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Author SHA1 Message Date
jcuny
debb6f898c after merge 2021-06-15 19:42:03 +02:00
jcuny
d0e296b204 JC general intro 2021-06-15 19:40:14 +02:00
jcuny
358a54e58f JC general intro 2021-06-15 19:39:59 +02:00
jcuny
bebc62185a merge with linjie 2021-06-15 14:32:26 +02:00
jcuny
a0335a6aff general conclusion 2021-06-15 14:13:20 +02:00
jcuny
c1d2ca33cf to merge with linjie 2021-06-14 15:01:08 +02:00
23 changed files with 622 additions and 534 deletions
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\section{General Conclusions}
The goals of this thesis are: first, to characterize the structural, solvation, thermodynamic properties of the newly identified low-energy isomers of ammonium/ammonia water clusters, protonated uracil water clusters; second, to analyse the collision-induced dissociation of protonated uracil water clusters, and pyrene dimer cation. These systems selected are relevant to many scientific fields. The organic/inorganic molecules included water clusters can be viewed as an intermediate state of matter between the dilute gas phase and solution and the study of them helps to understand the solvation effect on gas-phase molecules and ions to be explored. PAHs are abundant in the interstellar medium, which plays a significant role in many fields such as astrophysics, environment science, combustion science, organic solar cell and so on.
As stated in the general introduction, the goal of this thesis was to go a step further into the theoretical description of properties
of molecular clusters in the view to complement complex experimental measurements. It has focused on two different types of
molecular clusters. I have first investigated water clusters containing an impurity, \textit{i.e.} an additional ion or molecule.
First, I have studied ammonium and ammonia water clusters in order to thoroughly explore their PES to characterize in details
low-energy isomers for various cluster sizes. I have then tackled the study of 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 by S. Zamith and J.-M. l'Hermite. Finally, I have addressed the study of the pyrene dimer cation
to explore collision trajectories, dissociation mechanism, energy partition, mass spectra, and cross-section. These four studies have
been organized in two chapters, each one gathering two studies involving similar computational tools. Below are gathered the main
conclusions obtained along this thesis.
\textbf{Structural and energetic properties study}
\textbf{Structural and energetic properties.}
The structures and binding energies of the lowest-energy isomers of (H$_2$O)$_{1-10}${NH$_4$}$^+$ and (H$_2$O)$_{1-10}$NH$_3$
clusters were obtained through a synergistic use of SCC-DFTB and PTMD. The reported low energy isomers were further optimized at
the MP2/Def2TZVP level of theory. In order to improve the description of sp$^3$ nitrogen, I have proposed a modified set of N-H
parameters. Through comparing the configurations and binding energies of the lowest-energy isomers obtained at SCC-DFTB an
MP2/Def2TZVP levels and by comparing the corresponding results to the literature, I demonstrated that this modified set of NH
parameters is accurate enough to model both ammonia and ammonium water clusters. This work has thus allowed to report a number
of new low-energy isomers for the studied species. Finally, PTMD simulation of (H$_2$O)$_{20}${NH$_4$}$^+$ was conducted and the
heat capacity curve of this aggregate was obtained. It is in agreement with previous results reported in the literature.
A similar exploration of the PES of (H$_2$O)$_{1-7, 11, 12}$UH$^+$ clusters was also performed. The reported low-energy isomers
for these systems are all new and therefore constitute new data set to discuss and analyse the hydration properties of RNA nucleobases.
They also complement available structures already reported for the non-protonated (H$_2$O)$_{n}$UH$^+$ species. These structures
have also helped use to provide preliminary explanations to recent collision-induced measurements performed by S. Zamith and J.-M.
l'Hermite. In particular, I show that when there are only 1 or 2 water molecules, the excess proton is chemically bond to the uracil.
When there are 3 or 4 water molecules, the proton is still bound to the uracil but it has a tendency to be transferred toward an adjacent water
molecule. 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 bound to a water molecule which is separated from uracil by at least one other water molecule.
In the context of a direct dissociation mechanism, the nature of these isomers and the localisation of the proton as a function of
cluster size, helps in analysing the nature of the fragments and the location of the proton on them.
The structures and binding energies of lowest-energy isomers of clusters
(H$_2$O)$_{n=1-10}${NH$_4$}$^+$,
(H$_2$O)$_{n=1-10}$NH$_3$ and (H$_2$O)$_{n=1-7, 11, 12}$UH$^+$ were obtained through a combination of global (combination of SCC-DFTB and PTMD) and local (MP2/Def2TZVP) optimization.
Through comparing the configurations and binding energies of lowest-energy isomers of clusters (H$_2$O)$_{n=1-10}${NH$_4$}$^+$ and (H$_2$O)$_{n=1-10}$NH$_3$ at SCC-DFTB and MP2/Def2TZVP levels and the corresponding results in the literature, we proposed the proper N-H integral parameter 0.14 and bond parameter 1.28 in SCC-DFTB. Both structures and binding energies of clusters (H$_2$O)$_{n=1-10}${NH$_4$}$^+$ and (H$_2$O)$_{n=1-10}$NH$_3$ obtained with SCC-DFTB potential are in line with the MP2/Def2TZVP results, which confirms the good ability of SCC-DFTB to describe complex potential energy landscapes of molecular species and represents a first step towards to the modelling of complex aggregates of atmospheric interest.
The calculated results of clusters (H$_2$O)$_{n=1-7, 11, 12}$UH$^+$ show that when there are 1 or 2 water molecules, the proton is on the uracil. When there are 3 or 4 water molecules, the proton is still on the uracil but it has a tendency to be transferred to the water molecule which is directly bounded 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 bound to a water molecule which is separated from uracil by at least one other water molecule. The localization of the excess proton in different clusters (H$_2$O)$_{n=1-7, 11, 12}$UH$^+$ helps to understand the evaporation channels of clusters after collision.
These two studies finally provide a new proof that SCC-DFTB, when combined to efficient enhanced sampling methods, is a powerful
tool to explore complex potential energy surfaces of molecular aggregates. They have already given rise to two publications \cite{Simon2019,Braud2019}
and one other publication is in preparation.
\textbf{Collision-induced dissociation study}
\textbf{Collision-induced dissociation.}
The SCC-DFTB simulations conducted to model collision-induced dissociation of (H$_2$O)$_{1-7,11,12}$UH$^+$ clusters
and pyrene dimer cation were presented. These simulations have provided a wealth of important information to complement recent
experimental CID measurements.
The QM/MM dynamical simulations using SCC-DFTB method for collision-induced dissociation of low-energy protonated uracil water clusters (H$_2$O)$_{1-7,11,12}$UH$^+$ and pyrene dimer cation were performed, which provides a wealth of important information for recent experimental CID measurements.
For the collision simulations of (H$_2$O)$_{1-7,11,12}$UH$^+$ clusters at constant center of mass collision energy, the theoretical proportion
of formed neutral \textit{vs.} protonated uracil containing clusters, total fragmentation cross sections as well as the mass spectra of charged
fragments are consistent with the experimental data which highlights the accuracy of the simulations. They allow to probe which fragments
are formed on the short time scale and rationalize the location of the excess proton on these fragments. Analyses of the time evolution of
the fragments populations and theoretical and experimental branching ratios indicate that (H$_2$O)$_{1-7}$UH$^+$ engage a direct/shattering
mechanism (dissociation on a very short time scale) after collision whereas for (H$_2$O)$_{11-12}$UH$^+$ a significant contribution of structural
rearrangements occur. This suggests that a contribution of a statistical mechanism is more likely to occur for larger species such as
(H$_2$O)$_{11-12}$UH$^+$. Such study is almost unique as the modelling of the dissociation of aqueous aggregates is very scarce in the literature.
This study thus demonstrates that explicit molecular dynamics simulations at the SCC-DFTB level appear as a key tool to complement collision-induced
dissociation experiments of hydrated molecular clusters. This study opens new possibility in the domain and I hope it will motivate new experimental
measurements. One publication devoted to this study is in preparation.
For the explicit dynamical collision simulations of (H$_2$O)$_{1-7,11,12}$UH$^+$ at constant center of mass collision energy, the theoretical proportion of formed neutral \textit{vs.} protonated uracil containing clusters, total fragmentation cross sections as well as the mass spectra of charged fragments are consistent with the experimental data which highlights the accuracy of the simulations. They allow to probe which fragments are formed on the short time scale and rationalize the location of the excess proton on these fragments. The results show that this latter property is highly influenced by the nature of the aggregate undergoing the collision. Analyses of the time evolution of the fragments populations and theoretical and experimental branching ratios of (H$_2$O)$_{1-7, 11, 12}$UH$^+$ indicate that (H$_2$O)$_{1-7}$UH$^+$ engage a direct/shattering mechanism (dissociation on a very short time scale) after collision whereas for (H$_2$O)$_{11-12}$UH$^+$ a significant contribution of structural rearrangements occur. This suggests that a contribution of a statistical mechanism is more likely to occur for larger species such as (H$_2$O)$_{11-12}$UH$^+$.
This study demonstrates that explicit molecular dynamics simulations appear as a useful tool to complement collision-induced dissociation experiments of hydrated molecular clusters.
Dynamical simulations of collision between Py$_2^+$ and argon at different center of mass collision energies, between 2.5 and 30.0 eV, were conducted.
Collision process, dissociation path, energy partition and distribution, and the efficiency of energy transfer were deeply explored form these simulations that
have provided valuable reference for the CID study of larger PAH cation clusters. The simulated TOFMS of parent and dissociated products were obtained
from the combination of MD simulations and PST to address the short and long timescales dissociation, respectively. The agreement between the simulated
and measured mass spectra suggests that the main processes are captured by this approach. It appears that the TOFMS spectra mostly result from dimers
dissociating on short timescales (during the MD simulation) and the remaining minor contribution results from dimers dissociating at longer timescales
(the second step, during PST calculation). This indicates that Py$_2^+$ primarily engages a direct dissociation path after collision. The dynamical
simulations show that the outcome of the trajectories either toward a dissociation or a redistribution
of the transferred energy strongly depends on the initial collision conditions. Intramolecular fragmentation of the monomers occurs only for
collision energies above 25 eV. At low collision energies, the dissociation cross section increases with collision energies whereas it remains almost
constant for collision energies greater than 10-15~eV. The analysis of the kinetic energy partition as a function of the collision energy shows the
absorbed energy is shared between the dissociative modes and the heating of individual monomers. It shows that above 7.5~eV, increasing the
collision energy mostly results in an increase of the intramolecular energy. Finally, the analysis of energy transfer efficiency within the dimer suggests
that direct dissociation is too fast to allow significant thermalization of the system. On the other hand, when there is no dissociation, thermalization
can occur with a faster equilibration between the intramolecular modes of the two units than with the intermolecular modes.
This study has given rise to two publications.\cite{Zamith2020threshold,Zheng2021}
For the dynamical simulations of collision between Py$_2^+$ and argon at different center of mass collision energies between 2.5 and 30 eV, the collision process, dissociation path, energy partition and distribution, and the efficiency of energy transfer were deeply explored for the Py$_2^+$ system, which can provide valuable reference for the CID study of larger PAH cation clusters.
The simulated TOFMS of parent and dissociated products are obtained from the combination of MD simulations and PST to address the short and long timescales dissociation, respectively. The agreement between the simulated and measured mass spectra suggests that the main processes are captured by this approach. It appears that the TOFMS spectra mostly result from dimers dissociating on short timescales (during the MD simulation) and the remaining minor contribution is from dimers dissociating at longer timescales (the second step, during PST calculation). This indicates that Py$_2^+$ primarily engages a direct dissociation path after collision. The dynamical simulations allow to visualise the dissociation processes. It shows that the evolution of the trajectories either toward a dissociation or a redistribution of the transferred energy strongly depends on the initial collision conditions. Intramolecular fragmentation of the monomers occurred only for collision energies above 25 eV. At low collision energies, the dissociation cross section increases with collision energies whereas it remains almost constant for collision energies greater than 10-15~eV.
The analysis of the kinetic energy partition as a function of the collision energy shows the absorbed energy is shared between the dissociative modes and the heating of individual monomers. It shows that above 7.5~eV, increasing the collision energy mostly results in an increase of the intramolecular energy. Finally, the analysis of energy transfer efficiency within the dimer suggests that direct dissociation is too fast to allow significant thermalization of the system. On the other hand, when there is no dissociation, thermalization can occur with a faster equilibration between the intramolecular modes of the two units than with the intermolecular modes.
\break
%\break
\section{Perspectives}
Based on the work of this thesis, several perspectives can be implemented in the future:
This thesis has addressed various problems, on different molecular clusters, and has involved a range of theoretical methodologies that are not
common way in computational chemistry. Various and very exciting perspectives can be therefore be considered in future studies:
\begin{itemize}
\item[$\bullet$]
The proposed N-H integral parameter and bond parameter in SCC-DFTB can be used to explore the low-energy isomers and binding energies of clusters (NH$_3$)$_m$, (NH$_3$)$_m$H$^+$, (H$_2$O)$_n$(NH$_3$)$_m$, (H$_2$O)$_n$(NH$_3$)$_m$H$^+$ and mixed sulfate ammonia/ammonium water clusters and compare their results with the ones at MP2 level to see if these proposed parameters are proper for the calculation of these clusters.
The newly proposed set of N-H parameters could be used to explore the low-energy structures and properties of a much larger range of systems
of atmospheric interest. Indeed the structure of pure (NH$_3$)$_m$ clusters as well as (NH$_3$)$_m$H$^+$, (H$_2$O)$_n$(NH$_3$)$_m$, and
(H$_2$O)$_n$(NH$_3$)$_m$H$^+$ clusters have been hardly addressed in the literature mainly due to the lake of properly defined force field for
these systems. The transferability of SCC-DFTB would suggests that the potential I developed could also applied to these systems. This is an ongoing
work that I have recently initiated. More interesting and also complicated is the study of water clusters containing a mix of nitrogen and sulphur
compounds, for instance, ammonium and sulfate ion. These species, their conjugated basis and acid in combination with dimethylamine and
water molecules represent the basis for nucleation of atmospheric particles. The chemical complexity induced by their mixing in force field
simulations one the one hand, and the system size needed for proper molecular simulations on the other hand, suggest that SCC-DFTB
has a major role to play in the theoretical description of these species.
\item[$\bullet$] It would be of great interest to pursue dynamical simulations of protonated uracil water clusters by looking at the influence of collision energy, both lower or higher, on the dissociation mechanism as a function of the cluster size. Furthermore, inclusion of nuclear quantum effects in the simulations could also help to increase the accuracy of the model and improve the comparison with the experiments.
\item[$\bullet$] It would also be of great interest to pursue dynamical simulations of protonated uracil water clusters. Indeed, the work I have
presented in this thesis still suffers from some lacks. First, it would be of high interest to look at the influence of collision energy, both lower or
higher, on the dissociation mechanism as a function of the cluster size. By implementing a similar methodology as for the study of Py$_2^+$,
it would be possible to extract important new information about energy partition and dissociation mechanism. Those can be of interest to other
aqueous aggregates. In other important point is the inclusion of nuclear quantum effects in the simulations. Indeed, as the experiments are
performed at very low temperatures, the quantum nature of the proton can play an important role that has been neglected in the present thesis.
\item[$\bullet$] The dynamical simulations for collision-induced dissociation of pyrene dimer cation have been verified successfully. It is possible to do the dynamical simulations for collision-induced dissociation of PAHs water clusters to compare with the experimental results and to explain and complete the experiments.
\item[$\bullet$] The dynamical simulations for collision-induced dissociation of pyrene dimer cation can be extended to PAHs water clusters
to complement recent experiments on these systems.
\item[$\bullet$] All the simulations of water clusters in this thesis were performed in the electronic ground state, it would be interesting to investigate solvation effect on organic/inorganic molecule in both electronic ground and excited states using TD-DFTB method. It would be wonderful to calculate both absorption spectra from electronic ground state and emission spectra from electronic excited state of organic/inorganic molecule containing water clusters.
\item[$\bullet$] Finally, all the simulations of water clusters performed within this thesis were performed in the electronic ground state. To model
what can occur in the atmosphere or interstellar medium, it would be of interest to investigate solvation effects on organic/inorganic molecules
brought in an electronic excited state. To do so, the TD-DFTB method need to be implemented and tested as such simulation would involve a number
of additional theoretical complexities. This would allow to calculate both absorption spectra from electronic ground state and emission spectra from
electronic excited state of organic/inorganic molecule containing water clusters.
\end{itemize}
%The work of this thesis is focused on two aspects. First, to obtain the low-lying energy isomers of ammonium/ammonia water clusters and protonated uracil water clusters through exploring the potential energy surfaces using the combination of global and local optimizations. Then the structural, solvation, thermodynamics properties of the low-lying energy isomers were characterized. Second, the molecular dynamics simulations of collision-induced dissociation of protonated uracil water clusters and pyrene dimer cation were carried out to explore the collision trajectories, dissociation mechanism, energy partition, mass spectra, cross-section and do on.
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\babel@toc {english}{}
\contentsline {chapter}{\nonumberline Glossary}{xi}{chapter*.2}%
\contentsline {chapter}{\numberline {1}General Introduction}{1}{chapter.1}%
\contentsline {chapter}{\numberline {2}Computational Methods}{13}{chapter.2}%
\contentsline {section}{\numberline {2.1}Schr{\"o}dinger Equation}{15}{section.2.1}%
\contentsline {section}{\numberline {2.2}Born-Oppenheimer Approximation}{16}{section.2.2}%
\contentsline {section}{\numberline {2.3}Computation of Electronic Energy}{18}{section.2.3}%
\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}{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}{39}{subsection.2.4.2}%
\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}%
\contentsline {chapter}{Glossary}{xi}{chapter*.2}
\contentsline {chapter}{\numberline {1}General Introduction}{1}{chapter.1}
\contentsline {chapter}{\numberline {2}Computational Methods}{13}{chapter.2}
\contentsline {section}{\numberline {2.1}Schr{\"o}dinger Equation}{15}{section.2.1}
\contentsline {section}{\numberline {2.2}Born-Oppenheimer Approximation}{16}{section.2.2}
\contentsline {section}{\numberline {2.3}Computation of Electronic Energy}{18}{section.2.3}
\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}{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}{39}{subsection.2.4.2}
\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}{163}{chapter*.82}