\newlabel{sec:collisionwUH}{{4.3}{107}{Dynamical Simulation of Collision-Induced Dissociation of Protonated Uracil Water Clusters}{section.4.3}{}}
\@writefile{toc}{\contentsline{section}{\numberline{4.3}Dynamical Simulation of Collision-Induced Dissociation of Protonated Uracil Water Clusters}{107}{section.4.3}}
\@writefile{lof}{\contentsline{figure}{\numberline{4.4}{\ignorespaces Schematic representation of random argon orientations for the collision with the second lowest-energy isomer of cluster (H$_2$O)$_3$UH$^+$. 200 (a), 400 (b) and 600 (c) random argon orientations are generated with impact parameter being 0. ~200 orientations are generated with impact parameter being 0 and 6 (d), respectively.}}{109}{figure.caption.42}}
\newlabel{3b-sphere}{{4.4}{109}{Schematic representation of random argon orientations for the collision with the second lowest-energy isomer of cluster (H$_2$O)$_3$UH$^+$. 200 (a), 400 (b) and 600 (c) random argon orientations are generated with impact parameter being 0. ~200 orientations are generated with impact parameter being 0 and 6 (d), respectively}{figure.caption.42}{}}
\@writefile{lof}{\contentsline{figure}{\numberline{4.5}{\ignorespaces Schematic representation of random argon orientations for the collision with the second lowest-energy isomer of cluster (H$_2$O)$_{12}$UH$^+$. 200 (a), 400 (b) and 600 (c) random argon orientations are generated with impact parameter being 0. ~200 orientations are generated with impact parameter value being 0 and 7 (d), respectively.}}{110}{figure.caption.43}}
\newlabel{12f-sphere}{{4.5}{110}{Schematic representation of random argon orientations for the collision with the second lowest-energy isomer of cluster (H$_2$O)$_{12}$UH$^+$. 200 (a), 400 (b) and 600 (c) random argon orientations are generated with impact parameter being 0. ~200 orientations are generated with impact parameter value being 0 and 7 (d), respectively}{figure.caption.43}{}}
\@writefile{lot}{\contentsline{table}{\numberline{4.1}{\ignorespaces The proportions of $P_{NUL}$ and $\sigma_{frag}$ of first lowest-energy isomer and the isomer whose $P_{NUL}$ fits the experiment (in bold) of (H$_2$O)$_{1-5}$UH$^+$ with simulations of 200, 400, and 600 as initial conditions.\relax}}{112}{table.caption.44}}
\newlabel{tab:converge-1w-5w}{{4.1}{112}{The proportions of $P_{NUL}$ and $\sigma_{frag}$ of first lowest-energy isomer and the isomer whose $P_{NUL}$ fits the experiment (in bold) of (H$_2$O)$_{1-5}$UH$^+$ with simulations of 200, 400, and 600 as initial conditions.\relax}{table.caption.44}{}}
\@writefile{lot}{\contentsline{table}{\numberline{4.2}{\ignorespaces The proportions of $P_{NUL}$ and $\sigma_{frag}$ of first lowest-energy isomer and the isomer whose $P_{NUL}$ fits the experiment (in bold) of (H$_2$O)$_{6, 7, 11, 12}$UH$^+$ with simulations of 200, 400, and 600 as initial conditions.\relax}}{113}{table.caption.45}}
\newlabel{tab:converge-6w-12w}{{4.2}{113}{The proportions of $P_{NUL}$ and $\sigma_{frag}$ of first lowest-energy isomer and the isomer whose $P_{NUL}$ fits the experiment (in bold) of (H$_2$O)$_{6, 7, 11, 12}$UH$^+$ with simulations of 200, 400, and 600 as initial conditions.\relax}{table.caption.45}{}}
\@writefile{lof}{\contentsline{figure}{\numberline{4.6}{\ignorespaces Time-dependent proportions of the main fragments obtained from the dissociation of the lowest-energy isomers of (H$_2$O)$_1$UH$^+$ (left) and (H$_2$O)$_{2}$UH$^+$ (right).}}{114}{figure.caption.46}}
\newlabel{proporEachFrag-1a2a}{{4.6}{114}{Time-dependent proportions of the main fragments obtained from the dissociation of the lowest-energy isomers of (H$_2$O)$_1$UH$^+$ (left) and (H$_2$O)$_{2}$UH$^+$ (right)}{figure.caption.46}{}}
\@writefile{toc}{\contentsline{subsection}{\numberline{4.3.4}Proportion of Neutral Uracil Loss and Total Fragmentation Cross Sections for Small Clusters}{114}{subsection.4.3.4}}
\newlabel{small}{{4.3.4}{114}{Proportion of Neutral Uracil Loss and Total Fragmentation Cross Sections for Small Clusters}{subsection.4.3.4}{}}
\@writefile{lof}{\contentsline{figure}{\numberline{4.7}{\ignorespaces Time-dependent proportions of the main fragments obtained from the dissociation of the lowest-energy isomers of (H$_2$O)$_3$UH$^+$ (left) and (H$_2$O)$_{4}$UH$^+$ (right). Bottom panels correspond to a zoom over the lower proportions.}}{115}{figure.caption.47}}
\newlabel{proporEachFrag-3a4a-zoom}{{4.7}{115}{Time-dependent proportions of the main fragments obtained from the dissociation of the lowest-energy isomers of (H$_2$O)$_3$UH$^+$ (left) and (H$_2$O)$_{4}$UH$^+$ (right). Bottom panels correspond to a zoom over the lower proportions}{figure.caption.47}{}}
\@writefile{lof}{\contentsline{figure}{\numberline{4.8}{\ignorespaces Time-dependent proportions of the main fragments obtained from the dissociation of the lowest-energy isomers of (H$_2$O)$_5$UH$^+$ (left) and (H$_2$O)$_{6}$UH$^+$ (right). Bottom panels correspond to a zoom over the lower proportions.}}{116}{figure.caption.48}}
\newlabel{proporEachFrag-5a6a-zoom}{{4.8}{116}{Time-dependent proportions of the main fragments obtained from the dissociation of the lowest-energy isomers of (H$_2$O)$_5$UH$^+$ (left) and (H$_2$O)$_{6}$UH$^+$ (right). Bottom panels correspond to a zoom over the lower proportions}{figure.caption.48}{}}
\@writefile{lof}{\contentsline{figure}{\numberline{4.9}{\ignorespaces Time-dependent proportions of the main fragments obtained from the dissociation of the lowest-energy isomer of (H$_2$O)$_{11}$UH$^+$. Right panel corresponds to a zoom over the lower proportions.}}{116}{figure.caption.49}}
\newlabel{proporEachFrag-11a-zoom}{{4.9}{116}{Time-dependent proportions of the main fragments obtained from the dissociation of the lowest-energy isomer of (H$_2$O)$_{11}$UH$^+$. Right panel corresponds to a zoom over the lower proportions}{figure.caption.49}{}}
\@writefile{lot}{\contentsline{table}{\numberline{4.3}{\ignorespaces Relative energy $E_{rel.}$ (in kcal.mol$^{-1}$) at the MP2/Def2TZVP level, LEP, $P_{PU}$ (in \%), $P_{NUL}$ (in \%), $\sigma_{frag}$ (in \r A$^2$) of the considered low-energy isomers of (H$_2$O)$_{1-7, 11, 12}$UH$^+$ clusters. Isomers which $P_{NUL}$ fit best to the experimental value are indicated in bold. $P_{{NUL}_{exp}}$ and $\sigma_{{frag}_{exp}}$ are the experimental values for $P_{NUL}$ and $\sigma_{frag}$, respectively. For (H$_2$O)$_{12}$UH$^+$, experimental values were obtained for collision with Ne, whereas all other theoretical and experimental data are for collision with Ar.\relax}}{117}{table.caption.52}}
\newlabel{tab:full}{{4.3}{117}{Relative energy $E_{rel.}$ (in kcal.mol$^{-1}$) at the MP2/Def2TZVP level, LEP, $P_{PU}$ (in \%), $P_{NUL}$ (in \%), $\sigma_{frag}$ (in \AA$^2$) of the considered low-energy isomers of (H$_2$O)$_{1-7, 11, 12}$UH$^+$ clusters. Isomers which $P_{NUL}$ fit best to the experimental value are indicated in bold. $P_{{NUL}_{exp}}$ and $\sigma_{{frag}_{exp}}$ are the experimental values for $P_{NUL}$ and $\sigma_{frag}$, respectively. For (H$_2$O)$_{12}$UH$^+$, experimental values were obtained for collision with Ne, whereas all other theoretical and experimental data are for collision with Ar.\relax}{table.caption.52}{}}
\@writefile{lof}{\contentsline{figure}{\numberline{4.10}{\ignorespaces Time-dependent proportions of the main fragments obtained from the dissociation of the lowest-energy isomers of (H$_2$O)$_7$UH$^+$ (left) and (H$_2$O)$_{12}$UH$^+$ (right). Bottom panels correspond to a zoom over the lower proportions.}}{118}{figure.caption.50}}
\newlabel{proporEachFrag-7a12a-zoom}{{4.10}{118}{Time-dependent proportions of the main fragments obtained from the dissociation of the lowest-energy isomers of (H$_2$O)$_7$UH$^+$ (left) and (H$_2$O)$_{12}$UH$^+$ (right). Bottom panels correspond to a zoom over the lower proportions}{figure.caption.50}{}}
\@writefile{lof}{\contentsline{figure}{\numberline{4.11}{\ignorespaces Time-dependent proportions of the main fragments obtained from the dissociation of the the third lowest-energy isomer of (H$_2$O)$_7$UH$^+$ (left) and the third lowest-energy isomer (H$_2$O)$_{12}$UH$^+$ (right). Bottom panels correspond to a zoom over the lower proportions.}}{119}{figure.caption.51}}
\newlabel{proporEachFrag-7d12c-zoom}{{4.11}{119}{Time-dependent proportions of the main fragments obtained from the dissociation of the the third lowest-energy isomer of (H$_2$O)$_7$UH$^+$ (left) and the third lowest-energy isomer (H$_2$O)$_{12}$UH$^+$ (right). Bottom panels correspond to a zoom over the lower proportions}{figure.caption.51}{}}
\@writefile{lof}{\contentsline{figure}{\numberline{4.12}{\ignorespaces Selected low-energy configurations of (H$_2$O)$_{1-3}$UH$^+$. Relative energies at the MP2/Def2TZVP level are in kcal.mol$^{-1}$.}}{120}{figure.caption.53}}
\newlabel{fig-1a-3b}{{4.12}{120}{Selected low-energy configurations of (H$_2$O)$_{1-3}$UH$^+$. Relative energies at the MP2/Def2TZVP level are in kcal.mol$^{-1}$}{figure.caption.53}{}}
\@writefile{lof}{\contentsline{figure}{\numberline{4.13}{\ignorespaces Selected low-energy configurations of (H$_2$O)$_{4-5}$UH$^+$. Relative energies at the MP2/Def2TZVP level are in kcal.mol$^{-1}$.}}{121}{figure.caption.54}}
\newlabel{fig-4a-5d}{{4.13}{121}{Selected low-energy configurations of (H$_2$O)$_{4-5}$UH$^+$. Relative energies at the MP2/Def2TZVP level are in kcal.mol$^{-1}$}{figure.caption.54}{}}
\@writefile{lof}{\contentsline{figure}{\numberline{4.14}{\ignorespaces Selected low-energy configurations of (H$_2$O)$_{6}$UH$^+$. Relative energies at the MP2/Def2TZVP level are in kcal.mol$^{-1}$.}}{122}{figure.caption.55}}
\newlabel{fig-6a-6f}{{4.14}{122}{Selected low-energy configurations of (H$_2$O)$_{6}$UH$^+$. Relative energies at the MP2/Def2TZVP level are in kcal.mol$^{-1}$}{figure.caption.55}{}}
\@writefile{lof}{\contentsline{figure}{\numberline{4.15}{\ignorespaces Selected low-energy configurations of (H$_2$O)$_{7}$UH$^+$. Relative energies at the MP2/Def2TZVP level are in kcal.mol$^{-1}$.}}{123}{figure.caption.56}}
\newlabel{fig-7a-7d}{{4.15}{123}{Selected low-energy configurations of (H$_2$O)$_{7}$UH$^+$. Relative energies at the MP2/Def2TZVP level are in kcal.mol$^{-1}$}{figure.caption.56}{}}
\@writefile{lof}{\contentsline{figure}{\numberline{4.16}{\ignorespaces Theoretical (green and blue lines) and experimental (red line) $P_{NUL}$ values for the (H$_2$O)$_{1-7, 11, 12}$UH$^+$ clusters. Theory 1 (green line) is obtained from the isomers which $P_{NUL}$ matches best to the experimental data while Theory 2 (blue line) is obtained from lowest-energy isomers.}}{124}{figure.caption.57}}
\newlabel{neutralUloss-Ne-Ar}{{4.16}{124}{Theoretical (green and blue lines) and experimental (red line) $P_{NUL}$ values for the (H$_2$O)$_{1-7, 11, 12}$UH$^+$ clusters. Theory 1 (green line) is obtained from the isomers which $P_{NUL}$ matches best to the experimental data while Theory 2 (blue line) is obtained from lowest-energy isomers}{figure.caption.57}{}}
\@writefile{toc}{\contentsline{subsection}{\numberline{4.3.5}Behaviour at Larger Sizes, the Cases of (H$_2$O)$_{11, 12}$UH$^+$}{124}{subsection.4.3.5}}
\newlabel{large}{{4.3.5}{124}{Behaviour at Larger Sizes, the Cases of (H$_2$O)$_{11, 12}$UH$^+$}{subsection.4.3.5}{}}
\@writefile{lof}{\contentsline{figure}{\numberline{4.17}{\ignorespaces Theoretical (green and blue lines) and experimental (red line) $\sigma_{frag}$ values for the (H$_2$O)$_{1-7, 11, 12}$UH$^+$ clusters. Theory 1 (green line) is obtained from the isomers which $P_{NUL}$ matches best to the experimental data while Theory 2 (blue line) is obtained from lowest-energy isomers.}}{125}{figure.caption.58}}
\newlabel{cross-section-Ne-Ar}{{4.17}{125}{Theoretical (green and blue lines) and experimental (red line) $\sigma_{frag}$ values for the (H$_2$O)$_{1-7, 11, 12}$UH$^+$ clusters. Theory 1 (green line) is obtained from the isomers which $P_{NUL}$ matches best to the experimental data while Theory 2 (blue line) is obtained from lowest-energy isomers}{figure.caption.58}{}}
\@writefile{lof}{\contentsline{figure}{\numberline{4.18}{\ignorespaces Selected low-energy configurations of (H$_2$O)$_{11}$UH$^+$. Relative energies at the MP2/Def2TZVP level are in kcal.mol$^{-1}$.}}{127}{figure.caption.59}}
\newlabel{fig-11a-f}{{4.18}{127}{Selected low-energy configurations of (H$_2$O)$_{11}$UH$^+$. Relative energies at the MP2/Def2TZVP level are in kcal.mol$^{-1}$}{figure.caption.59}{}}
\@writefile{lof}{\contentsline{figure}{\numberline{4.19}{\ignorespaces Selected low-energy configurations of (H$_2$O)$_{12}$UH$^+$. Relative energies at the MP2/Def2TZVP level are in kcal.mol$^{-1}$.}}{127}{figure.caption.60}}
\newlabel{fig-12a-f}{{4.19}{127}{Selected low-energy configurations of (H$_2$O)$_{12}$UH$^+$. Relative energies at the MP2/Def2TZVP level are in kcal.mol$^{-1}$}{figure.caption.60}{}}
\@writefile{toc}{\contentsline{subsection}{\numberline{4.3.6}Mass Spectra of Fragments with Excess Proton}{128}{subsection.4.3.6}}
\newlabel{mass-spectra}{{4.3.6}{128}{Mass Spectra of Fragments with Excess Proton}{subsection.4.3.6}{}}
\@writefile{lof}{\contentsline{figure}{\numberline{4.20}{\ignorespaces Simulated mass spectra (positive area) of the charged fragments after 15~ps simulation time (fragments (H$_2$O)$_n$H$^+$ in red and (H$_2$O)$_n$UH$^+$ in blue for argon; (H$_2$O)$_n$H$^+$ in pink and (H$_2$O)$_n$UH$^+$ in green for neon) from isomers (a) 1a, (b) 2b, (c) 3b, (d) 4b. The counterparts in experiment are plotted (negative area).}}{128}{figure.caption.61}}
\newlabel{MS-BR-1w-4w-Ne-Ar-branch}{{4.20}{128}{Simulated mass spectra (positive area) of the charged fragments after 15~ps simulation time (fragments (H$_2$O)$_n$H$^+$ in red and (H$_2$O)$_n$UH$^+$ in blue for argon; (H$_2$O)$_n$H$^+$ in pink and (H$_2$O)$_n$UH$^+$ in green for neon) from isomers (a) 1a, (b) 2b, (c) 3b, (d) 4b. The counterparts in experiment are plotted (negative area)}{figure.caption.61}{}}
\@writefile{lof}{\contentsline{figure}{\numberline{4.21}{\ignorespaces Simulated mass spectra (positive area) of the charged fragments after 15~ps simulation time (fragments (H$_2$O)$_n$H$^+$ in red and (H$_2$O)$_n$UH$^+$ in blue) from isomers (e) 5d, (f) 6f, (g) 7d, and (h) 11d. The counterparts in experiment are plotted (negative area).}}{129}{figure.caption.62}}
\newlabel{MS-BR-5w-11w-Ne-Ar-branch}{{4.21}{129}{Simulated mass spectra (positive area) of the charged fragments after 15~ps simulation time (fragments (H$_2$O)$_n$H$^+$ in red and (H$_2$O)$_n$UH$^+$ in blue) from isomers (e) 5d, (f) 6f, (g) 7d, and (h) 11d. The counterparts in experiment are plotted (negative area)}{figure.caption.62}{}}
\@writefile{lof}{\contentsline{figure}{\numberline{4.22}{\ignorespaces Simulated mass spectra (positive area) of the charged fragments after 15~ps simulation time (fragments (H$_2$O)$_n$H$^+$ in red and (H$_2$O)$_n$UH$^+$ in blue) from isomers 12c. The counterparts in experiment obtained for collision with neon are plotted in negative area (H$_2$O)$_n$H$^+$ in pink and (H$_2$O)$_n$UH$^+$ in green).}}{130}{figure.caption.63}}
\newlabel{MS-BR-12w-Ne-branch}{{4.22}{130}{Simulated mass spectra (positive area) of the charged fragments after 15~ps simulation time (fragments (H$_2$O)$_n$H$^+$ in red and (H$_2$O)$_n$UH$^+$ in blue) from isomers 12c. The counterparts in experiment obtained for collision with neon are plotted in negative area (H$_2$O)$_n$H$^+$ in pink and (H$_2$O)$_n$UH$^+$ in green)}{figure.caption.63}{}}
\@writefile{lot}{\contentsline{table}{\numberline{4.4}{\ignorespaces Energies of different (H$_2$O)$_6$UH$^+$ fragments selected from the dissociation of 7d at SCC-DFTB level, and the lowest energies (H$_2$O)$_5$UH$^+$ and (H$_2$O) at SCC-DFTB level. The relative energy $\Delta E$ = $E_{(H_2O)_6UH^+}$ -($E_{(H_2O)_5UH^+}$ +$ E_{H_2O}$). All energies here are given in eV.\relax}}{131}{table.caption.64}}
\newlabel{tab:fragenergy}{{4.4}{131}{Energies of different (H$_2$O)$_6$UH$^+$ fragments selected from the dissociation of 7d at SCC-DFTB level, and the lowest energies (H$_2$O)$_5$UH$^+$ and (H$_2$O) at SCC-DFTB level. The relative energy $\Delta E$ = $E_{(H_2O)_6UH^+}$ -($E_{(H_2O)_5UH^+}$ +$ E_{H_2O}$). All energies here are given in eV.\relax}{table.caption.64}{}}
\@writefile{toc}{\contentsline{subsection}{\numberline{4.3.7}Conclusions about CID of (H$_2$O)$_{n}$UH$^+$}{131}{subsection.4.3.7}}
\newlabel{Concl}{{4.3.7}{131}{Conclusions about CID of (H$_2$O)$_{n}$UH$^+$}{subsection.4.3.7}{}}
\@writefile{toc}{\contentsline{section}{\numberline{4.4}Dynamical Simulation of Collision-Induced Dissociation for Pyrene Dimer Cation}{133}{section.4.4}}
\@writefile{lof}{\contentsline{figure}{\numberline{4.24}{\ignorespaces Normalized time of flight mass spectra of the parent pyrene dimer cation (a), and the pyrene fragment Py$^+$ (b) resulting from the collision of Py$_2^+$ with argon at a center of mass collision energy of 17.5~eV. The black line is for the experimental result whereas red and green curves are the MD+PST and PST model results. The blue curve is the PST subcontribution of the MD+PST model.}}{139}{figure.caption.66}}
\newlabel{expTOF}{{4.24}{139}{Normalized time of flight mass spectra of the parent pyrene dimer cation (a), and the pyrene fragment Py$^+$ (b) resulting from the collision of Py$_2^+$ with argon at a center of mass collision energy of 17.5~eV. The black line is for the experimental result whereas red and green curves are the MD+PST and PST model results. The blue curve is the PST subcontribution of the MD+PST model}{figure.caption.66}{}}
\@writefile{lof}{\contentsline{figure}{\numberline{4.25}{\ignorespaces Snapshots for two different molecular dynamics trajectories. Top and bottom: trajectories with impact parameter of 3.5~\r A{} and a collision energy of 17.5~eV, leading to dissociation and non-dissociation (top and bottom, respectively).}}{141}{figure.caption.67}}
\newlabel{collisions}{{4.25}{141}{Snapshots for two different molecular dynamics trajectories. Top and bottom: trajectories with impact parameter of 3.5~\AA{} and a collision energy of 17.5~eV, leading to dissociation and non-dissociation (top and bottom, respectively)}{figure.caption.67}{}}
\@writefile{lof}{\contentsline{figure}{\numberline{4.26}{\ignorespaces Distribution of transferred energy in rovibrational modes $\Delta E_{int}^{Py_2}$ for trajectories leading to dissociation at the end of MD (center of mass collision energy of 17.5~eV). The dashed line shows the distribution of transferred energy used in the LOC model.}}{143}{figure.caption.68}}
\newlabel{distriPerc-Etf-175eV-d-bin03}{{4.26}{143}{Distribution of transferred energy in rovibrational modes $\Delta E_{int}^{Py_2}$ for trajectories leading to dissociation at the end of MD (center of mass collision energy of 17.5~eV). The dashed line shows the distribution of transferred energy used in the LOC model}{figure.caption.68}{}}
\@writefile{lof}{\contentsline{figure}{\numberline{4.27}{\ignorespaces Snapshots for molecular dynamics trajectory with impact parameter of 0.5~\r A{} and a collision energy of 27.5 eV leading to intramolecular fragmentation.}}{144}{figure.caption.69}}
\newlabel{fragmentation}{{4.27}{144}{Snapshots for molecular dynamics trajectory with impact parameter of 0.5~\AA{} and a collision energy of 27.5 eV leading to intramolecular fragmentation}{figure.caption.69}{}}
\@writefile{lof}{\contentsline{figure}{\numberline{4.28}{\ignorespaces Opacity curves as a function of the impact parameter $b$ for several selected center of mass collision energies.}}{144}{figure.caption.70}}
\newlabel{opacitycurves}{{4.28}{144}{Opacity curves as a function of the impact parameter $b$ for several selected center of mass collision energies}{figure.caption.70}{}}
\@writefile{lof}{\contentsline{figure}{\numberline{4.29}{\ignorespaces Dissociation cross sections of Py$_2^+$ after collision with argon as a function of center of mass collision energy for the short (MD), experimental (MD+PST) and infinite timescales. Cross sections resulting from the LOC model are also plotted. $\sigma_\mathrm{MD}$ (0.1) denotes the dissociation cross section for short (MD) timescale with a time step of 0.1 fs.}}{146}{figure.caption.71}}
\newlabel{cross-section}{{4.29}{146}{Dissociation cross sections of Py$_2^+$ after collision with argon as a function of center of mass collision energy for the short (MD), experimental (MD+PST) and infinite timescales. Cross sections resulting from the LOC model are also plotted. $\sigma_\mathrm{MD}$ (0.1) denotes the dissociation cross section for short (MD) timescale with a time step of 0.1 fs}{figure.caption.71}{}}
\@writefile{lof}{\contentsline{figure}{\numberline{4.30}{\ignorespaces At the end of the MD collision simulations with a time step of 0.1 and 0.5 fs, the total transferred energy $\Delta E_{int}^{Py_2}$ to the rovibrational modes or restricted to the sole dissociated ($\Delta E_{int-d}^{Py_2}$) or undissociated ($\Delta E_{int-ud}^{Py_2}$) pyrene dimers as a function of collision energy. The transeferred energy to the monomers rovibrational modes for the dissociated dimers $\Delta E_{int-d}^{Py^1+Py^2}$ is also plotted.}}{147}{figure.caption.72}}
\newlabel{transferredE-Ar-300}{{4.30}{147}{At the end of the MD collision simulations with a time step of 0.1 and 0.5 fs, the total transferred energy $\Delta E_{int}^{Py_2}$ to the rovibrational modes or restricted to the sole dissociated ($\Delta E_{int-d}^{Py_2}$) or undissociated ($\Delta E_{int-ud}^{Py_2}$) pyrene dimers as a function of collision energy. The transeferred energy to the monomers rovibrational modes for the dissociated dimers $\Delta E_{int-d}^{Py^1+Py^2}$ is also plotted}{figure.caption.72}{}}
\@writefile{lot}{\contentsline{table}{\numberline{4.5}{\ignorespaces The kinetic energy partition after the collision of pyrene dimer with argon at different collision energies $E_{col}$. All energies are in eV.\relax}}{148}{table.caption.73}}
\newlabel{tab:table1}{{4.5}{148}{The kinetic energy partition after the collision of pyrene dimer with argon at different collision energies $E_{col}$. All energies are in eV.\relax}{table.caption.73}{}}
\@writefile{lof}{\contentsline{figure}{\numberline{4.31}{\ignorespaces Mean kinetic energy partition at the end of the MD simulations.}}{149}{figure.caption.74}}
\newlabel{Epartition-Ar-300-SP}{{4.31}{149}{Mean kinetic energy partition at the end of the MD simulations}{figure.caption.74}{}}
\@writefile{lot}{\contentsline{table}{\numberline{4.6}{\ignorespaces The kinetic energy partition and cross section at the end of MD simulations with time step being 0.1 and 0.5 at different collision energies of 20 and 25. All energies are in eV. Time step ($Tstep$) is in fs. Cross section $\sigma_{_{MD}}$ is in ~\r A.\relax}}{150}{table.caption.75}}
\newlabel{tab:table2}{{4.6}{150}{The kinetic energy partition and cross section at the end of MD simulations with time step being 0.1 and 0.5 at different collision energies of 20 and 25. All energies are in eV. Time step ($Tstep$) is in fs. Cross section $\sigma_{_{MD}}$ is in ~\AA .\relax}{table.caption.75}{}}
\@writefile{lof}{\contentsline{figure}{\numberline{4.32}{\ignorespaces Mean kinetic energy partition at the end of the MD simulations with time step being 0.5 fs at the center of mass collision energy from 2.5 to 25 eV. The mean kinetic energy partition with time step being 0.1 fs at center of mass collision energies of 20 and 25 eV are plotted with filled round circles.}}{150}{figure.caption.76}}
\newlabel{Epartition-Ar-300-Tstep-01}{{4.32}{150}{Mean kinetic energy partition at the end of the MD simulations with time step being 0.5 fs at the center of mass collision energy from 2.5 to 25 eV. The mean kinetic energy partition with time step being 0.1 fs at center of mass collision energies of 20 and 25 eV are plotted with filled round circles}{figure.caption.76}{}}
\@writefile{lof}{\contentsline{figure}{\numberline{4.33}{\ignorespaces Kinetic energy proportion after collision of Py$_2^+$ with argon as a function of collision energy.}}{151}{figure.caption.77}}
\newlabel{prot-Ar-300}{{4.33}{151}{Kinetic energy proportion after collision of Py$_2^+$ with argon as a function of collision energy}{figure.caption.77}{}}
\@writefile{lof}{\contentsline{figure}{\numberline{4.34}{\ignorespaces Kinetic energy partition for dissociated (-d) and undissociated (-ud) trajectories at the end of the MD simulation as a function of collision energy.}}{152}{figure.caption.78}}
\newlabel{Epartition-Ar-300-d-ud}{{4.34}{152}{Kinetic energy partition for dissociated (-d) and undissociated (-ud) trajectories at the end of the MD simulation as a function of collision energy}{figure.caption.78}{}}
\@writefile{lof}{\contentsline{figure}{\numberline{4.35}{\ignorespaces Timescales, as a function of center of mass collision energy, for argon to travel across some typical distances: a carbon-carbon bond (green), a carbon-hydrogen bond (purple) or the largest axis of the pyrene molecule (blue).}}{153}{figure.caption.79}}
\newlabel{figuretimescale}{{4.35}{153}{Timescales, as a function of center of mass collision energy, for argon to travel across some typical distances: a carbon-carbon bond (green), a carbon-hydrogen bond (purple) or the largest axis of the pyrene molecule (blue)}{figure.caption.79}{}}
\@writefile{lof}{\contentsline{figure}{\numberline{4.36}{\ignorespaces Instantaneous kinetic temperatures as a function of time for intra and intermolecular modes of the pyrene dimer at a collision energy of 22.5~eV. Impact parameters $b$ are (a) 2, (b) 3, (c) 0, (d) 2.5, (e) 2, and (f) 2~\r A{}. In cases (a) and (b) dissociation takes place whereas in the other cases the dimer remains undissociated at the end of the MD simulation. In (c) to (f) the lower panel is a vertical zoom of the corresponding intramolecular parts in upper panel.}}{154}{figure.caption.80}}
\newlabel{T-time-zoom_abcdef}{{4.36}{154}{Instantaneous kinetic temperatures as a function of time for intra and intermolecular modes of the pyrene dimer at a collision energy of 22.5~eV. Impact parameters $b$ are (a) 2, (b) 3, (c) 0, (d) 2.5, (e) 2, and (f) 2~\AA{}. In cases (a) and (b) dissociation takes place whereas in the other cases the dimer remains undissociated at the end of the MD simulation. In (c) to (f) the lower panel is a vertical zoom of the corresponding intramolecular parts in upper panel}{figure.caption.80}{}}
\@writefile{lof}{\contentsline{figure}{\numberline{4.37}{\ignorespaces Instantaneous kinetic energies as a function of time for intra and intermolecular modes of the pyrene dimer at a collision energy of 22.5 eV. Impact parameters $b$ are (a) 2, (b) 3, (c) 0, (d) 2.5, (e) 2, and (f) 2 \r A{}. In cases (a) and (b), dissociation takes place whereas in the other cases the dimer remains undissociated at the end of the MD simulation.}}{155}{figure.caption.81}}
\newlabel{E-time-abcdef}{{4.37}{155}{Instantaneous kinetic energies as a function of time for intra and intermolecular modes of the pyrene dimer at a collision energy of 22.5 eV. Impact parameters $b$ are (a) 2, (b) 3, (c) 0, (d) 2.5, (e) 2, and (f) 2 \AA{}. In cases (a) and (b), dissociation takes place whereas in the other cases the dimer remains undissociated at the end of the MD simulation}{figure.caption.81}{}}
\@writefile{toc}{\contentsline{subsection}{\numberline{4.4.5}Conclusions about CID of Py$_2^+$}{156}{subsection.4.4.5}}
