Ce travail qui a été effectué au sein du groupe radiochimie de l'IPN Orsay, participe à l'enrichissement des connaissances destinées à la compréhension du comportement des radionucléides à travers l'environnement. Le comportement et l'évolution des radionucléides sont des phénomènes souvent complexes à caractériser expérimentalement qui dépendent des interactions aux interfaces eau / surface minérale, lesquelles peuvent être modélisées grâce à des méthodes théoriques. Lors de cette étude, nous avons choisi d'utiliser des méthodes de dynamique moléculaire (DM), lesquelles permettent de considérer explicitement les effets du solvant, de la température et d'étudier la dynamique de l'ion uranyle. Dans un premier temps, des méthodes de dynamique moléculaire Car-Parrinello basées sur la théorie de la fonctionnelle de la densité (DFT) ont permis de caractériser finement les structures d'équilibres de l'ion uranyle en solution et à l'interface eau/ face (001) de gibbsite. Dans le cas d'un pH faible, les complexes d'adsorption présents à l’interface eau/ face (001) de gibbsite ont été identifiés et comparées aux données expérimentales disponibles. Leurs énergies relatives et les énergies d'activations impliquées dans le processus de sorption ont également été déterminées. Dans un deuxième temps, des méthodes de dynamique moléculaire classique ont été employées afin de modéliser des systèmes de plus grande taille, donc plus réalistes, sur des échelles de temps plus longues. La comparaison des résultats DM Car-Parrinello / DM classique a montré qu’une dynamique classique utilisée avec les potentiels non polarisables de Guilbaud, CLAYFF et SPC/E, permet de modéliser le comportement de l’ion uranyle à l’interface eau/ face (001) de gibbsite. Les longs temps de simulation permettent de mettre en avant le caractère diffusif de l’ion uranyle à l’interface eau/ face (001) de la gibbsite. Enfin, L’effet d’une élévation de la température a été étudié. La rétention de l’ion uranyle diminue avec la température. / This work was performed in the radiochemistry group of the IPN Orsay, it participates in the advancement of knowledge for understanding the behavior of radionuclides through the environment. The behavior and the evolution of the radionuclides, which are often complex phenomena to characterize experimentally, depend on interactions at the interfaces water / mineral surface and can be modeled using theoretical methods. In this study, we chose to use dynamics molecular methods (DM), which can explicitly consider the effects of solvent, temperature and allow to study the dynamics of the uranyl ion. At first, methods of Car-Parrinello dynamics molecular, based on the density functional theory (DFT), were used to characterize the structures of the uranyl ion in solution and at the interface water / (001) face of gibbsite. For low pH condition, the adsorption complexes present at the interface water / (001) face of gibbsite were identified and compared with available experimental data. Their relative energies and activation energies involved in the sorption process were also determined. Secondly, the classical molecular dynamics methods were used to model larger systems, thus more realistic, on longer time scales. Comparing the results DM Car-Parrinello / classical DM showed a classical dynamics, which use the non-polarizable Guilbaud, CLAYFF and SPC/E potentials, can model the behavior of the uranyl ion at the interface water / face (001) of gibbsite. The long simulation times, allow to show particularly the diffusive character of the uranyl ion to the interface water / face (001) of gibbsite. Finally, the effect of temperature rise was studied. Retention of the uranyl ion decreases with temperature.

Biomolecular systems, in particular those involving proteins and their constituents, have been the focus of much research in the last century. The relationship between experiment, development of models and simulation has enabled vast improvements in our knowledge of subjects such as protein folding and the processes by which key biomolecules affect the human body. In particular, vital information can be obtained from understanding the building blocks of polypeptides and proteins involved in these processes. This work focuses on simulating two such building blocks; glutamate, the salt of the proteinogenic amino acid, glutamic acid, and glycine-proline-glutamate, or GPE, a related tripeptide. Both are important in neurotransmission processes in the brain. Glutamate is the most abundant neurotransmitter in the central nervous system and GPE is an important neuroprotective agent. This work aims to elucidate the key structural properties of aqueous solutions of glutamate and GPE, focusing on the solute-solute as well as the solute-solvent interactions. Both systems were considered with classical empirical potentials using the CHARMM22 force-fi eld. The glutamate system has also been studied using Car-Parrinello Molecular Dynamics and classical parallel tempering. In both the aqueous glutamate and GPE systems the molecules formed a large proportion of bifurcated bonding motifs with both carboxyl groups, but not with the amin (N-terminal) of the molecules. Bifurcated bonds form between solute molecules as well as in the solute-solvent interactions. The structure of the glutamate solution was found to be dependent on the initial con figuration and thus the parallel tempering simulations enabled better sampling of the conformational landscape. In addition, in the glutamate system single water molecules form a stable structure by bonding to both the amine (N-terminal) and C -carboxyl within the same glutamate molecule.

Ce travail de thèse est consacré à la rationalisation de verres de tellure, au fort potentiel applicatif. Les résultats ont été obtenus en utilisant la dynamique moléculaire ab initio et le calcul de paramètres RMN sur différents noyaux. Pour valider nos modèles de verres, les résultats théoriques sont comparés aux données expérimentales disponibles, comme les facteurs de structure neutroniques ou des rayons X, ainsi que les spectres RMN du solide. La première partie décrit les méthodes théoriques employées, tandis que les deux chapitres qui suivent se concentrent sur l’utilisation du formalisme GIPAW pour le calcul des paramètres RMN du 73Ge et du 125Te sur des systèmes cristallins et/ou moléculaires. Dans le cas du 125Te, nous avons calibré une fonction linéaire qui relie l’écrantage isotrope calculé au déplacement chimique isotrope. Pour le 73Ge, nous avons pris en compte des effets thermiques pour obtenir des paramètres RMN moyens, en considérant plusieurs configurations extraites d’une dynamique moléculaire à 300 K. La partie suivante est une étude structurale du verre GeTe4, où l’impact de la taille des cellules modélisées et de la fonctionnelle utilisée, ont été analysés. Une confrontation des facteurs de structure théoriques avec ceux obtenus expérimentalement, permet la description de la première sphère de coordination des tellures et des germaniums. La comparaison des spectres RMN expérimentaux et théoriques du 125Te ne vient pas infirmer ces résultats. Les cinquième et sixième chapitres portent sur l’étude des systèmes ternaires Ge-Te-Se et Ge-Ga-Te. La validation de nos modèles par la RMN des 77Se, 125Te, 69Ga et 71Ga, et par les facteurs de structure, nous a permis de caractériser le rôle du sélénium ou du gallium sur la structuration de ces verres. Le dernier chapitre est consacré à l’étude de verre de chalcohalogénures du système binaire Te-Cl. La RMN du solide, les méthodes de diffractions de neutrons et des rayons X, combinées à des calculs ab initio ont permis de faire évoluer les précédents modèles structuraux proposés. / This thesis is devoted to the rationalisation of telluride glasses, with a high applicative potential. Results have been obtained using ab initio molecular dynamics and NMR parameters calculations on different nuclei. In order to validate our glasses models, theoretical results have been compared to available experimental data, as neutron or X-rays scattering structure factors or NMR spectra. The first part describes theoretical methods employed, whereas the two next chapters focus on the use of GIPAW formalism to obtain NMR parameters of 73Ge and 125Te, on crystalline and/or molecular systems. In the case of 125Te, we calibrated a linear function that relates calculated isotropic shielding and isotropic chemical shift. For the 73Ge, we took into account thermal effect to get averaged NMR parameters, by considering several configurations taken from a 300 K molecular dynamics. The next part is a structural study of amorphous GeTe4, where the impact of the size of simulated cells and the functional used, has been analysed. A comparison of theoretical and experimental structure factors, allowed a description of germanium and tellurium first coordination sphere. The comparison of experimental and theoretical 125Te NMR spectra did not disprove these results. Fifth and sixth parts deal with glasses of ternary systems Ge-Se-Te and Ge-Ga-Te. The validation of our models with 77Se, 125Te, 69Ga and 71Ga NMR and structure factors, permitted us to characterize the role of selenium or gallium on glasses structures. Last chapter is dedicated to chalcohalide glasses from the binary system Te-Cl. Solid state NMR, X-rays and neutron diffraction, combined with ab initio calculations, let us make changes in previews suggested structural models.

Ce travail qui a été effectué au sein du groupe radiochimie de l'IPN Orsay, participe à l'enrichissement des connaissances destinées à la compréhension du comportement des radionucléides à travers l'environnement. Le comportement et l'évolution des radionucléides sont des phénomènes souvent complexes à caractériser expérimentalement qui dépendent des interactions aux interfaces eau / surface minérale, lesquelles peuvent être modélisées grâce à des méthodes théoriques. Lors de cette étude, nous avons choisi d'utiliser des méthodes de dynamique moléculaire (DM), lesquelles permettent de considérer explicitement les effets du solvant, de la température et d'étudier la dynamique de l'ion uranyle. Dans un premier temps, des méthodes de dynamique moléculaire Car-Parrinello basées sur la théorie de la fonctionnelle de la densité (DFT) ont permis de caractériser finement les structures d'équilibres de l'ion uranyle en solution et à l'interface eau/ face (001) de gibbsite. Dans le cas d'un pH faible, les complexes d'adsorption présents à l'interface eau/ face (001) de gibbsite ont été identifiés et comparées aux données expérimentales disponibles. Leurs énergies relatives et les énergies d'activations impliquées dans le processus de sorption ont également été déterminées. Dans un deuxième temps, des méthodes de dynamique moléculaire classique ont été employées afin de modéliser des systèmes de plus grande taille, donc plus réalistes, sur des échelles de temps plus longues. La comparaison des résultats DM Car-Parrinello / DM classique a montré qu'une dynamique classique utilisée avec les potentiels non polarisables de Guilbaud, CLAYFF et SPC/E, permet de modéliser le comportement de l'ion uranyle à l'interface eau/ face (001) de gibbsite. Les longs temps de simulation permettent de mettre en avant le caractère diffusif de l'ion uranyle à l'interface eau/ face (001) de la gibbsite. Enfin, L'effet d'une élévation de la température a été étudié. La rétention de l'ion uranyle diminue avec la température.

Water is known to take on highly organized structures to influence the reactivity of chemical and biological systems; despite this, water is often only implicitly or approximately included in theoretical studies of biochemical systems, if not omitted entirely. Many of the current models for biological processes predate an understanding of the complex behaviour of water, yet these models have not been updated. This thesis presents an exploration of how a better of water might affect the models used to describe neurotransmission. Two classes of systems are investigated, representing the two main categories of neurotransmission: that which occurs along the length of a neuron, and that which occurs between one neuron and another cell. Lipid bilayers are studied using molecular dynamics, and neurotransmitters are studied using Car-Parrinello molecular dynamics. The results indicate that water structures may play a more specific role in neurotransmission than was previously thought.

Abstract This thesis focuses on the molecular-level chemistry of the solvation of aluminum salts. Fundamental aspects such as, structural characteristics of the aluminum molecules, hydrolysis, acidity, solvation structure, effect of counter ions, and chemical stability are discussed herein. Static computations augmented with the conductor-like screening model (COSMO) were used to investigate hundreds of planar and cyclic configurations of dimeric, trimeric, tetrameric, and pentameric aluminum complexes. Car–Parrinello molecular dynamics (CPMD) calculations were used to expand investigations to aqueous environments. This thesis consists of four articles and one additional article. The first paper focuses on the structural analysis of the hydrolysis products of AlCl3 · 6H2O. Dimeric, trimeric, and tetrameric aluminum (chloro)hydroxides were investigated in both gas and liquid phase. The liquid environment was modeled by using COSMO. The second and the additional paper concentrate on the chemistry of aluminum sulfate complexes. The second article focuses on identifying hydrolysis products of AlCl3 · 6H2O in the presence of sulfate (H2SO4). The additional paper focuses on the structural characteristics of the hydrolysis products of Al2 (SO4)3 · 18H2O. Structural information was deduced from the ESI MS results with the aid of computational methods. Detected cationic structures closely resembled the aluminum chlorohydrate analogues introduced in the first paper. The third and fourth articles are devoted to the hydrolysis, stability, and dynamics of dimeric and pentameric aluminum (chloro)hydroxides in aquatic environments. During the CPMD simulations, several spontaneous associative hydration reactions were detected in the primary hydration shell of the complexes. Dimeric aluminum chlorohydrates were detected to be stable in liquid conditions, whereas the pentameric aluminum complexes experienced significant topological changes during the simulations. Constrained simulations were used to reveal the role of chloride ions in the hydrolysis processes of dimeric complexes. The effect of the empirical van der Waals corrections to the dynamics of the simulations was also tested for the pentameric system. The results of this thesis showed unequivocally that computational chemistry provides effective tools for structural analysis of inorganic complexes such as, aluminum chlorohydrates and sulfates in both gas and liquid phase. In addition, calculations provided answers to the anomalies detected in the experiments. Hence, theoretical methods are highly recommended to be used alongside with conventional experimental methods in the interpretation of the aluminum species in aqueous solutions and to widen the overall chemical perspective of the hydrolysis of aluminum salts.

No description available.

<p>The aqueous solvation of metal ions is one of the long-standing and complex problems in chemistry, with implications for and applications in a broad range of biochemical and electrochemical systems, where water is the all-pervasive medium.</p><p>This thesis describes computer simulations of Al³⁺(<i>aq</i>), Fe²⁺(<i>aq</i>), Fe³⁺(<i>aq</i>) and Cu²⁺(<i>aq</i>). Various aspects of the solvation of these polyvalent metal ions in water are addressed, at different levels of theory, using Car-Parrinello molecular dynamics, classical molecular dynamics and quantum-mechanical cluster calculations. Polyvalent metal ions are particularly interesting because of their large influence on the solvent structure, dynamics and thermodynamics, as well as on the properties of the individual solvent molecules. Polyvalent metal ions in aqueous solution also constitute a challenging subject for computer simulations since a sophisticated interaction model is needed to incorporate the large many-body effects. </p><p>All the ion-water coordination figures in this thesis are octahedral, except in the Cu²⁺(<i>aq</i>) solution, where the ion is penta-coordinated with four equatorial neighbours in a plane and one axial neighbour located ~0.45 Å further out from the ion. The equatorial ion-water bonds have covalent character, while the axial water molecule is only electrostatically bound. For all the ions, the OD stretching frequencies of the first-shell water molecules are much more downshifted than in liquid water. In the case of Cu²⁺(<i>aq</i>), however, only the OD frequencies of the equatorial water molecules are downshifted with respect to bulk water whereas the OD frequencies of the axial water molecule are slightly upshifted. </p><p>Various limitations of the Car-Parrinello molecular dynamics simulations have been explored and compared, such as finite system-size effects and shortcomings in the electronic structure calculations. The Car-Parrinello simulations are found to give reasonable descriptions of the polyvalent metal ions in aqueous solution.</p>

The aqueous solvation of metal ions is one of the long-standing and complex problems in chemistry, with implications for and applications in a broad range of biochemical and electrochemical systems, where water is the all-pervasive medium. This thesis describes computer simulations of Al3+(aq), Fe2+(aq), Fe3+(aq) and Cu2+(aq). Various aspects of the solvation of these polyvalent metal ions in water are addressed, at different levels of theory, using Car-Parrinello molecular dynamics, classical molecular dynamics and quantum-mechanical cluster calculations. Polyvalent metal ions are particularly interesting because of their large influence on the solvent structure, dynamics and thermodynamics, as well as on the properties of the individual solvent molecules. Polyvalent metal ions in aqueous solution also constitute a challenging subject for computer simulations since a sophisticated interaction model is needed to incorporate the large many-body effects. All the ion-water coordination figures in this thesis are octahedral, except in the Cu2+(aq) solution, where the ion is penta-coordinated with four equatorial neighbours in a plane and one axial neighbour located ~0.45 Å further out from the ion. The equatorial ion-water bonds have covalent character, while the axial water molecule is only electrostatically bound. For all the ions, the OD stretching frequencies of the first-shell water molecules are much more downshifted than in liquid water. In the case of Cu2+(aq), however, only the OD frequencies of the equatorial water molecules are downshifted with respect to bulk water whereas the OD frequencies of the axial water molecule are slightly upshifted. Various limitations of the Car-Parrinello molecular dynamics simulations have been explored and compared, such as finite system-size effects and shortcomings in the electronic structure calculations. The Car-Parrinello simulations are found to give reasonable descriptions of the polyvalent metal ions in aqueous solution.

Ce mémoire traite de la dynamique des molécules envisageant une description classique pour les noyaux et quantique pour la structure électronique. Les approches "Born-Oppenheimer" et "Car-Parrinello" sont discutées et un nouvel algorithme est présenté puis validé de par la bonne conservation de l'énergie totale au cours du temps. Il est ensuiote étendu pour simuler l'ensemble canonique et appliqué à la détermination de caractéristiques spectroscopiques de systèmes moléculaires. L'estimation de quantités, telle l'énergie libre, est considérée à l'aide de la théorie de l'ensemble "blue-moon". Cette méthode est appliquée à deux réactions chimiques, mettant en évidence la mise en défaut de l'approche traditionnelle basée sur l'approximation harmonique. Enfin, l'estimation de l'énergie de point zéro au delà de cette approximation est abordée.