65 lines
6.2 KiB
TeX
65 lines
6.2 KiB
TeX
\babel@toc {english}{}
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\contentsline {chapter}{Glossary}{xi}{chapter*.2}
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\contentsline {chapter}{\numberline {1}General Introduction}{1}{chapter.1}
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\contentsline {chapter}{\numberline {2}Computational Methods}{13}{chapter.2}
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\contentsline {section}{\numberline {2.1}Schr{\"o}dinger Equation}{15}{section.2.1}
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\contentsline {section}{\numberline {2.2}Born-Oppenheimer Approximation}{16}{section.2.2}
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\contentsline {section}{\numberline {2.3}Computation of Electronic Energy}{18}{section.2.3}
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\contentsline {subsection}{\numberline {2.3.1}Wavefunction based Methods}{19}{subsection.2.3.1}
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\contentsline {subsection}{\numberline {2.3.2}Density Functional Theory}{21}{subsection.2.3.2}
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\contentsline {subsection}{\numberline {2.3.3}Density Functional based Tight-Binding Theory}{26}{subsection.2.3.3}
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\contentsline {subsection}{\numberline {2.3.4}Force Field Methods}{34}{subsection.2.3.4}
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\contentsline {section}{\numberline {2.4}Exploration of PES}{36}{section.2.4}
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\contentsline {subsection}{\numberline {2.4.1}Monte Carlo Simulations}{37}{subsection.2.4.1}
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\contentsline {subsection}{\numberline {2.4.2}Classical Molecular Dynamics}{40}{subsection.2.4.2}
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\contentsline {subsection}{\numberline {2.4.3}Parallel-Tempering Molecular Dynamics}{45}{subsection.2.4.3}
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\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}{49}{chapter.3}
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\contentsline {section}{\numberline {3.1}Computational Details}{50}{section.3.1}
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\contentsline {subsection}{\numberline {3.1.1}SCC-DFTB Potential}{50}{subsection.3.1.1}
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\contentsline {subsection}{\numberline {3.1.2}SCC-DFTB Exploration of PES}{50}{subsection.3.1.2}
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\contentsline {subsection}{\numberline {3.1.3}MP2 Geometry Optimizations, Relative and Binding Energies}{51}{subsection.3.1.3}
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\contentsline {subsection}{\numberline {3.1.4}Structure Classification}{53}{subsection.3.1.4}
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\contentsline {section}{\numberline {3.2}Structural and Energetic Properties of Ammonium/Ammonia including Water Clusters}{53}{section.3.2}
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\contentsline {subsection}{\numberline {3.2.1}General introduction}{53}{subsection.3.2.1}
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\contentsline {subsection}{\numberline {3.2.2}Results and Discussion}{55}{subsection.3.2.2}
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\contentsline {subsubsection}{\numberline {3.2.2.1}Dissociation Curves and SCC-DFTB Potential}{55}{subsubsection.3.2.2.1}
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\contentsline {subsubsection}{\numberline {3.2.2.2}Small Species: (H$_2$O)$_{1-3}${NH$_4$}$^+$ and (H$_2$O)$_{1-3}${NH$_3$}}{59}{subsubsection.3.2.2.2}
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\contentsline {subsubsection}{\numberline {3.2.2.3}Properties of (H$_2$O)$_{4-10}${NH$_4$}$^+$ Clusters}{59}{subsubsection.3.2.2.3}
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\contentsline {subsection}{\numberline {3.2.3}Conclusions for Ammonium/Ammonia Including Water Clusters}{59}{subsection.3.2.3}
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\contentsline {section}{\numberline {3.3}Structural and Energetic Properties of Protonated Uracil Water Clusters}{59}{section.3.3}
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\contentsline {subsection}{\numberline {3.3.1}General introduction}{59}{subsection.3.3.1}
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\contentsline {subsection}{\numberline {3.3.2}Results and Discussion}{61}{subsection.3.3.2}
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\contentsline {subsubsection}{\numberline {3.3.2.1}Experimental Results}{61}{subsubsection.3.3.2.1}
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\contentsline {subsubsection}{\numberline {3.3.2.2}Calculated Structures of Protonated Uracil Water Clusters}{67}{subsubsection.3.3.2.2}
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\contentsline {subsection}{\numberline {3.3.3}Conclusions on (H$_2$O)$_{n}$UH$^+$ clusters}{76}{subsection.3.3.3}
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\contentsline {chapter}{\numberline {4}Dynamical Simulation of Collision-Induced Dissociation}{81}{chapter.4}
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\contentsline {section}{\numberline {4.1}Experimental Methods}{81}{section.4.1}
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\contentsline {subsection}{\numberline {4.1.1}Principle of TCID}{83}{subsection.4.1.1}
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\contentsline {subsection}{\numberline {4.1.2}Experimental Setup}{84}{subsection.4.1.2}
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\contentsline {section}{\numberline {4.2}Computational Details}{86}{section.4.2}
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\contentsline {subsection}{\numberline {4.2.1}SCC-DFTB Potential}{86}{subsection.4.2.1}
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\contentsline {subsection}{\numberline {4.2.2}Collision Trajectories}{87}{subsection.4.2.2}
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\contentsline {subsection}{\numberline {4.2.3}Trajectory Analysis}{88}{subsection.4.2.3}
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\contentsline {section}{\numberline {4.3}Dynamical Simulation of Collision-Induced Dissociation of Protonated Uracil Water Clusters}{89}{section.4.3}
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\contentsline {subsection}{\numberline {4.3.1}Introduction}{89}{subsection.4.3.1}
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\contentsline {subsection}{\numberline {4.3.2}Results and Discussion}{90}{subsection.4.3.2}
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\contentsline {subsubsection}{\numberline {4.3.2.1}Statistical Convergence}{90}{subsubsection.4.3.2.1}
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\contentsline {subsection}{\numberline {4.3.3}Time-Dependent Proportion of Fragments}{93}{subsection.4.3.3}
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\contentsline {subsection}{\numberline {4.3.4}Proportion of Neutral Uracil Loss and Total Fragmentation Cross Sections for Small Clusters}{96}{subsection.4.3.4}
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\contentsline {subsection}{\numberline {4.3.5}Behaviour at Larger Sizes, the Cases of (H$_2$O)$_{11, 12}$UH$^+$}{106}{subsection.4.3.5}
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\contentsline {subsection}{\numberline {4.3.6}Mass Spectra of Fragments with Excess Proton}{110}{subsection.4.3.6}
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\contentsline {subsection}{\numberline {4.3.7}Conclusions about CID of (H$_2$O)$_{n}$UH$^+$}{113}{subsection.4.3.7}
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\contentsline {section}{\numberline {4.4}Dynamical Simulation of Collision-Induced Dissociation for Pyrene Dimer Cation}{115}{section.4.4}
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\contentsline {subsection}{\numberline {4.4.1}Introduction}{115}{subsection.4.4.1}
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\contentsline {subsection}{\numberline {4.4.2}Calculation of Energies}{117}{subsection.4.4.2}
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\contentsline {subsection}{\numberline {4.4.3}Simulation of the Experimental TOFMS}{119}{subsection.4.4.3}
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\contentsline {subsection}{\numberline {4.4.4}Results and Discussion}{121}{subsection.4.4.4}
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\contentsline {subsubsection}{\numberline {4.4.4.1}TOFMS Comparison}{121}{subsubsection.4.4.4.1}
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\contentsline {subsubsection}{\numberline {4.4.4.2}Molecular Dynamics Analysis}{122}{subsubsection.4.4.4.2}
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\contentsline {subsection}{\numberline {4.4.5}Conclusions about CID of Py$_2^+$}{138}{subsection.4.4.5}
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\contentsline {chapter}{\numberline {5}General Conclusions and Perspectives}{141}{chapter.5}
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\contentsline {section}{\numberline {5.1}General Conclusions}{141}{section.5.1}
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\contentsline {section}{\numberline {5.2}Perspectives}{144}{section.5.2}
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\contentsline {chapter}{References}{145}{chapter*.71}
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