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figu uracile + biblio ammonia

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jcuny 2021-06-14 04:44:43 +02:00
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18 changed files with 35650 additions and 5394 deletions
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thesis/3/structure_stability.tex
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@ -1,4 +1,4 @@
% 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
@ -83,7 +83,7 @@ level. See below for the details on MP2/Def2TZVP calculations.
%\figuremacro{uracil}{Structures of the two protonated uracil isomers, u178 (keto-enol form) and u138 (di-keto form), used as initial conditions in the PTMD simulations.}
\begin{figure}[h!]
\includegraphics[width=0.5\linewidth]{a-b.pdf}
\includegraphics[width=0.5\linewidth]{uracil.pdf}
\centering
\caption{Structures of the two protonated uracil isomers, u178 (keto-enol form) and u138 (di-keto form), used as initial conditions in the PTMD simulations.}
\label{uracil_s}
@ -494,7 +494,7 @@ For cluster (H$_2$O)$_{10}${NH$_3$}, 10$^\prime$-a to 10$^\prime$-e are the firs
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$_4$}$^+$ Clusters}
\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}
@ -579,7 +579,7 @@ section~\ref{exp_cid} of chapter~4, where these details are important to explici
\subsubsection{Experimental Results} \label{exp_ur}
\textbf{Time of flight of mass spectrum(TOFMS) .}
\textbf{Time of flight of mass spectrum(TOFMS).}
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,
\begin{align}
@ -632,9 +632,16 @@ This analysis based on PA is however quite crude. Indeed, it assumes that the pr
As discussed in section~\ref{sec:ammoniumwater}, we 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_s} at MP2/Def2TZVP and SCC-DFTB levels of theory. Both $D_\textrm{NH}$ = 0.12 and
(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
$D_\textrm{NH}$ = 0.14 lead to consistent binding energies. So, to be consistent with the work performed in the previous section, we
have used $D_\textrm{NH}$ = 0.14 in the following.
have used $D_\textrm{NH}$ = 0.12 in the following.
\begin{figure}[h!]
\includegraphics[width=0.5\linewidth]{a-b.pdf}
\centering
\caption{Structure of two (H$_2$O)U isomers used for binding energy calculations.}
\label{uracil_i}
\end{figure}
\begin{table}
%\footnotesize
@ -721,7 +728,7 @@ water molecule. Upon direct dissociation, the excess proton and the uracil can t
collision-induced dissociation experiments and theoretical calculation allows to probe the solvation and protonation properties of organic molecules such as nucleobases.
This is a step toward a better understanding of the role of water in the chemistry of in vivo DNA and RNA bases. However, the knowledge of the lowest-energy isomers
of the species involved in CID experiments is not enough to understand all the collision process. To get a deeper understanding of the collision mechanism, an explicit
modelling of the collision is needed?. This question is addressed in the next chapter of this thesis.
modelling of the collision is needed. This question is addressed in the next chapter of this thesis.
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@article{Bandow2006,
title={Larger water clusters with edges and corners on their way to ice: Structural trends elucidated with an improved parallel evolutionary algorithm},
author={Bandow, Bernhard and Hartke, Bernd},
journal={J. Phys. Chem. A},
volume={110},
number={17},
pages={5809--5822},
year={2006},
publisher={ACS Publications}}
@article{Kazimirski2003,
title={Search for low energy structures of water clusters (H2O) n, n= 20- 22, 48, 123, and 293},
author={Kazimirski, Jan K and Buch, Victoria},
journal={J. Phys. Chem. A},
volume={107},
number={46},
pages={9762--9775},
year={2003},
publisher={ACS Publications}}
@article{Pickard2005,
title={Comparison of model chemistry and density functional theory thermochemical predictions with experiment for formation of ionic clusters of the ammonium cation complexed with water and ammonia; atmospheric implications},
author={Pickard IV, Frank C and Dunn, Meghan E and Shields, George C},
journal={J. Phys. Chem. A},
volume={109},
number={22},
pages={4905--4910},
year={2005},
publisher={ACS Publications}}
@article{Lee2004,
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},
number={15},
pages={2949--2958},
year={2004},
publisher={ACS Publications}}
@article{Boys2002,
title={The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors},
author={Boys, SF and Bernardi, F},

192
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28
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@ -2424,6 +2424,34 @@
differential overlap based semiempirical molecular orbital technique}.
\newblock {\em Theor. Chem. Acc.}, {\bf 110}(4):254--266, 2003.
\bibitem{Lee2004}
{\sc Han~Myoung Lee, P~Tarakeshwar, Jungwon Park, Maciej~Roman Ko{\l}aski,
Yeo~Jin Yoon, Hai-Bo Yi, Woo~Youn Kim, and Kwang~S Kim}.
\newblock {\bf Insights into the Structures, Energetics, and Vibrations of
Monovalent Cation-(Water) 1-6 Clusters}.
\newblock {\em J. Phys. Chem. A}, {\bf 108}(15):2949--2958, 2004.
\bibitem{Pickard2005}
{\sc Frank~C Pickard~IV, Meghan~E Dunn, and George~C Shields}.
\newblock {\bf Comparison of model chemistry and density functional theory
thermochemical predictions with experiment for formation of ionic clusters of
the ammonium cation complexed with water and ammonia; atmospheric
implications}.
\newblock {\em J. Phys. Chem. A}, {\bf 109}(22):4905--4910, 2005.
\bibitem{Kazimirski2003}
{\sc Jan~K Kazimirski and Victoria Buch}.
\newblock {\bf Search for low energy structures of water clusters (H2O) n, n=
20- 22, 48, 123, and 293}.
\newblock {\em J. Phys. Chem. A}, {\bf 107}(46):9762--9775, 2003.
\bibitem{Bandow2006}
{\sc Bernhard Bandow and Bernd Hartke}.
\newblock {\bf Larger water clusters with edges and corners on their way to
ice: Structural trends elucidated with an improved parallel evolutionary
algorithm}.
\newblock {\em J. Phys. Chem. A}, {\bf 110}(17):5809--5822, 2006.
\bibitem{Maclot2011}
{\sc Sylvain Maclot, Michael Capron, R{\'e}mi Maisonny, Arkadiusz {\L}awicki,
Alain M{\'e}ry, Jimmy Rangama, Jean-Yves Chesnel, Sadia Bari, Ronnie

100
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@ -12,81 +12,81 @@ A level-1 auxiliary file: 4/collision.aux
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@ -98,45 +98,45 @@ Warning--empty year in Magnasco2009
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\backcite {Keesee1989}{{53}{3.2.1}{subsection.3.2.1}}
\backcite {Gilligan2000}{{53}{3.2.1}{subsection.3.2.1}}
\backcite {Sennikov2005}{{53}{3.2.1}{subsection.3.2.1}}
\backcite {Cabellos2016}{{53}{3.2.1}{subsection.3.2.1}}
\backcite {Orabi2013}{{53}{3.2.1}{subsection.3.2.1}}
\backcite {Bommer2016}{{53}{3.2.1}{subsection.3.2.1}}
\backcite {Rodgers2003}{{53}{3.2.1}{subsection.3.2.1}}
\backcite {Van2004}{{53}{3.2.1}{subsection.3.2.1}}
\backcite {Gibb2004}{{53}{3.2.1}{subsection.3.2.1}}
\backcite {Parise2005}{{53}{3.2.1}{subsection.3.2.1}}
\backcite {Boogert2015}{{53}{3.2.1}{subsection.3.2.1}}
\backcite {Dulieu2010}{{53}{3.2.1}{subsection.3.2.1}}
\backcite {Michoulier2018}{{53}{3.2.1}{subsection.3.2.1}}
\backcite {Kulmala2004}{{53}{3.2.1}{subsection.3.2.1}}
\backcite {Ziereis1986}{{53}{3.2.1}{subsection.3.2.1}}
\backcite {Perkins1984}{{53}{3.2.1}{subsection.3.2.1}}
\backcite {Arnold1997}{{53}{3.2.1}{subsection.3.2.1}}
\backcite {Dunne2016}{{53}{3.2.1}{subsection.3.2.1}}
\backcite {Kirkby2011}{{53}{3.2.1}{subsection.3.2.1}}
\backcite {Douady2009}{{53}{3.2.1}{subsection.3.2.1}}
\backcite {Perkins1984}{{53}{3.2.1}{subsection.3.2.1}}
\backcite {Herbine1985}{{53}{3.2.1}{subsection.3.2.1}}
\backcite {Stockman1992}{{53}{3.2.1}{subsection.3.2.1}}
\backcite {Hulthe1997}{{53}{3.2.1}{subsection.3.2.1}}
\backcite {Wang1998}{{53}{3.2.1}{subsection.3.2.1}}
\backcite {Chang1998}{{53}{3.2.1}{subsection.3.2.1}}
\backcite {Jiang1999}{{53}{3.2.1}{subsection.3.2.1}}
\backcite {Hvelplund2010}{{53}{3.2.1}{subsection.3.2.1}}
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\backcite {Bacelo2002}{{53}{3.2.1}{subsection.3.2.1}}
\backcite {Galashev2013}{{53}{3.2.1}{subsection.3.2.1}}
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\backcite {Bacelo2002}{{54}{3.2.1}{subsection.3.2.1}}
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\backcite {Lee1996}{{54}{3.2.1}{subsection.3.2.1}}
\backcite {Skurski1998}{{54}{3.2.1}{subsection.3.2.1}}
\backcite {Donaldson1999}{{54}{3.2.1}{subsection.3.2.1}}
\backcite {Sadlej1999}{{54}{3.2.1}{subsection.3.2.1}}
\backcite {Lee1996}{{54}{3.2.1}{subsection.3.2.1}}
\backcite {Bacelo2002}{{54}{3.2.1}{subsection.3.2.1}}
\backcite {Douady2008}{{54}{3.2.1}{subsection.3.2.1}}
\backcite {Kozack1992polar}{{54}{3.2.1}{subsection.3.2.1}}
\backcite {Morrell2010}{{54}{3.2.1}{subsection.3.2.1}}
\backcite {Pei2015}{{54}{3.2.1}{subsection.3.2.1}}
\backcite {Walters2018}{{54}{3.2.1}{subsection.3.2.1}}
\backcite {Korchagina2017}{{55}{3.2.1}{subsection.3.2.1}}
\backcite {Choi2010}{{55}{3.2.1}{subsection.3.2.1}}
\backcite {Choi2013}{{55}{3.2.1}{subsection.3.2.1}}
\backcite {Simon2019}{{55}{3.2.1}{subsection.3.2.1}}
\backcite {Simon2012}{{55}{3.2.1}{subsection.3.2.1}}
\backcite {Simon2013water}{{55}{3.2.1}{subsection.3.2.1}}
\backcite {Korchagina2016}{{55}{3.2.1}{subsection.3.2.1}}
\backcite {Simon2017formation}{{55}{3.2.1}{subsection.3.2.1}}
\backcite {Winget2003}{{55}{3.2.1}{subsection.3.2.1}}
\backcite {Gaus2013para}{{55}{3.2.1}{subsection.3.2.1}}
\backcite {Rapacioli2009}{{55}{3.2.1}{subsection.3.2.1}}
\backcite {Thompson2003}{{55}{3.2.1}{subsection.3.2.1}}
\backcite {Simon2019}{{55}{3.2.1}{subsection.3.2.1}}
\backcite {Gaus2013para}{{58}{3.2.2.1}{figure.caption.11}}
\backcite {Winget2003}{{58}{3.2.2.1}{figure.caption.11}}
\backcite {Wang1998}{{59}{3.2.2.2}{subsubsection.3.2.2.2}}
\backcite {Jiang1999}{{59}{3.2.2.2}{subsubsection.3.2.2.2}}
\backcite {Wang1998}{{59}{3.2.2.2}{subsubsection.3.2.2.2}}
\backcite {Jiang1999}{{59}{3.2.2.2}{subsubsection.3.2.2.2}}
\backcite {Douady2008}{{59}{3.2.2.2}{subsubsection.3.2.2.2}}
\backcite {Douady2009}{{61}{3.2.2.2}{table.caption.16}}
\backcite {Wang1998}{{61}{3.2.2.2}{table.caption.16}}
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\backcite {Douady2008}{{61}{3.2.2.2}{table.caption.16}}
\backcite {Morrell2010}{{61}{3.2.2.2}{table.caption.16}}
\backcite {Wang1998}{{61}{3.2.2.3}{subsubsection.3.2.2.3}}
\backcite {Jiang1999}{{61}{3.2.2.3}{subsubsection.3.2.2.3}}
\backcite {Douady2008}{{61}{3.2.2.3}{subsubsection.3.2.2.3}}
\backcite {Wang1998}{{61}{3.2.2.3}{subsubsection.3.2.2.3}}
\backcite {Chang1998}{{61}{3.2.2.3}{subsubsection.3.2.2.3}}
\backcite {Jiang1999}{{61}{3.2.2.3}{subsubsection.3.2.2.3}}
\backcite {Douady2008}{{63}{3.2.2.3}{table.caption.18}}
\backcite {Morrell2010}{{63}{3.2.2.3}{table.caption.18}}
\backcite {Jiang1999}{{64}{3.2.2.3}{table.caption.18}}
\backcite {Douady2008}{{64}{3.2.2.3}{table.caption.18}}
\backcite {Morrell2010}{{64}{3.2.2.3}{table.caption.18}}
\backcite {Wang1998}{{64}{3.2.2.3}{table.caption.18}}
\backcite {Douady2008}{{64}{3.2.2.3}{table.caption.18}}
\backcite {Douady2008}{{65}{3.2.2.3}{table.caption.18}}
\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 {Jiang1999}{{55}{3.2.1}{subsection.3.2.1}}
\backcite {Hvelplund2010}{{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 {Lee1996}{{55}{3.2.1}{subsection.3.2.1}}
\backcite {Skurski1998}{{55}{3.2.1}{subsection.3.2.1}}
\backcite {Donaldson1999}{{56}{3.2.1}{subsection.3.2.1}}
\backcite {Sadlej1999}{{56}{3.2.1}{subsection.3.2.1}}
\backcite {Lee1996}{{56}{3.2.1}{subsection.3.2.1}}
\backcite {Bacelo2002}{{56}{3.2.1}{subsection.3.2.1}}
\backcite {Douady2008}{{56}{3.2.1}{subsection.3.2.1}}
\backcite {Kozack1992polar}{{56}{3.2.1}{subsection.3.2.1}}
\backcite {Morrell2010}{{56}{3.2.1}{subsection.3.2.1}}
\backcite {Pei2015}{{56}{3.2.1}{subsection.3.2.1}}
\backcite {Walters2018}{{56}{3.2.1}{subsection.3.2.1}}
\backcite {Korchagina2017}{{56}{3.2.1}{subsection.3.2.1}}
\backcite {Choi2010}{{56}{3.2.1}{subsection.3.2.1}}
\backcite {Choi2013}{{56}{3.2.1}{subsection.3.2.1}}
\backcite {Simon2019}{{56}{3.2.1}{subsection.3.2.1}}
\backcite {Simon2012}{{56}{3.2.1}{subsection.3.2.1}}
\backcite {Simon2013water}{{56}{3.2.1}{subsection.3.2.1}}
\backcite {Korchagina2016}{{56}{3.2.1}{subsection.3.2.1}}
\backcite {Simon2017formation}{{56}{3.2.1}{subsection.3.2.1}}
\backcite {Winget2003}{{57}{3.2.1}{subsection.3.2.1}}
\backcite {Gaus2013para}{{57}{3.2.1}{subsection.3.2.1}}
\backcite {Rapacioli2009}{{57}{3.2.1}{subsection.3.2.1}}
\backcite {Thompson2003}{{57}{3.2.1}{subsection.3.2.1}}
\backcite {Simon2019}{{57}{3.2.1}{subsection.3.2.1}}
\backcite {Gaus2013para}{{60}{3.2.2.1}{figure.caption.11}}
\backcite {Winget2003}{{60}{3.2.2.1}{figure.caption.11}}
\backcite {Wang1998}{{61}{3.2.2.2}{subsubsection.3.2.2.2}}
\backcite {Jiang1999}{{61}{3.2.2.2}{subsubsection.3.2.2.2}}
\backcite {Wang1998}{{61}{3.2.2.2}{subsubsection.3.2.2.2}}
\backcite {Jiang1999}{{61}{3.2.2.2}{subsubsection.3.2.2.2}}
\backcite {Douady2008}{{61}{3.2.2.2}{subsubsection.3.2.2.2}}
\backcite {Douady2009}{{63}{3.2.2.2}{table.caption.16}}
\backcite {Wang1998}{{63}{3.2.2.2}{table.caption.16}}
\backcite {Jiang1999}{{63}{3.2.2.2}{table.caption.16}}
\backcite {Douady2008}{{63}{3.2.2.2}{table.caption.16}}
\backcite {Morrell2010}{{63}{3.2.2.2}{table.caption.16}}
\backcite {Lee2004}{{63}{3.2.2.2}{table.caption.16}}
\backcite {Wang1998}{{63}{3.2.2.3}{subsubsection.3.2.2.3}}
\backcite {Jiang1999}{{63}{3.2.2.3}{subsubsection.3.2.2.3}}
\backcite {Douady2008}{{63}{3.2.2.3}{subsubsection.3.2.2.3}}
\backcite {Lee2004}{{63}{3.2.2.3}{subsubsection.3.2.2.3}}
\backcite {Pickard2005}{{63}{3.2.2.3}{subsubsection.3.2.2.3}}
\backcite {Wang1998}{{63}{3.2.2.3}{subsubsection.3.2.2.3}}
\backcite {Chang1998}{{63}{3.2.2.3}{subsubsection.3.2.2.3}}
\backcite {Jiang1999}{{63}{3.2.2.3}{subsubsection.3.2.2.3}}
\backcite {Douady2008}{{65}{3.2.2.3}{table.caption.18}}
\backcite {Morrell2010}{{65}{3.2.2.3}{table.caption.18}}
\backcite {Douady2008}{{65}{3.2.2.3}{figure.caption.19}}
\backcite {Douady2008}{{65}{3.2.2.3}{figure.caption.19}}
\backcite {Jiang1999}{{65}{3.2.2.3}{table.caption.18}}
\backcite {Douady2008}{{66}{3.2.2.3}{table.caption.18}}
\backcite {Morrell2010}{{66}{3.2.2.3}{table.caption.18}}
\backcite {Wang1998}{{66}{3.2.2.3}{table.caption.18}}
\backcite {Douady2008}{{66}{3.2.2.3}{table.caption.18}}
\backcite {Douady2008}{{67}{3.2.2.3}{table.caption.18}}
\backcite {Douady2008}{{67}{3.2.2.3}{table.caption.18}}
\backcite {Morrell2010}{{67}{3.2.2.3}{table.caption.18}}
\backcite {Douady2008}{{67}{3.2.2.3}{figure.caption.19}}
\backcite {Douady2008}{{67}{3.2.2.3}{figure.caption.19}}
\backcite {Douady2008}{{67}{3.2.2.3}{figure.caption.19}}
\backcite {Douady2008}{{67}{3.2.2.3}{figure.caption.19}}
\backcite {Lee1996}{{68}{3.2.2.4}{subsubsection.3.2.2.4}}
\backcite {Bacelo2002}{{68}{3.2.2.4}{subsubsection.3.2.2.4}}
\backcite {Bacelo2002}{{68}{3.2.2.4}{subsubsection.3.2.2.4}}
\backcite {Douady2009}{{73}{3.2.2.5}{subsubsection.3.2.2.5}}
\backcite {Douady2009}{{73}{3.2.2.5}{subsubsection.3.2.2.5}}
\backcite {Castrovilli2017}{{75}{3.3.1}{subsection.3.3.1}}
\backcite {Maclot2011}{{75}{3.3.1}{subsection.3.3.1}}
\backcite {Domaracka2012}{{75}{3.3.1}{subsection.3.3.1}}
\backcite {Markush2016}{{75}{3.3.1}{subsection.3.3.1}}
\backcite {Wincel2009}{{75}{3.3.1}{subsection.3.3.1}}
\backcite {Boudaiffa2000}{{75}{3.3.1}{subsection.3.3.1}}
\backcite {Smyth2011}{{75}{3.3.1}{subsection.3.3.1}}
\backcite {Siefermann2011}{{75}{3.3.1}{subsection.3.3.1}}
\backcite {Alizadeh2013}{{75}{3.3.1}{subsection.3.3.1}}
\backcite {Rasmussen2010}{{76}{3.3.1}{subsection.3.3.1}}
\backcite {Coates2018}{{76}{3.3.1}{subsection.3.3.1}}
\backcite {Nelson1994}{{76}{3.3.1}{subsection.3.3.1}}
\backcite {Sadr2014}{{76}{3.3.1}{subsection.3.3.1}}
\backcite {Molina2016}{{76}{3.3.1}{subsection.3.3.1}}
\backcite {Bakker2008}{{76}{3.3.1}{subsection.3.3.1}}
\backcite {Shishkin2000}{{76}{3.3.1}{subsection.3.3.1}}
\backcite {Gadre2000}{{76}{3.3.1}{subsection.3.3.1}}
\backcite {Van2001diffu}{{76}{3.3.1}{subsection.3.3.1}}
\backcite {Gaigeot2001}{{76}{3.3.1}{subsection.3.3.1}}
\backcite {Danilov2006}{{76}{3.3.1}{subsection.3.3.1}}
\backcite {Bacchus2015}{{76}{3.3.1}{subsection.3.3.1}}
\backcite {Gadre2000}{{76}{3.3.1}{subsection.3.3.1}}
\backcite {Van2001diffu}{{76}{3.3.1}{subsection.3.3.1}}
\backcite {Gaigeot2001}{{76}{3.3.1}{subsection.3.3.1}}
\backcite {Danilov2006}{{76}{3.3.1}{subsection.3.3.1}}
\backcite {Bacchus2015}{{76}{3.3.1}{subsection.3.3.1}}
\backcite {Gaigeot2001}{{76}{3.3.1}{subsection.3.3.1}}
\backcite {Shishkin2000}{{76}{3.3.1}{subsection.3.3.1}}
\backcite {Bacchus2015}{{76}{3.3.1}{subsection.3.3.1}}
\backcite {Danilov2006}{{76}{3.3.1}{subsection.3.3.1}}
\backcite {Bacchus2015}{{76}{3.3.1}{subsection.3.3.1}}
\backcite {Gadre2000}{{76}{3.3.1}{subsection.3.3.1}}
\backcite {Danilov2006}{{77}{3.3.1}{subsection.3.3.1}}
\backcite {Bacchus2015}{{77}{3.3.1}{subsection.3.3.1}}
\backcite {Braud2019}{{77}{3.3.1}{subsection.3.3.1}}
\backcite {Dalleska1993}{{78}{3.3.2.1}{figure.caption.23}}
\backcite {Zamith2012}{{78}{3.3.2.1}{figure.caption.23}}
\backcite {Myers2007}{{79}{3.3.2.1}{equation.3.3.3}}
\backcite {Zamith2012}{{79}{3.3.2.1}{equation.3.3.3}}
\backcite {Dalleska1993}{{79}{3.3.2.1}{equation.3.3.3}}
\backcite {Dalleska1993}{{79}{3.3.2.1}{equation.3.3.3}}
\backcite {Hansen2009}{{79}{3.3.2.1}{equation.3.3.3}}
\backcite {Wincel2009}{{79}{3.3.2.1}{equation.3.3.3}}
\backcite {Bakker2008}{{79}{3.3.2.1}{equation.3.3.3}}
\backcite {Dalleska1993}{{79}{3.3.2.1}{equation.3.3.3}}
\backcite {Hansen2009}{{79}{3.3.2.1}{equation.3.3.3}}
\backcite {Wincel2009}{{79}{3.3.2.1}{equation.3.3.3}}
\backcite {Dalleska1993}{{80}{3.14}{figure.caption.24}}
\backcite {Zamith2012}{{80}{3.14}{figure.caption.24}}
\backcite {Kurinovich2002}{{81}{3.3.2.1}{figure.caption.25}}
\backcite {Magnera1991}{{81}{3.3.2.1}{figure.caption.25}}
\backcite {Cheng1998}{{81}{3.3.2.1}{figure.caption.25}}
\backcite {Cheng1998}{{81}{3.3.2.1}{figure.caption.25}}
\backcite {Magnera1991}{{82}{3.16}{figure.caption.26}}
\backcite {Cheng1998}{{82}{3.16}{figure.caption.26}}
\backcite {Kurinovich2002}{{82}{3.16}{figure.caption.26}}
\backcite {Bakker2008}{{82}{3.3.2.1}{figure.caption.26}}
\backcite {Wolken2000}{{84}{3.3.2.2}{table.caption.27}}
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\backcite {Dontot2019}{{103}{4.2.2}{subsection.4.2.2}}
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\backcite {Nelson1994}{{78}{3.3.1}{subsection.3.3.1}}
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\backcite {Danilov2006}{{78}{3.3.1}{subsection.3.3.1}}
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\backcite {Dalleska1993}{{80}{3.3.2.1}{figure.caption.23}}
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\backcite {Dalleska1993}{{82}{3.14}{figure.caption.24}}
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\backcite {Kurinovich2002}{{83}{3.3.2.1}{figure.caption.25}}
\backcite {Magnera1991}{{83}{3.3.2.1}{figure.caption.25}}
\backcite {Cheng1998}{{83}{3.3.2.1}{figure.caption.25}}
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\backcite {Bakker2008}{{83}{3.3.2.1}{figure.caption.26}}
\backcite {Magnera1991}{{84}{3.16}{figure.caption.26}}
\backcite {Cheng1998}{{84}{3.16}{figure.caption.26}}
\backcite {Kurinovich2002}{{84}{3.16}{figure.caption.26}}
\backcite {Wolken2000}{{86}{3.3.2.2}{table.caption.28}}
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\backcite {Zundel1968}{{90}{3.3.2.2}{figure.caption.34}}
\backcite {Molina2015}{{94}{3.3.2.2}{figure.caption.38}}
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\backcite {Gauthier1991}{{100}{4.1}{section.4.1}}
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\backcite {Coates2017}{{100}{4.1}{section.4.1}}
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\backcite {Li1992}{{101}{4.1}{section.4.1}}
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\backcite {Zamith2012}{{101}{4.1}{section.4.1}}
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\backcite {Spasov2000}{{101}{4.1}{section.4.1}}
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\backcite {Baer1996}{{101}{4.1.1}{subsection.4.1.1}}
\backcite {Armentrout2008}{{102}{4.1.1}{subsection.4.1.1}}
\backcite {Rodgers1998}{{102}{4.1.1}{equation.4.1.1}}
\backcite {Armentrout2007}{{102}{4.1.1}{equation.4.1.1}}
\backcite {Braud2017}{{102}{4.1.2}{figure.caption.39}}
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\BOOKMARK [3][]{subsubsection.3.2.2.2}{3.2.2.2 Small Species: \(H2O\)1-3NH4+ and \(H2O\)1-3NH3}{subsection.3.2.2}% 26
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@ -14,53 +14,53 @@
\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}{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}{53}{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$_4$}$^+$ Clusters}{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*.81}
\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}