130 lines
12 KiB
TeX
130 lines
12 KiB
TeX
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\chapter{General Conclusions and Perspectives}
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\section{General Conclusions}
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As stated in the general introduction, the goal of this thesis was to go a step further into the theoretical description of properties
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of molecular clusters in the view to complement complex experimental measurements. It has focused on two different types of
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molecular clusters. I have first investigated water clusters containing an impurity, \textit{i.e.} an additional ion or molecule.
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First, I have studied ammonium and ammonia water clusters in order to thoroughly explore their PES to characterize in details
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low-energy isomers for various cluster sizes. I have then tackled the study of protonated uracil water clusters through two aspects:
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characterize low-energy isomers and model collision-induced dissociation experiments to probe dissociation mechanism in relation
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with recent experimental measurements by S. Zamith and J.-M. l'Hermite. Finally, I have addressed the study of the pyrene dimer cation
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to explore collision trajectories, dissociation mechanism, energy partition, mass spectra, and cross-section. These four studies have
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been organized in two chapters, each one gathering two studies involving similar computational tools. Below are gathered the main
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conclusions obtained along this thesis.
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\textbf{Structural and energetic properties.}
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The structures and binding energies of the lowest-energy isomers of (H$_2$O)$_{1-10}${NH$_4$}$^+$ and (H$_2$O)$_{1-10}$NH$_3$
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clusters were obtained through a synergistic use of SCC-DFTB and PTMD. The reported low energy isomers were further optimized at
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the MP2/Def2TZVP level of theory. In order to improve the description of sp$^3$ nitrogen, I have proposed a modified set of N-H
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parameters. Through comparing the configurations and binding energies of the lowest-energy isomers obtained at SCC-DFTB an
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MP2/Def2TZVP levels and by comparing the corresponding results to the literature, I demonstrated that this modified set of NH
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parameters is accurate enough to model both ammonia and ammonium water clusters. This work has thus allowed to report a number
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of new low-energy isomers for the studied species. Finally, PTMD simulation of (H$_2$O)$_{20}${NH$_4$}$^+$ was conducted and the
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heat capacity curve of this aggregate was obtained. It is in agreement with previous results reported in the literature.
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A similar exploration of the PES of (H$_2$O)$_{1-7, 11, 12}$UH$^+$ clusters was also performed. The reported low-energy isomers
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for these systems are all new and therefore constitute new data set to discuss and analyse the hydration properties of RNA nucleobases.
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They also complement available structures already reported for the non-protonated (H$_2$O)$_{n}$UH$^+$ species. These structures
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have also helped use to provide preliminary explanations to recent collision-induced measurements performed by S. Zamith and J.-M.
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l'Hermite. In particular, I show that when there are only 1 or 2 water molecules, the excess proton is chemically bond to the uracil.
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When there are 3 or 4 water molecules, the proton is still bound to the uracil but it has a tendency to be transferred toward an adjacent water
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molecule. From $n$ = 5 and above, clusters contain enough water molecules to allow for a net separation between uracil and the
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excess proton. The latter is often bound to a water molecule which is separated from uracil by at least one other water molecule.
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In the context of a direct dissociation mechanism, the nature of these isomers and the localisation of the proton as a function of
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cluster size, helps in analysing the nature of the fragments and the location of the proton on them.
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These two studies finally provide a new proof that SCC-DFTB, when combined to efficient enhanced sampling methods, is a powerful
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tool to explore complex potential energy surfaces of molecular aggregates. They have already given rise to two publications \cite{Simon2019,Braud2019}
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and one other publication is in preparation.
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\textbf{Collision-induced dissociation.}
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The SCC-DFTB simulations conducted to model collision-induced dissociation of (H$_2$O)$_{1-7,11,12}$UH$^+$ clusters
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and pyrene dimer cation were presented. These simulations have provided a wealth of important information to complement recent
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experimental CID measurements.
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For the collision simulations of (H$_2$O)$_{1-7,11,12}$UH$^+$ clusters at constant center of mass collision energy, the theoretical proportion
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of formed neutral \textit{vs.} protonated uracil containing clusters, total fragmentation cross sections as well as the mass spectra of charged
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fragments are consistent with the experimental data which highlights the accuracy of the simulations. They allow to probe which fragments
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are formed on the short time scale and rationalize the location of the excess proton on these fragments. Analyses of the time evolution of
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the fragments populations and theoretical and experimental branching ratios indicate that (H$_2$O)$_{1-7}$UH$^+$ engage a direct/shattering
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mechanism (dissociation on a very short time scale) after collision whereas for (H$_2$O)$_{11-12}$UH$^+$ a significant contribution of structural
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rearrangements occur. This suggests that a contribution of a statistical mechanism is more likely to occur for larger species such as
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(H$_2$O)$_{11-12}$UH$^+$. Such study is almost unique as the modelling of the dissociation of aqueous aggregates is very scarce in the literature.
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This study thus demonstrates that explicit molecular dynamics simulations at the SCC-DFTB level appear as a key tool to complement collision-induced
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dissociation experiments of hydrated molecular clusters. This study opens new possibility in the domain and I hope it will motivate new experimental
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measurements. One publication devoted to this study is in preparation.
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Dynamical simulations of collision between Py$_2^+$ and argon at different center of mass collision energies, between 2.5 and 30.0 eV, were conducted.
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Collision process, dissociation path, energy partition and distribution, and the efficiency of energy transfer were deeply explored form these simulations that
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have provided valuable reference for the CID study of larger PAH cation clusters. The simulated TOFMS of parent and dissociated products were obtained
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from the combination of MD simulations and PST to address the short and long timescales dissociation, respectively. The agreement between the simulated
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and measured mass spectra suggests that the main processes are captured by this approach. It appears that the TOFMS spectra mostly result from dimers
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dissociating on short timescales (during the MD simulation) and the remaining minor contribution results from dimers dissociating at longer timescales
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(the second step, during PST calculation). This indicates that Py$_2^+$ primarily engages a direct dissociation path after collision. The dynamical
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simulations show that the outcome of the trajectories either toward a dissociation or a redistribution
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of the transferred energy strongly depends on the initial collision conditions. Intramolecular fragmentation of the monomers occurs only for
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collision energies above 25 eV. At low collision energies, the dissociation cross section increases with collision energies whereas it remains almost
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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
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absorbed energy is shared between the dissociative modes and the heating of individual monomers. It shows that above 7.5~eV, increasing the
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collision energy mostly results in an increase of the intramolecular energy. Finally, the analysis of energy transfer efficiency within the dimer suggests
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that direct dissociation is too fast to allow significant thermalization of the system. On the other hand, when there is no dissociation, thermalization
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can occur with a faster equilibration between the intramolecular modes of the two units than with the intermolecular modes.
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This study has given rise to two publications.\cite{Zamith2020threshold,Zheng2021}
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%\break
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\section{Perspectives}
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This thesis has addressed various problems, on different molecular clusters, and has involved a range of theoretical methodologies that are not
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common way in computational chemistry. Various and very exciting perspectives can be therefore be considered in future studies:
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\begin{itemize}
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\item[$\bullet$]
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The newly proposed set of N-H parameters could be used to explore the low-energy structures and properties of a much larger range of systems
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of atmospheric interest. Indeed the structure of pure (NH$_3$)$_m$ clusters as well as (NH$_3$)$_m$H$^+$, (H$_2$O)$_n$(NH$_3$)$_m$, and
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(H$_2$O)$_n$(NH$_3$)$_m$H$^+$ clusters have been hardly addressed in the literature mainly due to the lake of properly defined force field for
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these systems. The transferability of SCC-DFTB would suggests that the potential I developed could also applied to these systems. This is an ongoing
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work that I have recently initiated. More interesting and also complicated is the study of water clusters containing a mix of nitrogen and sulphur
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compounds, for instance, ammonium and sulfate ion. These species, their conjugated basis and acid in combination with dimethylamine and
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water molecules represent the basis for nucleation of atmospheric particles. The chemical complexity induced by their mixing in force field
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simulations one the one hand, and the system size needed for proper molecular simulations on the other hand, suggest that SCC-DFTB
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has a major role to play in the theoretical description of these species.
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\item[$\bullet$] It would also be of great interest to pursue dynamical simulations of protonated uracil water clusters. Indeed, the work I have
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presented in this thesis still suffers from some lacks. First, it would be of high interest to look at the influence of collision energy, both lower or
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higher, on the dissociation mechanism as a function of the cluster size. By implementing a similar methodology as for the study of Py$_2^+$,
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it would be possible to extract important new information about energy partition and dissociation mechanism. Those can be of interest to other
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aqueous aggregates. In other important point is the inclusion of nuclear quantum effects in the simulations. Indeed, as the experiments are
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performed at very low temperatures, the quantum nature of the proton can play an important role that has been neglected in the present thesis.
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\item[$\bullet$] The dynamical simulations for collision-induced dissociation of pyrene dimer cation can be extended to PAHs water clusters
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to complement recent experiments on these systems.
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\item[$\bullet$] Finally, all the simulations of water clusters performed within this thesis were performed in the electronic ground state. To model
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what can occur in the atmosphere or interstellar medium, it would be of interest to investigate solvation effects on organic/inorganic molecules
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brought in an electronic excited state. To do so, the TD-DFTB method need to be implemented and tested as such simulation would involve a number
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of additional theoretical complexities. This would allow to calculate both absorption spectra from electronic ground state and emission spectra from
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electronic excited state of organic/inorganic molecule containing water clusters.
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\end{itemize}
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