A similar exploration of the PES of (H$_2$O)$_{1-7, 11, 12}$UH$^+$ clusters was also performed. The reported low-energy isomers
for these systems are all new and therefore constitute new data set to discuss and analyse the hydration properties of nucleobases found
in RNA. The complement available structures already reported for the non-protonated (H$_2$O)$_{n}$UH$^+$ species. These structures
have also helped use to understand recent collision-induced measurements performed by S. Zamith and J.-M. l'Hermite.
The theoretical results show that
when there are 1 or 2 water molecules, the proton located is on the uracil. When there are 3 or 4 water molecules, the proton is still on the uracil but it has a tendency to be transferred to the water molecule which is directly bounded to uracil \textit{i.e.}, forming a strongly bound U–H$_2$OH$^+$ complex.
From n = 5 and above, clusters contain enough water molecules to allow for a net separation between uracil and the excess proton: The latter is often bound to a water molecule which is separated from uracil by at least one other water molecule. The localization of the excess proton in different clusters (H$_2$O)$_{n=1-7, 11, 12}$UH$^+$ helps to understand the evaporation channels of clusters after collision.
The QM/MM dynamical simulations using SCC-DFTB method for collision-induced dissociation of low-energy protonated uracil water clusters (H$_2$O)$_{1-7,11,12}$UH$^+$ and pyrene dimer cation were performed, which provides a wealth of important information for recent experimental CID measurements.
For the explicit dynamical collision simulations of (H$_2$O)$_{1-7,11,12}$UH$^+$ at constant center of mass collision energy, the theoretical proportion of formed neutral \textit{vs.} protonated uracil containing clusters, total fragmentation cross sections as well as the mass spectra of charged fragments are consistent with the experimental data which highlights the accuracy of the simulations. They allow to probe which fragments are formed on the short time scale and rationalize the location of the excess proton on these fragments. The results show that this latter property is highly influenced by the nature of the aggregate undergoing the collision. Analyses of the time evolution of the fragments populations and theoretical and experimental branching ratios of (H$_2$O)$_{1-7, 11, 12}$UH$^+$ indicate that (H$_2$O)$_{1-7}$UH$^+$ engage a direct/shattering mechanism (dissociation on a very short time scale) after collision whereas for (H$_2$O)$_{11-12}$UH$^+$ a significant contribution of structural rearrangements occur. This suggests that a contribution of a statistical mechanism is more likely to occur for larger species such as (H$_2$O)$_{11-12}$UH$^+$.
This study demonstrates that explicit molecular dynamics simulations appear as a useful tool to complement collision-induced dissociation experiments of hydrated molecular clusters.
For the dynamical simulations of collision between Py$_2^+$ and argon at different center of mass collision energies between 2.5 and 30 eV, the collision process, dissociation path, energy partition and distribution, and the efficiency of energy transfer were deeply explored for the Py$_2^+$ system, which can provide valuable reference for the CID study of larger PAH cation clusters.
The simulated TOFMS of parent and dissociated products are obtained from the combination of MD simulations and PST to address the short and long timescales dissociation, respectively. The agreement between the simulated and measured mass spectra suggests that the main processes are captured by this approach. It appears that the TOFMS spectra mostly result from dimers dissociating on short timescales (during the MD simulation) and the remaining minor contribution is from dimers dissociating at longer timescales (the second step, during PST calculation). This indicates that Py$_2^+$ primarily engages a direct dissociation path after collision. The dynamical simulations allow to visualise the dissociation processes. It shows that the evolution of the trajectories either toward a dissociation or a redistribution of the transferred energy strongly depends on the initial collision conditions. Intramolecular fragmentation of the monomers occurred only for collision energies above 25 eV. At low collision energies, the dissociation cross section increases with collision energies whereas it remains almost constant for collision energies greater than 10-15~eV.
The analysis of the kinetic energy partition as a function of the collision energy shows the absorbed energy is shared between the dissociative modes and the heating of individual monomers. It shows that above 7.5~eV, increasing the collision energy mostly results in an increase of the intramolecular energy. Finally, the analysis of energy transfer efficiency within the dimer suggests that direct dissociation is too fast to allow significant thermalization of the system. On the other hand, when there is no dissociation, thermalization can occur with a faster equilibration between the intramolecular modes of the two units than with the intermolecular modes.
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\section{Perspectives}
Based on the work of this thesis, several perspectives can be implemented in the future:
\begin{itemize}
\item[$\bullet$]
The proposed N-H integral parameter and bond parameter in SCC-DFTB can be used to explore the low-energy isomers and binding energies of clusters (NH$_3$)$_m$, (NH$_3$)$_m$H$^+$, (H$_2$O)$_n$(NH$_3$)$_m$, (H$_2$O)$_n$(NH$_3$)$_m$H$^+$ and mixed sulfate ammonia/ammonium water clusters and compare their results with the ones at MP2 level to see if these proposed parameters are proper for the calculation of these clusters.
\item[$\bullet$] It would be of great interest to pursue dynamical simulations of protonated uracil water clusters by looking at the influence of collision energy, both lower or higher, on the dissociation mechanism as a function of the cluster size. Furthermore, inclusion of nuclear quantum effects in the simulations could also help to increase the accuracy of the model and improve the comparison with the experiments.
\item[$\bullet$] The dynamical simulations for collision-induced dissociation of pyrene dimer cation have been verified successfully. It is possible to do the dynamical simulations for collision-induced dissociation of PAHs water clusters to compare with the experimental results and to explain and complete the experiments.
\item[$\bullet$] All the simulations of water clusters in this thesis were performed in the electronic ground state, it would be interesting to investigate solvation effect on organic/inorganic molecule in both electronic ground and excited states using TD-DFTB method. It would be wonderful to calculate both absorption spectra from electronic ground state and emission spectra from electronic excited state of organic/inorganic molecule containing water clusters.
\end{itemize}
%The work of this thesis is focused on two aspects. First, to obtain the low-lying energy isomers of ammonium/ammonia water clusters and protonated uracil water clusters through exploring the potential energy surfaces using the combination of global and local optimizations. Then the structural, solvation, thermodynamics properties of the low-lying energy isomers were characterized. Second, the molecular dynamics simulations of collision-induced dissociation of protonated uracil water clusters and pyrene dimer cation were carried out to explore the collision trajectories, dissociation mechanism, energy partition, mass spectra, cross-section and do on.
