jcuny/These_linjie_JC
1
0
Fork 0
Code Issues Pull Requests Projects Releases Wiki Activity

general conclusion

Browse Source
This commit is contained in:
jcuny 2021-06-15 14:13:20 +02:00
parent c1d2ca33cf
commit a0335a6aff
1 changed files with 29 additions and 8 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

37
thesis/5/general_conclusion.tex
View File

@ -5,18 +5,39 @@
\section{General Conclusions}
The goals of this thesis are: first, to characterize the structural, solvation, thermodynamic properties of the newly identified low-energy isomers of ammonium/ammonia water clusters, protonated uracil water clusters; second, to analyse the collision-induced dissociation of protonated uracil water clusters, and pyrene dimer cation. These systems selected are relevant to many scientific fields. The organic/inorganic molecules included water clusters can be viewed as an intermediate state of matter between the dilute gas phase and solution and the study of them helps to understand the solvation effect on gas-phase molecules and ions to be explored. PAHs are abundant in the interstellar medium, which plays a significant role in many fields such as astrophysics, environment science, combustion science, organic solar cell and so on.
As stated in the general introduction, the goal of this thesis was to go a step further into the theoretical description of properties
of molecular clusters in the view to complement complex experimental measurements. It has focused on two different types of
molecular clusters. First, we have focused on water clusters containing an impurity, \textit{i.e.} an additional ion or molecule. We
have first focused our studies on ammonium and ammonia water clusters in order to thoroughly explore their PES to characterize in details
low-energy isomers for various cluster sizes. We have then tackled the study of protonated uracil water clusters through two aspects:
characterize low-energy isomers and model collision-induced dissociation experiments to probe dissociation mechanism in relation
with recent experimental measurements by S. Zamith and J.-M. l'Hermite. Finally, we addressed the study of the pyrene dimer cation
to explore collision trajectories, dissociation mechanism, energy partition, mass spectra, and cross-section. These four studies have
been organized in two chapters, each one gathering two studies involving similar computational tools. Below are gathered the main
conclusions obtained along this thesis.
\textbf{Structural and energetic properties study}
The structures and binding energies of lowest-energy isomers of clusters
(H$_2$O)$_{n=1-10}${NH$_4$}$^+$,
(H$_2$O)$_{n=1-10}$NH$_3$ and (H$_2$O)$_{n=1-7, 11, 12}$UH$^+$ were obtained through a combination of global (combination of SCC-DFTB and PTMD) and local (MP2/Def2TZVP) optimization.
Through comparing the configurations and binding energies of lowest-energy isomers of clusters (H$_2$O)$_{n=1-10}${NH$_4$}$^+$ and (H$_2$O)$_{n=1-10}$NH$_3$ at SCC-DFTB and MP2/Def2TZVP levels and the corresponding results in the literature, we proposed the proper N-H integral parameter 0.14 and bond parameter 1.28 in SCC-DFTB. Both structures and binding energies of clusters (H$_2$O)$_{n=1-10}${NH$_4$}$^+$ and (H$_2$O)$_{n=1-10}$NH$_3$ obtained with SCC-DFTB potential are in line with the MP2/Def2TZVP results, which confirms the good ability of SCC-DFTB to describe complex potential energy landscapes of molecular species and represents a first step towards to the modelling of complex aggregates of atmospheric interest.
\textbf{Structural and energetic properties.}
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$_3$
clusters were obtained through a synergistic use of SCC-DFTB and PTMD. The reported low energy isomers were further optimized at
the MP2/Def2TZVP level of theory. In order to improve the description of sp$^3$ nitrogen, we have proposed a modified set of N-H
parameters. Through comparing the configurations and binding energies of the lowest-energy isomers obtained at SCC-DFTB an
MP2/Def2TZVP levels and by comparing the corresponding results to the literature, we demonstrate that this modified set of NH
parameters is accurate enough to model both ammonia and ammonium water clusters. This work has thus allowed to report a number
of new low-energy isomers for the studied species. Finally, PTMD simulation of (H$_2$O)$_{20}${NH$_4$}$^+$ was conducted and the
heat capacity curve of this aggregate was obtained. It is in agreement with previous results reported in the literature.
The calculated results of clusters (H$_2$O)$_{n=1-7, 11, 12}$UH$^+$ show that when there are 1 or 2 water molecules, the proton 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.
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.
Overall, SCC-DFTB super powerfull continue to demonsdtret blablabl
\textbf{Collision-induced dissociation study}
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.