article{Elstner1998 : , I'm skipping whatever remains of this entry Warning--can't use both volume and number fields in Castleman1978 +Warning--empty journal in Shields2010 +Warning--empty year in Shields2010 Warning--empty journal in Finlayson1986 Warning--empty journal in Fleming1986 Warning--empty journal in Slater1968 Warning--empty year in Magnasco2009 +Warning--empty year in Oliveira2009 +Warning--empty year in Unger1993 Warning--empty title in GaussianCode Warning--empty journal in GaussianCode Warning--empty year in GaussianCode -You've used 484 entries, +You've used 483 entries, 2776 wiz_defined-function locations, - 3607 strings with 98136 characters, -and the built_in function-call counts, 223751 in all, are: -= -- 23367 -> -- 9299 + 3553 strings with 95663 characters, +and the built_in function-call 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-- 1878 +warning$ -- 12 +while$ -- 1750 +width$ -- 486 +write$ -- 5280 +(There were 22 error messages) diff --git a/thesis/thesis.brf b/thesis/thesis.brf index 55449f0..bebf8a7 100644 --- a/thesis/thesis.brf +++ b/thesis/thesis.brf @@ -202,7 +202,6 @@ \backcite {dftb2}{{19}{2.3}{section.2.3}} \backcite {Elstner1998}{{19}{2.3}{section.2.3}} \backcite {Elstner2014}{{19}{2.3}{section.2.3}} -\backcite {Cremer1993}{{19}{2.3}{section.2.3}} \backcite {Singh1986}{{19}{2.3}{section.2.3}} \backcite {Gao1996}{{19}{2.3}{section.2.3}} \backcite {Mordasini1998}{{19}{2.3}{section.2.3}} @@ -215,7 +214,7 @@ \backcite {Helgaker2014}{{20}{2.3.1}{equation.2.3.15}} \backcite {Roothaan1951}{{20}{2.3.1}{equation.2.3.15}} \backcite {Blinder2018}{{20}{2.3.1}{equation.2.3.15}} -\backcite {koch1999}{{21}{2.3.1}{equation.2.3.15}} +\backcite {koch1999}{{20}{2.3.1}{equation.2.3.15}} \backcite {Moskowitz1965}{{21}{2.3.1}{equation.2.3.15}} \backcite {Lowdin1995}{{21}{2.3.1}{equation.2.3.15}} \backcite {Jensen2017}{{21}{2.3.1}{equation.2.3.15}} @@ -235,145 +234,145 @@ \backcite {Head1994}{{21}{2.3.1}{equation.2.3.15}} \backcite {Magnasco2009}{{21}{2.3.1}{equation.2.3.15}} \backcite {Dacosta2011}{{21}{2.3.1}{equation.2.3.15}} +\backcite {Kohn1965}{{21}{2.3.2}{subsection.2.3.2}} +\backcite {kohn1999nobel}{{21}{2.3.2}{subsection.2.3.2}} +\backcite {Hohenberg1964}{{22}{2.3.2}{subsection.2.3.2}} +\backcite {Levy1979}{{22}{2.3.2}{subsection.2.3.2}} \backcite {Kohn1965}{{22}{2.3.2}{subsection.2.3.2}} -\backcite {kohn1999nobel}{{22}{2.3.2}{subsection.2.3.2}} \backcite {Thomas1927}{{22}{2.3.2}{equation.2.3.16}} \backcite {Fermi1928}{{22}{2.3.2}{equation.2.3.16}} -\backcite {Hohenberg1964}{{22}{2.3.2}{equation.2.3.16}} -\backcite {Levy1979}{{22}{2.3.2}{equation.2.3.16}} -\backcite {Kohn1965}{{22}{2.3.2}{equation.2.3.16}} \backcite {Kohn1965}{{23}{2.3.2}{equation.2.3.18}} -\backcite {Kohn1965}{{26}{2.3.2}{equation.2.3.28}} -\backcite {Kohn1965}{{26}{2.3.2}{equation.2.3.28}} -\backcite {Herman1969}{{26}{2.3.2}{equation.2.3.28}} -\backcite {Perdew1996}{{26}{2.3.2}{equation.2.3.28}} +\backcite {Kohn1965}{{25}{2.3.2}{equation.2.3.27}} +\backcite {Kohn1965}{{25}{2.3.2}{equation.2.3.27}} +\backcite {Herman1969}{{25}{2.3.2}{equation.2.3.27}} +\backcite {Perdew1996}{{25}{2.3.2}{equation.2.3.27}} +\backcite {Becke1993}{{25}{2.3.2}{equation.2.3.27}} \backcite {Becke1993}{{26}{2.3.2}{equation.2.3.28}} -\backcite {Becke1993}{{26}{2.3.2}{equation.2.3.29}} -\backcite {Becke1988}{{26}{2.3.2}{equation.2.3.29}} -\backcite {Lee1988}{{26}{2.3.2}{equation.2.3.29}} -\backcite {Stephens1994}{{26}{2.3.2}{equation.2.3.29}} -\backcite {Adamo1999}{{26}{2.3.2}{equation.2.3.29}} -\backcite {Henderson2009}{{26}{2.3.2}{equation.2.3.29}} -\backcite {Krukau2006}{{26}{2.3.2}{equation.2.3.29}} -\backcite {Zhao2008}{{26}{2.3.2}{equation.2.3.29}} -\backcite {Li2018}{{26}{2.3.2}{equation.2.3.29}} -\backcite {Foulkes1989}{{27}{2.3.3}{subsection.2.3.3}} -\backcite 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{Mayer1983}{{33}{2.3.3}{equation.2.3.53}} -\backcite {Cances1997}{{33}{2.3.3}{equation.2.3.53}} -\backcite {Lu2012}{{33}{2.3.3}{equation.2.3.53}} -\backcite {Lewis1995}{{33}{2.3.3}{equation.2.3.54}} -\backcite {Gianturco1999}{{33}{2.3.3}{equation.2.3.54}} -\backcite {Elstner2001}{{33}{2.3.3}{equation.2.3.54}} -\backcite {Wu2002}{{33}{2.3.3}{equation.2.3.54}} -\backcite {Grimme2004}{{33}{2.3.3}{equation.2.3.54}} -\backcite {Zimmerli2004}{{33}{2.3.3}{equation.2.3.54}} -\backcite {Neumann2005}{{33}{2.3.3}{equation.2.3.54}} -\backcite {Goursot2007}{{33}{2.3.3}{equation.2.3.54}} -\backcite {Frenkel2001}{{34}{2.3.4}{subsection.2.3.4}} -\backcite {Jones1924}{{34}{2.3.4}{subsection.2.3.4}} -\backcite {Lennard1924}{{34}{2.3.4}{subsection.2.3.4}} -\backcite {Morse1929}{{34}{2.3.4}{subsection.2.3.4}} -\backcite {Born1932}{{34}{2.3.4}{subsection.2.3.4}} -\backcite {Stillinger1985}{{34}{2.3.4}{subsection.2.3.4}} -\backcite {Kaplan2006}{{34}{2.3.4}{subsection.2.3.4}} -\backcite {Bahar1997}{{34}{2.3.4}{subsection.2.3.4}} -\backcite {Morse1929}{{34}{2.3.4}{equation.2.3.56}} -\backcite {Girifalco1959}{{34}{2.3.4}{equation.2.3.56}} -\backcite {Jones1924}{{34}{2.3.4}{equation.2.3.57}} -\backcite {Lennard1924}{{34}{2.3.4}{equation.2.3.57}} -\backcite {Lennard1931}{{35}{2.3.4}{equation.2.3.57}} -\backcite {Monticelli2013}{{35}{2.3.4}{equation.2.3.58}} -\backcite {Metropolis1987}{{37}{2.4.1}{subsection.2.4.1}} -\backcite {Metropolis1949}{{37}{2.4.1}{subsection.2.4.1}} -\backcite {Kroese2014}{{37}{2.4.1}{subsection.2.4.1}} -\backcite {Rosenbluth1955}{{38}{2.4.1}{subsection.2.4.1}} -\backcite {Binder1993}{{38}{2.4.1}{subsection.2.4.1}} -\backcite {Baeurle2009}{{38}{2.4.1}{subsection.2.4.1}} -\backcite {Alder1957}{{41}{2.4.2}{subsection.2.4.2}} -\backcite {Gibson1960}{{41}{2.4.2}{subsection.2.4.2}} -\backcite {Rahman1964}{{41}{2.4.2}{subsection.2.4.2}} -\backcite {Frenkel2001}{{41}{2.4.2}{subsection.2.4.2}} -\backcite {Allen2017}{{41}{2.4.2}{subsection.2.4.2}} -\backcite {Cicccotti1987}{{41}{2.4.2}{subsection.2.4.2}} -\backcite {Van1990}{{41}{2.4.2}{subsection.2.4.2}} -\backcite {Berne1998}{{41}{2.4.2}{subsection.2.4.2}} -\backcite {Tuckerman2000}{{41}{2.4.2}{subsection.2.4.2}} -\backcite {Karplus2002}{{41}{2.4.2}{subsection.2.4.2}} -\backcite {Rapaport2004}{{41}{2.4.2}{subsection.2.4.2}} -\backcite {Tavan2005}{{41}{2.4.2}{subsection.2.4.2}} -\backcite {Van2006}{{41}{2.4.2}{subsection.2.4.2}} -\backcite {Karplus2002}{{41}{2.4.2}{subsection.2.4.2}} -\backcite {Parrinello1980}{{41}{2.4.2}{subsection.2.4.2}} -\backcite {Ballone1988}{{41}{2.4.2}{subsection.2.4.2}} -\backcite {Gutierrez1996}{{41}{2.4.2}{subsection.2.4.2}} -\backcite {Briant1975}{{41}{2.4.2}{subsection.2.4.2}} -\backcite {Postma1982}{{41}{2.4.2}{subsection.2.4.2}} -\backcite {Honeycutt1987}{{41}{2.4.2}{subsection.2.4.2}} -\backcite {Dang1997}{{41}{2.4.2}{subsection.2.4.2}} -\backcite {Coveney2016}{{41}{2.4.2}{subsection.2.4.2}} -\backcite {Charati1998}{{41}{2.4.2}{subsection.2.4.2}} -\backcite {Yeh2004}{{41}{2.4.2}{subsection.2.4.2}} -\backcite {Braga2014}{{41}{2.4.2}{subsection.2.4.2}} -\backcite {Pranami2015}{{41}{2.4.2}{subsection.2.4.2}} -\backcite {Yeh2004}{{41}{2.4.2}{subsection.2.4.2}} -\backcite {Mondello1997}{{41}{2.4.2}{subsection.2.4.2}} -\backcite {Hess2002}{{41}{2.4.2}{subsection.2.4.2}} -\backcite {Zhang2015}{{41}{2.4.2}{subsection.2.4.2}} -\backcite {Aragon1976}{{41}{2.4.2}{subsection.2.4.2}} -\backcite {Vuilleumier1999}{{41}{2.4.2}{subsection.2.4.2}} -\backcite {Pavone2006}{{41}{2.4.2}{subsection.2.4.2}} -\backcite {Brancato2006}{{41}{2.4.2}{subsection.2.4.2}} +\backcite {Mulliken1955}{{30}{2.3.3}{equation.2.3.44}} +\backcite {Mulliken1955}{{31}{2.3.3}{equation.2.3.47}} +\backcite {Bader1985}{{32}{2.3.3}{equation.2.3.51}} +\backcite {Bader1990}{{32}{2.3.3}{equation.2.3.51}} +\backcite {Glendening1998}{{32}{2.3.3}{equation.2.3.51}} +\backcite {Glendening2012}{{32}{2.3.3}{equation.2.3.51}} +\backcite {Singh1984}{{32}{2.3.3}{equation.2.3.51}} +\backcite {Besler1990}{{32}{2.3.3}{equation.2.3.51}} +\backcite {Li1998}{{32}{2.3.3}{equation.2.3.51}} +\backcite {Kalinowski2004}{{32}{2.3.3}{equation.2.3.51}} +\backcite {Kelly2005}{{32}{2.3.3}{equation.2.3.51}} +\backcite {Rapacioli2009corr}{{32}{2.3.3}{equation.2.3.51}} +\backcite {Mayer1983}{{32}{2.3.3}{equation.2.3.52}} +\backcite {Cances1997}{{32}{2.3.3}{equation.2.3.52}} +\backcite {Lu2012}{{32}{2.3.3}{equation.2.3.52}} +\backcite {Lewis1995}{{32}{2.3.3}{equation.2.3.53}} +\backcite {Gianturco1999}{{32}{2.3.3}{equation.2.3.53}} +\backcite {Elstner2001}{{32}{2.3.3}{equation.2.3.53}} +\backcite {Wu2002}{{32}{2.3.3}{equation.2.3.53}} +\backcite {Grimme2004}{{32}{2.3.3}{equation.2.3.53}} +\backcite {Zimmerli2004}{{32}{2.3.3}{equation.2.3.53}} +\backcite {Neumann2005}{{32}{2.3.3}{equation.2.3.53}} +\backcite {Goursot2007}{{32}{2.3.3}{equation.2.3.53}} +\backcite {Frenkel2001}{{33}{2.3.4}{subsection.2.3.4}} +\backcite {Jones1924}{{33}{2.3.4}{subsection.2.3.4}} +\backcite {Lennard1924}{{33}{2.3.4}{subsection.2.3.4}} +\backcite {Morse1929}{{33}{2.3.4}{subsection.2.3.4}} +\backcite {Born1932}{{33}{2.3.4}{subsection.2.3.4}} +\backcite {Stillinger1985}{{33}{2.3.4}{subsection.2.3.4}} +\backcite {Kaplan2006}{{33}{2.3.4}{subsection.2.3.4}} +\backcite {Bahar1997}{{33}{2.3.4}{subsection.2.3.4}} +\backcite {Morse1929}{{34}{2.3.4}{equation.2.3.55}} +\backcite {Girifalco1959}{{34}{2.3.4}{equation.2.3.55}} +\backcite {Jones1924}{{34}{2.3.4}{equation.2.3.56}} +\backcite {Lennard1924}{{34}{2.3.4}{equation.2.3.56}} +\backcite {Lennard1931}{{34}{2.3.4}{equation.2.3.56}} +\backcite {Monticelli2013}{{34}{2.3.4}{equation.2.3.57}} +\backcite {Metropolis1987}{{36}{2.4.1}{subsection.2.4.1}} +\backcite {Metropolis1949}{{36}{2.4.1}{subsection.2.4.1}} +\backcite {Kroese2014}{{36}{2.4.1}{subsection.2.4.1}} +\backcite {Rosenbluth1955}{{37}{2.4.1}{subsection.2.4.1}} +\backcite {Binder1993}{{37}{2.4.1}{subsection.2.4.1}} +\backcite {Baeurle2009}{{37}{2.4.1}{subsection.2.4.1}} +\backcite {Alder1957}{{40}{2.4.2}{subsection.2.4.2}} +\backcite {Gibson1960}{{40}{2.4.2}{subsection.2.4.2}} +\backcite {Rahman1964}{{40}{2.4.2}{subsection.2.4.2}} +\backcite {Frenkel2001}{{40}{2.4.2}{subsection.2.4.2}} +\backcite {Allen2017}{{40}{2.4.2}{subsection.2.4.2}} +\backcite {Cicccotti1987}{{40}{2.4.2}{subsection.2.4.2}} +\backcite {Van1990}{{40}{2.4.2}{subsection.2.4.2}} +\backcite {Berne1998}{{40}{2.4.2}{subsection.2.4.2}} +\backcite {Tuckerman2000}{{40}{2.4.2}{subsection.2.4.2}} +\backcite {Karplus2002}{{40}{2.4.2}{subsection.2.4.2}} +\backcite {Rapaport2004}{{40}{2.4.2}{subsection.2.4.2}} +\backcite {Tavan2005}{{40}{2.4.2}{subsection.2.4.2}} +\backcite {Van2006}{{40}{2.4.2}{subsection.2.4.2}} +\backcite {Karplus2002}{{40}{2.4.2}{subsection.2.4.2}} +\backcite {Parrinello1980}{{40}{2.4.2}{subsection.2.4.2}} +\backcite {Ballone1988}{{40}{2.4.2}{subsection.2.4.2}} +\backcite {Gutierrez1996}{{40}{2.4.2}{subsection.2.4.2}} +\backcite {Briant1975}{{40}{2.4.2}{subsection.2.4.2}} +\backcite {Postma1982}{{40}{2.4.2}{subsection.2.4.2}} +\backcite {Honeycutt1987}{{40}{2.4.2}{subsection.2.4.2}} +\backcite {Dang1997}{{40}{2.4.2}{subsection.2.4.2}} +\backcite {Coveney2016}{{40}{2.4.2}{subsection.2.4.2}} +\backcite {Charati1998}{{40}{2.4.2}{subsection.2.4.2}} +\backcite {Yeh2004}{{40}{2.4.2}{subsection.2.4.2}} +\backcite {Braga2014}{{40}{2.4.2}{subsection.2.4.2}} +\backcite {Pranami2015}{{40}{2.4.2}{subsection.2.4.2}} +\backcite {Yeh2004}{{40}{2.4.2}{subsection.2.4.2}} +\backcite {Mondello1997}{{40}{2.4.2}{subsection.2.4.2}} +\backcite {Hess2002}{{40}{2.4.2}{subsection.2.4.2}} +\backcite {Zhang2015}{{40}{2.4.2}{subsection.2.4.2}} +\backcite {Aragon1976}{{40}{2.4.2}{subsection.2.4.2}} +\backcite {Vuilleumier1999}{{40}{2.4.2}{subsection.2.4.2}} +\backcite {Pavone2006}{{40}{2.4.2}{subsection.2.4.2}} +\backcite {Brancato2006}{{40}{2.4.2}{subsection.2.4.2}} \backcite {Beck2000}{{41}{2.4.2}{subsection.2.4.2}} \backcite {Wang2003}{{41}{2.4.2}{subsection.2.4.2}} \backcite {Wei1994}{{41}{2.4.2}{subsection.2.4.2}} \backcite {Light2000}{{41}{2.4.2}{subsection.2.4.2}} -\backcite {Batina1991}{{42}{2.4.2}{equation.2.4.72}} -\backcite {Butcher2008}{{42}{2.4.2}{equation.2.4.72}} -\backcite {Gear1966}{{42}{2.4.2}{equation.2.4.72}} -\backcite {Diethelm2002}{{42}{2.4.2}{equation.2.4.72}} -\backcite {Runge1895}{{42}{2.4.2}{equation.2.4.72}} -\backcite {Kutta1901}{{42}{2.4.2}{equation.2.4.72}} -\backcite {Butcher1996}{{42}{2.4.2}{equation.2.4.72}} -\backcite {Butcher2015}{{42}{2.4.2}{equation.2.4.72}} -\backcite {Verlet1967}{{42}{2.4.2}{equation.2.4.72}} -\backcite {Fraige2004}{{42}{2.4.2}{equation.2.4.72}} -\backcite {Swope1982}{{42}{2.4.2}{equation.2.4.72}} -\backcite {Ray1981}{{44}{2.4.2}{equation.2.4.81}} -\backcite {Ray1999}{{44}{2.4.2}{equation.2.4.81}} -\backcite {Nose1984}{{44}{2.4.2}{equation.2.4.81}} -\backcite {Nose1984M}{{44}{2.4.2}{equation.2.4.81}} -\backcite {Hoover1985}{{44}{2.4.2}{equation.2.4.81}} -\backcite {Hunenberger2005}{{44}{2.4.2}{equation.2.4.81}} -\backcite {Torrie1977}{{45}{2.4.3}{subsection.2.4.3}} -\backcite {Hansmann1993}{{45}{2.4.3}{subsection.2.4.3}} -\backcite {Marchi1999}{{45}{2.4.3}{subsection.2.4.3}} -\backcite {Bartels2000}{{45}{2.4.3}{subsection.2.4.3}} -\backcite {Darve2001}{{45}{2.4.3}{subsection.2.4.3}} -\backcite {Laio2002}{{45}{2.4.3}{subsection.2.4.3}} -\backcite {Iannuzzi2003}{{45}{2.4.3}{subsection.2.4.3}} -\backcite {Barducci2011}{{45}{2.4.3}{subsection.2.4.3}} -\backcite {Kirkpatrick1983}{{45}{2.4.3}{subsection.2.4.3}} -\backcite {Van1987}{{45}{2.4.3}{subsection.2.4.3}} +\backcite {Batina1991}{{42}{2.4.2}{equation.2.4.71}} +\backcite {Butcher2008}{{42}{2.4.2}{equation.2.4.71}} +\backcite {Gear1966}{{42}{2.4.2}{equation.2.4.71}} +\backcite {Diethelm2002}{{42}{2.4.2}{equation.2.4.71}} +\backcite {Runge1895}{{42}{2.4.2}{equation.2.4.71}} +\backcite {Kutta1901}{{42}{2.4.2}{equation.2.4.71}} +\backcite {Butcher1996}{{42}{2.4.2}{equation.2.4.71}} +\backcite {Butcher2015}{{42}{2.4.2}{equation.2.4.71}} +\backcite {Verlet1967}{{42}{2.4.2}{equation.2.4.71}} +\backcite {Fraige2004}{{42}{2.4.2}{equation.2.4.71}} +\backcite {Swope1982}{{42}{2.4.2}{equation.2.4.71}} +\backcite {Ray1981}{{43}{2.4.2}{equation.2.4.80}} +\backcite {Ray1999}{{43}{2.4.2}{equation.2.4.80}} +\backcite {Nose1984}{{44}{2.4.2}{equation.2.4.80}} +\backcite {Nose1984M}{{44}{2.4.2}{equation.2.4.80}} +\backcite {Hoover1985}{{44}{2.4.2}{equation.2.4.80}} +\backcite {Hunenberger2005}{{44}{2.4.2}{equation.2.4.80}} +\backcite {Torrie1977}{{44}{2.4.3}{subsection.2.4.3}} +\backcite {Hansmann1993}{{44}{2.4.3}{subsection.2.4.3}} +\backcite {Marchi1999}{{44}{2.4.3}{subsection.2.4.3}} +\backcite {Bartels2000}{{44}{2.4.3}{subsection.2.4.3}} +\backcite {Darve2001}{{44}{2.4.3}{subsection.2.4.3}} +\backcite {Laio2002}{{44}{2.4.3}{subsection.2.4.3}} +\backcite {Iannuzzi2003}{{44}{2.4.3}{subsection.2.4.3}} +\backcite {Barducci2011}{{44}{2.4.3}{subsection.2.4.3}} +\backcite {Kirkpatrick1983}{{44}{2.4.3}{subsection.2.4.3}} +\backcite {Van1987}{{44}{2.4.3}{subsection.2.4.3}} \backcite {Swendsen1986}{{45}{2.4.3}{subsection.2.4.3}} \backcite {Geyer1991}{{45}{2.4.3}{subsection.2.4.3}} \backcite {Hukushima1996}{{45}{2.4.3}{subsection.2.4.3}} @@ -386,359 +385,358 @@ \backcite {Unger1993}{{47}{2.4.4}{subsection.2.4.4}} \backcite {Sivanandam2008}{{47}{2.4.4}{subsection.2.4.4}} \backcite {Toledo2014}{{47}{2.4.4}{subsection.2.4.4}} -\backcite {deMonNano2009}{{52}{3.1.1}{subsection.3.1.1}} -\backcite {Elstner1998}{{52}{3.1.1}{subsection.3.1.1}} -\backcite {Gaus2013para}{{52}{3.1.1}{subsection.3.1.1}} -\backcite {Li1998}{{52}{3.1.1}{subsection.3.1.1}} -\backcite {Rapacioli2009corr}{{52}{3.1.1}{subsection.3.1.1}} -\backcite {Thompson2003}{{52}{3.1.1}{subsection.3.1.1}} -\backcite {Rapacioli2009corr}{{52}{3.1.1}{subsection.3.1.1}} -\backcite {Elstner2001}{{52}{3.1.1}{subsection.3.1.1}} -\backcite {Zhechkov2005}{{52}{3.1.1}{subsection.3.1.1}} -\backcite {Simon2012}{{52}{3.1.1}{subsection.3.1.1}} -\backcite {Odutola1980}{{52}{3.1.1}{subsection.3.1.1}} -\backcite {Earl2005}{{52}{3.1.2}{subsection.3.1.2}} -\backcite {Sugita1999}{{52}{3.1.2}{subsection.3.1.2}} -\backcite {Sugita2000}{{52}{3.1.2}{subsection.3.1.2}} -\backcite {Elstner1998}{{52}{3.1.2}{subsection.3.1.2}} -\backcite {Nose1984M}{{53}{3.1.2}{subsection.3.1.2}} -\backcite {Hoover1985}{{53}{3.1.2}{subsection.3.1.2}} -\backcite {Douady2009}{{53}{3.1.2}{subsection.3.1.2}} -\backcite {Nose1984M}{{53}{3.1.2}{subsection.3.1.2}} -\backcite {Hoover1985}{{53}{3.1.2}{subsection.3.1.2}} -\backcite {Wolken2000}{{53}{3.1.2}{subsection.3.1.2}} -\backcite {Pedersen2014}{{53}{3.1.2}{subsection.3.1.2}} -\backcite {Weigend2005}{{53}{3.1.3}{subsection.3.1.3}} -\backcite {Weigend2006}{{53}{3.1.3}{subsection.3.1.3}} -\backcite {GaussianCode}{{53}{3.1.3}{subsection.3.1.3}} -\backcite {Boys2002}{{54}{3.1.3}{subsection.3.1.3}} -\backcite {Tielens2005}{{55}{3.2.1}{subsection.3.2.1}} -\backcite {Keesee1989}{{55}{3.2.1}{subsection.3.2.1}} -\backcite {Gilligan2000}{{55}{3.2.1}{subsection.3.2.1}} -\backcite {Sennikov2005}{{55}{3.2.1}{subsection.3.2.1}} -\backcite {Cabellos2016}{{55}{3.2.1}{subsection.3.2.1}} -\backcite {Orabi2013}{{55}{3.2.1}{subsection.3.2.1}} -\backcite {Bommer2016}{{55}{3.2.1}{subsection.3.2.1}} -\backcite {Rodgers2003}{{55}{3.2.1}{subsection.3.2.1}} -\backcite {Van2004}{{55}{3.2.1}{subsection.3.2.1}} -\backcite {Gibb2004}{{55}{3.2.1}{subsection.3.2.1}} -\backcite {Parise2005}{{55}{3.2.1}{subsection.3.2.1}} -\backcite {Boogert2015}{{55}{3.2.1}{subsection.3.2.1}} -\backcite {Dulieu2010}{{55}{3.2.1}{subsection.3.2.1}} -\backcite {Michoulier2018}{{55}{3.2.1}{subsection.3.2.1}} -\backcite {Kulmala2004}{{55}{3.2.1}{subsection.3.2.1}} -\backcite {Ziereis1986}{{55}{3.2.1}{subsection.3.2.1}} -\backcite {Perkins1984}{{55}{3.2.1}{subsection.3.2.1}} -\backcite {Arnold1997}{{55}{3.2.1}{subsection.3.2.1}} -\backcite {Dunne2016}{{55}{3.2.1}{subsection.3.2.1}} -\backcite {Kirkby2011}{{55}{3.2.1}{subsection.3.2.1}} -\backcite {Douady2009}{{55}{3.2.1}{subsection.3.2.1}} -\backcite {Perkins1984}{{55}{3.2.1}{subsection.3.2.1}} -\backcite {Herbine1985}{{55}{3.2.1}{subsection.3.2.1}} -\backcite {Stockman1992}{{55}{3.2.1}{subsection.3.2.1}} -\backcite {Hulthe1997}{{55}{3.2.1}{subsection.3.2.1}} -\backcite {Wang1998}{{55}{3.2.1}{subsection.3.2.1}} -\backcite {Chang1998}{{55}{3.2.1}{subsection.3.2.1}} -\backcite {Jiang1999}{{55}{3.2.1}{subsection.3.2.1}} -\backcite {Hvelplund2010}{{55}{3.2.1}{subsection.3.2.1}} -\backcite {Douady2008}{{55}{3.2.1}{subsection.3.2.1}} -\backcite {Morrell2010}{{55}{3.2.1}{subsection.3.2.1}} -\backcite {Bacelo2002}{{55}{3.2.1}{subsection.3.2.1}} -\backcite {Galashev2013}{{55}{3.2.1}{subsection.3.2.1}} -\backcite {Perkins1984}{{55}{3.2.1}{subsection.3.2.1}} -\backcite {Hulthe1997}{{55}{3.2.1}{subsection.3.2.1}} -\backcite {Hvelplund2010}{{55}{3.2.1}{subsection.3.2.1}} -\backcite {Chang1998}{{55}{3.2.1}{subsection.3.2.1}} -\backcite 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Binary files a/thesis/thesis.pdf and b/thesis/thesis.pdf differ diff --git a/thesis/thesis.synctex.gz b/thesis/thesis.synctex.gz index fb26718..d554202 100644 Binary files a/thesis/thesis.synctex.gz and b/thesis/thesis.synctex.gz differ diff --git a/thesis/thesis.toc b/thesis/thesis.toc index 484ab19..95e7b49 100644 --- a/thesis/thesis.toc +++ b/thesis/thesis.toc @@ -8,59 +8,59 @@ \contentsline {subsection}{\numberline {2.3.1}Wavefunction based Methods}{19}{subsection.2.3.1}% \contentsline {subsection}{\numberline {2.3.2}Density Functional Theory}{21}{subsection.2.3.2}% \contentsline {subsection}{\numberline {2.3.3}Density Functional based Tight-Binding Theory}{26}{subsection.2.3.3}% -\contentsline {subsection}{\numberline {2.3.4}Force Field Methods}{34}{subsection.2.3.4}% -\contentsline {section}{\numberline {2.4}Exploration of PES}{36}{section.2.4}% -\contentsline {subsection}{\numberline {2.4.1}Monte Carlo Simulations}{37}{subsection.2.4.1}% +\contentsline {subsection}{\numberline {2.3.4}Force Field Methods}{33}{subsection.2.3.4}% +\contentsline {section}{\numberline {2.4}Exploration of PES}{35}{section.2.4}% +\contentsline {subsection}{\numberline {2.4.1}Monte Carlo Simulations}{36}{subsection.2.4.1}% \contentsline {subsection}{\numberline {2.4.2}Classical Molecular Dynamics}{40}{subsection.2.4.2}% -\contentsline {subsection}{\numberline {2.4.3}Parallel-Tempering Molecular Dynamics}{45}{subsection.2.4.3}% -\contentsline {subsection}{\numberline {2.4.4}Global Optimization}{47}{subsection.2.4.4}% -\contentsline {chapter}{\numberline {3}Exploration of Structural and Energetic Properties}{51}{chapter.3}% -\contentsline {section}{\numberline {3.1}Computational Details}{52}{section.3.1}% -\contentsline {subsection}{\numberline {3.1.1}SCC-DFTB Potential}{52}{subsection.3.1.1}% -\contentsline {subsection}{\numberline {3.1.2}SCC-DFTB Exploration of PES}{52}{subsection.3.1.2}% -\contentsline {subsection}{\numberline {3.1.3}MP2 Geometry Optimizations, Relative and Binding Energies}{53}{subsection.3.1.3}% -\contentsline {subsection}{\numberline {3.1.4}Structure Classification}{54}{subsection.3.1.4}% -\contentsline {section}{\numberline {3.2}Structural and Energetic Properties of Ammonium/Ammonia including Water Clusters}{55}{section.3.2}% -\contentsline {subsection}{\numberline {3.2.1}General introduction}{55}{subsection.3.2.1}% -\contentsline {subsection}{\numberline {3.2.2}Results and Discussion}{57}{subsection.3.2.2}% -\contentsline {subsubsection}{\numberline {3.2.2.1}Dissociation Curves and SCC-DFTB Potential}{57}{subsubsection.3.2.2.1}% -\contentsline {subsubsection}{\numberline {3.2.2.2}Small Species: (H$_2$O)$_{1-3}${NH$_4$}$^+$ and (H$_2$O)$_{1-3}${NH$_3$}}{60}{subsubsection.3.2.2.2}% -\contentsline {subsubsection}{\numberline {3.2.2.3}Properties of (H$_2$O)$_{4-10}${NH$_4$}$^+$ Clusters}{63}{subsubsection.3.2.2.3}% -\contentsline {subsubsection}{\numberline {3.2.2.4}Properties of (H$_2$O)$_{4-10}${NH$_3$} Clusters}{70}{subsubsection.3.2.2.4}% -\contentsline {subsubsection}{\numberline {3.2.2.5}Properties of (H$_2$O)$_{20}${NH$_4$}$^+$ Cluster}{75}{subsubsection.3.2.2.5}% -\contentsline {subsection}{\numberline {3.2.3}Conclusions for Ammonium/Ammonia Including Water Clusters}{76}{subsection.3.2.3}% -\contentsline {section}{\numberline {3.3}Structural and Energetic Properties of Protonated Uracil Water Clusters}{77}{section.3.3}% -\contentsline {subsection}{\numberline {3.3.1}General introduction}{77}{subsection.3.3.1}% -\contentsline {subsection}{\numberline {3.3.2}Results and Discussion}{79}{subsection.3.3.2}% -\contentsline {subsubsection}{\numberline {3.3.2.1}Experimental Results}{79}{subsubsection.3.3.2.1}% -\contentsline {subsubsection}{\numberline {3.3.2.2}Calculated Structures of Protonated Uracil Water Clusters}{85}{subsubsection.3.3.2.2}% -\contentsline {subsection}{\numberline {3.3.3}Conclusions on (H$_2$O)$_{n}$UH$^+$ clusters}{94}{subsection.3.3.3}% -\contentsline {chapter}{\numberline {4}Dynamical Simulation of Collision-Induced Dissociation}{99}{chapter.4}% -\contentsline {section}{\numberline {4.1}Experimental Methods}{99}{section.4.1}% -\contentsline {subsection}{\numberline {4.1.1}Principle of TCID}{101}{subsection.4.1.1}% -\contentsline {subsection}{\numberline {4.1.2}Experimental Setup}{102}{subsection.4.1.2}% -\contentsline {section}{\numberline {4.2}Computational Details}{104}{section.4.2}% -\contentsline {subsection}{\numberline {4.2.1}SCC-DFTB Potential}{104}{subsection.4.2.1}% -\contentsline {subsection}{\numberline {4.2.2}Collision Trajectories}{105}{subsection.4.2.2}% -\contentsline {subsection}{\numberline {4.2.3}Trajectory Analysis}{106}{subsection.4.2.3}% -\contentsline {section}{\numberline {4.3}Dynamical Simulation of Collision-Induced Dissociation of Protonated Uracil Water Clusters}{107}{section.4.3}% -\contentsline {subsection}{\numberline {4.3.1}Introduction}{107}{subsection.4.3.1}% -\contentsline {subsection}{\numberline {4.3.2}Results and Discussion}{108}{subsection.4.3.2}% -\contentsline {subsubsection}{\numberline {4.3.2.1}Statistical Convergence}{108}{subsubsection.4.3.2.1}% -\contentsline {subsection}{\numberline {4.3.3}Time-Dependent Proportion of Fragments}{111}{subsection.4.3.3}% -\contentsline {subsection}{\numberline {4.3.4}Proportion of Neutral Uracil Loss and Total Fragmentation Cross Sections for Small Clusters}{114}{subsection.4.3.4}% -\contentsline {subsection}{\numberline {4.3.5}Behaviour at Larger Sizes, the Cases of (H$_2$O)$_{11, 12}$UH$^+$}{124}{subsection.4.3.5}% -\contentsline {subsection}{\numberline {4.3.6}Mass Spectra of Fragments with Excess Proton}{128}{subsection.4.3.6}% -\contentsline {subsection}{\numberline {4.3.7}Conclusions about CID of (H$_2$O)$_{n}$UH$^+$}{131}{subsection.4.3.7}% -\contentsline {section}{\numberline {4.4}Dynamical Simulation of Collision-Induced Dissociation for Pyrene Dimer Cation}{133}{section.4.4}% -\contentsline {subsection}{\numberline {4.4.1}Introduction}{133}{subsection.4.4.1}% -\contentsline {subsection}{\numberline {4.4.2}Calculation of Energies}{135}{subsection.4.4.2}% -\contentsline {subsection}{\numberline {4.4.3}Simulation of the Experimental TOFMS}{137}{subsection.4.4.3}% -\contentsline {subsection}{\numberline {4.4.4}Results and Discussion}{139}{subsection.4.4.4}% -\contentsline {subsubsection}{\numberline {4.4.4.1}TOFMS Comparison}{139}{subsubsection.4.4.4.1}% -\contentsline {subsubsection}{\numberline {4.4.4.2}Molecular Dynamics Analysis}{140}{subsubsection.4.4.4.2}% -\contentsline {subsection}{\numberline {4.4.5}Conclusions about CID of Py$_2^+$}{156}{subsection.4.4.5}% -\contentsline {chapter}{\numberline {5}General Conclusions and Perspectives}{159}{chapter.5}% -\contentsline {section}{\numberline {5.1}General Conclusions}{159}{section.5.1}% -\contentsline {section}{\numberline {5.2}Perspectives}{162}{section.5.2}% -\contentsline {chapter}{References}{163}{chapter*.82}% +\contentsline {subsection}{\numberline {2.4.3}Parallel-Tempering Molecular Dynamics}{44}{subsection.2.4.3}% +\contentsline {subsection}{\numberline {2.4.4}Global Optimization}{46}{subsection.2.4.4}% +\contentsline {chapter}{\numberline {3}Exploration of Structural and Energetic Properties}{49}{chapter.3}% +\contentsline {section}{\numberline {3.1}Computational Details}{50}{section.3.1}% +\contentsline {subsection}{\numberline {3.1.1}SCC-DFTB Potential}{50}{subsection.3.1.1}% +\contentsline {subsection}{\numberline {3.1.2}SCC-DFTB Exploration of PES}{50}{subsection.3.1.2}% +\contentsline {subsection}{\numberline {3.1.3}MP2 Geometry Optimizations, Relative and Binding Energies}{51}{subsection.3.1.3}% +\contentsline {subsection}{\numberline {3.1.4}Structure Classification}{52}{subsection.3.1.4}% +\contentsline {section}{\numberline {3.2}Structural and Energetic Properties of Ammonium/Ammonia including Water Clusters}{53}{section.3.2}% +\contentsline {subsection}{\numberline {3.2.1}General introduction}{53}{subsection.3.2.1}% +\contentsline {subsection}{\numberline {3.2.2}Results and Discussion}{55}{subsection.3.2.2}% +\contentsline {subsubsection}{\numberline {3.2.2.1}Dissociation Curves and SCC-DFTB Potential}{55}{subsubsection.3.2.2.1}% +\contentsline {subsubsection}{\numberline {3.2.2.2}Small Species: (H$_2$O)$_{1-3}${NH$_4$}$^+$ and (H$_2$O)$_{1-3}${NH$_3$}}{58}{subsubsection.3.2.2.2}% +\contentsline {subsubsection}{\numberline {3.2.2.3}Properties of (H$_2$O)$_{4-10}${NH$_4$}$^+$ Clusters}{61}{subsubsection.3.2.2.3}% +\contentsline {subsubsection}{\numberline {3.2.2.4}Properties of (H$_2$O)$_{4-10}${NH$_3$} Clusters}{68}{subsubsection.3.2.2.4}% +\contentsline {subsubsection}{\numberline {3.2.2.5}Properties of (H$_2$O)$_{20}${NH$_4$}$^+$ Cluster}{73}{subsubsection.3.2.2.5}% +\contentsline {subsection}{\numberline {3.2.3}Conclusions for Ammonium/Ammonia Including Water Clusters}{74}{subsection.3.2.3}% +\contentsline {section}{\numberline {3.3}Structural and Energetic Properties of Protonated Uracil Water Clusters}{75}{section.3.3}% +\contentsline {subsection}{\numberline {3.3.1}General introduction}{75}{subsection.3.3.1}% +\contentsline {subsection}{\numberline {3.3.2}Results and Discussion}{77}{subsection.3.3.2}% +\contentsline {subsubsection}{\numberline {3.3.2.1}Experimental Results}{77}{subsubsection.3.3.2.1}% +\contentsline {subsubsection}{\numberline {3.3.2.2}Calculated Structures of Protonated Uracil Water Clusters}{83}{subsubsection.3.3.2.2}% +\contentsline {subsection}{\numberline {3.3.3}Conclusions on (H$_2$O)$_{n}$UH$^+$ clusters}{92}{subsection.3.3.3}% +\contentsline {chapter}{\numberline {4}Dynamical Simulation of Collision-Induced Dissociation}{97}{chapter.4}% +\contentsline {section}{\numberline {4.1}Experimental Methods}{97}{section.4.1}% +\contentsline {subsection}{\numberline {4.1.1}Principle of TCID}{99}{subsection.4.1.1}% +\contentsline {subsection}{\numberline {4.1.2}Experimental Setup}{100}{subsection.4.1.2}% +\contentsline {section}{\numberline {4.2}Computational Details}{102}{section.4.2}% +\contentsline {subsection}{\numberline {4.2.1}SCC-DFTB Potential}{102}{subsection.4.2.1}% +\contentsline {subsection}{\numberline {4.2.2}Collision Trajectories}{103}{subsection.4.2.2}% +\contentsline {subsection}{\numberline {4.2.3}Trajectory Analysis}{104}{subsection.4.2.3}% +\contentsline {section}{\numberline {4.3}Dynamical Simulation of Collision-Induced Dissociation of Protonated Uracil Water Clusters}{105}{section.4.3}% +\contentsline {subsection}{\numberline {4.3.1}Introduction}{105}{subsection.4.3.1}% +\contentsline {subsection}{\numberline {4.3.2}Results and Discussion}{106}{subsection.4.3.2}% +\contentsline {subsubsection}{\numberline {4.3.2.1}Statistical Convergence}{106}{subsubsection.4.3.2.1}% +\contentsline {subsection}{\numberline {4.3.3}Time-Dependent Proportion of Fragments}{109}{subsection.4.3.3}% +\contentsline {subsection}{\numberline {4.3.4}Proportion of Neutral Uracil Loss and Total Fragmentation Cross Sections for Small Clusters}{112}{subsection.4.3.4}% +\contentsline {subsection}{\numberline {4.3.5}Behaviour at Larger Sizes, the Cases of (H$_2$O)$_{11, 12}$UH$^+$}{122}{subsection.4.3.5}% +\contentsline {subsection}{\numberline {4.3.6}Mass Spectra of Fragments with Excess Proton}{126}{subsection.4.3.6}% +\contentsline {subsection}{\numberline {4.3.7}Conclusions about CID of (H$_2$O)$_{n}$UH$^+$}{129}{subsection.4.3.7}% +\contentsline {section}{\numberline {4.4}Dynamical Simulation of Collision-Induced Dissociation for Pyrene Dimer Cation}{131}{section.4.4}% +\contentsline {subsection}{\numberline {4.4.1}Introduction}{131}{subsection.4.4.1}% +\contentsline {subsection}{\numberline {4.4.2}Calculation of Energies}{133}{subsection.4.4.2}% +\contentsline {subsection}{\numberline {4.4.3}Simulation of the Experimental TOFMS}{135}{subsection.4.4.3}% +\contentsline {subsection}{\numberline {4.4.4}Results and Discussion}{137}{subsection.4.4.4}% +\contentsline {subsubsection}{\numberline {4.4.4.1}TOFMS Comparison}{137}{subsubsection.4.4.4.1}% +\contentsline {subsubsection}{\numberline {4.4.4.2}Molecular Dynamics Analysis}{138}{subsubsection.4.4.4.2}% +\contentsline {subsection}{\numberline {4.4.5}Conclusions about CID of Py$_2^+$}{154}{subsection.4.4.5}% +\contentsline {chapter}{\numberline {5}General Conclusions and Perspectives}{157}{chapter.5}% +\contentsline {section}{\numberline {5.1}General Conclusions}{157}{section.5.1}% +\contentsline {section}{\numberline {5.2}Perspectives}{160}{section.5.2}% +\contentsline {chapter}{References}{161}{chapter*.82}%