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\babel @toc { english} { }
\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} { 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 { 2.4.2} 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}
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\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}
