\BOOKMARK [0][]{chapter*.2}{Glossary}{}% 1
\BOOKMARK [0][]{chapter.1}{1 General Introduction}{}% 2
\BOOKMARK [0][]{chapter.2}{2 Computational Methods}{}% 3
\BOOKMARK [1][]{section.2.1}{2.1 Schr\366dinger Equation}{chapter.2}% 4
\BOOKMARK [1][]{section.2.2}{2.2 Born-Oppenheimer Approximation}{chapter.2}% 5
\BOOKMARK [1][]{section.2.3}{2.3 Computation of Electronic Energy}{chapter.2}% 6
\BOOKMARK [2][]{subsection.2.3.1}{2.3.1 Wavefunction based Methods}{section.2.3}% 7
\BOOKMARK [2][]{subsection.2.3.2}{2.3.2 Density Functional Theory}{section.2.3}% 8
\BOOKMARK [2][]{subsection.2.3.3}{2.3.3 Density Functional based Tight-Binding Theory}{section.2.3}% 9
\BOOKMARK [2][]{subsection.2.3.4}{2.3.4 Force Field Methods}{section.2.3}% 10
\BOOKMARK [1][]{section.2.4}{2.4 Exploration of PES}{chapter.2}% 11
\BOOKMARK [2][]{subsection.2.4.1}{2.4.1 Monte Carlo Simulations}{section.2.4}% 12
\BOOKMARK [2][]{subsection.2.4.2}{2.4.2 Classical Molecular Dynamics}{section.2.4}% 13
\BOOKMARK [2][]{subsection.2.4.3}{2.4.3 Parallel-Tempering Molecular Dynamics}{section.2.4}% 14
\BOOKMARK [2][]{subsection.2.4.4}{2.4.4 Global Optimization}{section.2.4}% 15
\BOOKMARK [0][]{chapter.3}{3 Exploration of Structural and Energetic Properties}{}% 16
\BOOKMARK [1][]{section.3.1}{3.1 Computational Details}{chapter.3}% 17
\BOOKMARK [2][]{subsection.3.1.1}{3.1.1 SCC-DFTB Potential}{section.3.1}% 18
\BOOKMARK [2][]{subsection.3.1.2}{3.1.2 SCC-DFTB Exploration of PES}{section.3.1}% 19
\BOOKMARK [2][]{subsection.3.1.3}{3.1.3 MP2 Geometry Optimizations, Relative and Binding Energies}{section.3.1}% 20
\BOOKMARK [2][]{subsection.3.1.4}{3.1.4 Structure Classification}{section.3.1}% 21
\BOOKMARK [1][]{section.3.2}{3.2 Structural and Energetic Properties of Ammonium/Ammonia including Water Clusters}{chapter.3}% 22
\BOOKMARK [2][]{subsection.3.2.1}{3.2.1 General introduction}{section.3.2}% 23
\BOOKMARK [2][]{subsection.3.2.2}{3.2.2 Results and Discussion}{section.3.2}% 24
\BOOKMARK [3][]{subsubsection.3.2.2.1}{3.2.2.1 Dissociation Curves and SCC-DFTB Potential}{subsection.3.2.2}% 25
\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
\BOOKMARK [3][]{subsubsection.3.2.2.3}{3.2.2.3 Properties of \(H2O\)4-10NH4+ Clusters}{subsection.3.2.2}% 27
\BOOKMARK [2][]{subsection.3.2.3}{3.2.3 Conclusions for Ammonium/Ammonia Including Water Clusters}{section.3.2}% 28
\BOOKMARK [1][]{section.3.3}{3.3 Structural and Energetic Properties of Protonated Uracil Water Clusters}{chapter.3}% 29
\BOOKMARK [2][]{subsection.3.3.1}{3.3.1 General introduction}{section.3.3}% 30
\BOOKMARK [2][]{subsection.3.3.2}{3.3.2 Results and Discussion}{section.3.3}% 31
\BOOKMARK [3][]{subsubsection.3.3.2.1}{3.3.2.1 Experimental Results}{subsection.3.3.2}% 32
\BOOKMARK [3][]{subsubsection.3.3.2.2}{3.3.2.2 Calculated Structures of Protonated Uracil Water Clusters}{subsection.3.3.2}% 33
\BOOKMARK [2][]{subsection.3.3.3}{3.3.3 Conclusions on \(H2O\)nUH+ clusters}{section.3.3}% 34
\BOOKMARK [0][]{chapter.4}{4 Dynamical Simulation of Collision-Induced Dissociation}{}% 35
\BOOKMARK [1][]{section.4.1}{4.1 Experimental Methods}{chapter.4}% 36
\BOOKMARK [2][]{subsection.4.1.1}{4.1.1 Principle of TCID}{section.4.1}% 37
\BOOKMARK [2][]{subsection.4.1.2}{4.1.2 Experimental Setup}{section.4.1}% 38
\BOOKMARK [1][]{section.4.2}{4.2 Computational Details}{chapter.4}% 39
\BOOKMARK [2][]{subsection.4.2.1}{4.2.1 SCC-DFTB Potential}{section.4.2}% 40
\BOOKMARK [2][]{subsection.4.2.2}{4.2.2 Collision Trajectories}{section.4.2}% 41
\BOOKMARK [2][]{subsection.4.2.3}{4.2.3 Trajectory Analysis}{section.4.2}% 42
\BOOKMARK [1][]{section.4.3}{4.3 Dynamical Simulation of Collision-Induced Dissociation of Protonated Uracil Water Clusters}{chapter.4}% 43
\BOOKMARK [2][]{subsection.4.3.1}{4.3.1 Introduction}{section.4.3}% 44
\BOOKMARK [2][]{subsection.4.3.2}{4.3.2 Results and Discussion}{section.4.3}% 45
\BOOKMARK [3][]{subsubsection.4.3.2.1}{4.3.2.1 Statistical Convergence}{subsection.4.3.2}% 46
\BOOKMARK [2][]{subsection.4.3.3}{4.3.3 Time-Dependent Proportion of Fragments}{section.4.3}% 47
\BOOKMARK [2][]{subsection.4.3.4}{4.3.4 Proportion of Neutral Uracil Loss and Total Fragmentation Cross Sections for Small Clusters}{section.4.3}% 48
\BOOKMARK [2][]{subsection.4.3.5}{4.3.5 Behaviour at Larger Sizes, the Cases of \(H2O\)11, 12UH+}{section.4.3}% 49
\BOOKMARK [2][]{subsection.4.3.6}{4.3.6 Mass Spectra of Fragments with Excess Proton}{section.4.3}% 50
\BOOKMARK [2][]{subsection.4.3.7}{4.3.7 Conclusions about CID of \(H2O\)nUH+}{section.4.3}% 51
\BOOKMARK [1][]{section.4.4}{4.4 Dynamical Simulation of Collision-Induced Dissociation for Pyrene Dimer Cation}{chapter.4}% 52
\BOOKMARK [2][]{subsection.4.4.1}{4.4.1 Introduction}{section.4.4}% 53
\BOOKMARK [2][]{subsection.4.4.2}{4.4.2 Calculation of Energies}{section.4.4}% 54
\BOOKMARK [2][]{subsection.4.4.3}{4.4.3 Simulation of the Experimental TOFMS}{section.4.4}% 55
\BOOKMARK [2][]{subsection.4.4.4}{4.4.4 Results and Discussion}{section.4.4}% 56
\BOOKMARK [3][]{subsubsection.4.4.4.1}{4.4.4.1 TOFMS Comparison}{subsection.4.4.4}% 57
\BOOKMARK [3][]{subsubsection.4.4.4.2}{4.4.4.2 Molecular Dynamics Analysis}{subsection.4.4.4}% 58
\BOOKMARK [2][]{subsection.4.4.5}{4.4.5 Conclusions about CID of Py2+}{section.4.4}% 59
\BOOKMARK [0][]{chapter.5}{5 General Conclusions and Perspectives}{}% 60
\BOOKMARK [1][]{section.5.1}{5.1 General Conclusions}{chapter.5}% 61
\BOOKMARK [1][]{section.5.2}{5.2 Perspectives}{chapter.5}% 62
\BOOKMARK [0][]{chapter*.71}{References}{}% 63