Nous nous intéressons à l'utilisation de la technologie manycore des cartes graphiques dans le cadre de la Chimie théorique. Nous soutenons la nécessité pour ce domaine d'être capable de tirer profit de cette technologie. Nous montrons la faisabilité et les limites de l'utilisation de cartes graphiques en Chimie théorique par le portage sur GPU de deux méthodes de calcul en modélisation moléculaire. Ces deux méthodes n’intégrerons ultérieurement au programme de docking moléculaire AlgoGen. L'accélération et la performance énergétique ont été examinées au cours de ce travail.Le premier programme NCIplot implémente la méthodologie NCI qui permet de détecter et de caractériser les interactions non-covalentes dans un système chimique. L'approche NCI se révèle être idéale pour l'utilisation de cartes graphiques comme notre analyse et nos résultats le montrent. Le meilleur portage que nous avons obtenu, a permis de constater des facteurs d'accélération allant jusqu'à 100 fois plus vite par rapport au programme NCIplot. Nous diffusons actuellement librement notre portage GPU : cuNCI.Le second travail de portage sur GPU se base sur GAMESS qui est un logiciel complexe de portée internationale implémentant de nombreuses méthodes quantiques. Nous nous sommes intéressés à la méthode combinée DFTB/FMO/PCM pour le calcul quantique de l'énergie potentielle d'un complexe. Nous sommes intervenus dans la partie du programme calculant l'effet du solvant. Ce cas s'avère moins favorable à l'utilisation de cartes graphiques, cependant nous avons su obtenir une accélération. / In this research work we are interested in the use of the manycore technology of graphics cards in the framework of approaches coming from the field of Theoretical Chemistry. We support the need for Theoretical Chemistry to be able to take advantage of the use of graphics cards. We show the feasibility as well as the limits of the use of graphics cards in the framework of the theoretical chemistry through two usage of GPU on different approaches.We first base our research work on the GPU implementation of the NCIplot program. The NCIplot program has been distributed since 2011 by Julia CONTRERAS-GARCIA implementing the NCI methodology published in 2010. The NCI approach is proving to be an ideal candidate for the use of graphics cards as demonstrated by our analysis of the NCIplot program, as well as the performance achieved by our GPU implementations. Our best implementation (VHY) shows an acceleration factors up to 100 times faster than the NCIplot program. We are currently freely distributing this implementation in the cuNCI program.The second GPU accelerated work is based on the software GAMESS-US, a free competitor of GAUSSIAN. GAMESS is an international software that implements many quantum methods. We were interested in the simultaneous use of DTFB, FMO and PCM methods. The frame is less favorable to the use of graphics cards however we have been able to accelerate the part carried by two K20X graphics cards.

The main goal of this work is to search for new stable porous carbon-based materials, which have the ability to accommodate and store hydrogen gas. Theoretical and experimental studies suggest a close relation between the nano-scale structure of the material and its storage capacity. In order to design materials with a high storage capacity, a compromise between the size and the shape of the nanopores must be considered. Therefore, a number of different carbon-based materials have been investigated: carbon foams, dislocated graphite, graphite intercalated by C60 molecules, and metal-organic frameworks. The structures of interest include experimentally well-known as well as hypothetical systems. The studies were focused on the determination of important properties and special features, which may result in high storage capacities. Although the variety of possible pure carbon structures and metal-organic frameworks is almost infinite, the materials described in this work possess the main structural characteristics, which are important for gas storage.

The main goal of this work is to search for new stable porous carbon-based materials, which have the ability to accommodate and store hydrogen gas. Theoretical and experimental studies suggest a close relation between the nano-scale structure of the material and its storage capacity. In order to design materials with a high storage capacity, a compromise between the size and the shape of the nanopores must be considered. Therefore, a number of different carbon-based materials have been investigated: carbon foams, dislocated graphite, graphite intercalated by C60 molecules, and metal-organic frameworks. The structures of interest include experimentally well-known as well as hypothetical systems. The studies were focused on the determination of important properties and special features, which may result in high storage capacities. Although the variety of possible pure carbon structures and metal-organic frameworks is almost infinite, the materials described in this work possess the main structural characteristics, which are important for gas storage.

This thesis discusses the chemistry and physics of Cu and H2O on ZnO surfaces, based primarily on results from quantum chemical calculations. The underlying context is heterogeneous catalysis, where Cu/ZnO-mixtures are used in the industrial synthesis of methanol and in the water gas shift reaction. Electron transfer between small Cu clusters and ZnO is central to this thesis, as are the design and use of models that can describe realistic and very large-scale ZnO surface structures while still retaining the electronic nature of the system. Method and model enhancements as well as tests and validations constitute a large part of this thesis. The thesis demonstrates that the charges of small Cu clusters, adsorbed on the non-polar ZnO(10-10) surface, depend on whether the Cu clusters contain an even or odd number of atoms, and whether water is present (water can induce electron transfer from Cu to ZnO). On the polar Zn-terminated ZnO(0001) surface, Cu becomes negatively charged, which causes it to attract positively charged subsurface defects and to wet the ZnO(0001) surface at elevated temperatures. When a Cu cluster on a ZnO surface becomes positively charged, this happens because it donates an electron to the ZnO conduction band. Hence, it is necessary to use a method which describes the ZnO band gap correctly, and we show that a hybrid density functional, which includes a fraction of Hartree-Fock exchange, fulfills this requirement. When the ZnO conduction band becomes populated by electrons from Cu, band-filling occurs, which affects the adsorption energy. The band-filling correction is presented as a means to extrapolate the calculated adsorption energy under periodic boundary conditions to the zero coverage (isolated adsorbate, infinite supercell) limit. A part of this thesis concerns the parameterization of the computationally very efficient SCC-DFTB method (density functional based tight binding with self-consistent charges), in a multi-scale modeling approach. Our findings suggest that the SCC-DFTB method satisfactorily describes the interaction between ZnO surfaces and water, as well as the stabilities of different surface reconstructions (such as triangularly and hexagonally shaped pits) at the polar ZnO(0001) and ZnO(000-1) surfaces.

The nature and role of defects is of primary importance to understand the physical properties of C and BN single walled nanotubes. Transmission electron microscopy (TEM) is a well known powerful tool to study the structure of defects in materials. However, in the case of SWNTs, the electron irradiation of the TEM may knock out atoms. This effect may alter the native structure of the tube, and has also been proposed as a potential tool for nanoengineering of nanotubular structures. Here we develop a theoretical description of the irradiation mechanism. First, the anisotropy of the emission energy threshold is obtained via density functional based calculations. Then, we numerically derive the total Mott cross section for different emission sites of carbon and boron nitride nanotubes with different chiralities. Using a dedicated STEM microscope with experimental conditions optimised on the basis of derived cross-sections, we are able to control the generation of defects in nanotubular systems. Either point or line defects can be obtained with a spatial resolution of a few nanometers. The structure, energetics and electronics of point and line defects in BN systems have been investigated. Stability of mono- and di- vacancy defects in hexagonal boron nitride layers is investigated, and their activation energies and reaction paths for diffusion have been derived using the nudged elastic band method (NEB) combined with density functional based techniques. We demonstrate that the appearance of extended linear defects under electron irradiation is more favorable than a random distribution of point defects and this is due to the existence of preferential sites for atom emission in the presence of pre-existing defects, rather than thermal vacancy nucleation and migration.

Les agrégats de molécules d'eau constituent une classe d'espèces chimiques importante du fait de leur rôle central dans de nombreux processus physico-chimiques et biologiques terrestres, en particulier, les processus atmosphériques. Leurs propriétés physiques et chimiques sont particulièrement sensibles aux effets de taille et aux effets de température, ce qui les rend particulièrement difficile à caractériser expérimentalement. Ainsi, mes travaux de thèse ont porté sur l'étude théorique des propriétés structurales, dynamiques et thermodynamiques ainsi que sur la réactivité de divers agrégats de molécules d'eau avec pour objectif de mettre en place des outils de modélisation adaptés, permettant une description plus fine de ces systèmes. Pour cela, nous avons utilisé des approches de dynamique moléculaire de type "parallel-tempering" qui ont été couplées avec des calculs d'énergie et de gradient réalisés par la méthode Self-Consistent-Charge Density-Functional based Tight-Binding (SCC-DFTB). Trois grands volets ont été abordés au cours de ces travaux. Dans la première partie, l'analyse détaillée des structures des agrégats d'eau (H2O)nSO24- et (H2O)nH2SO4 avec n=1-20 est présentée. Nous avons mis en évidence l'influence de la nature de l'impureté soufrée sur le réseau de liaisons hydrogène de ces agrégats. La deuxième partie de cette thèse porte sur l'étude de la transition de phase "solide-liquide" dans divers agrégats de molécules d'eau. En plus des agrégats soufrés évoqués ci-dessus, nous avons également étudié des agrégats d'eau protonés contenant de 19 à 23 molécules d'eau. Pour mieux comprendre le mécanisme de transition de phase, nous avons considéré divers changements structuraux associés à la transition tels que l'évolution des distributions d'angles intermoléculaires et l'évolution du nombre de cycles de molécules dans l'agrégat. Nous avons également caractérisé la transition de phase au travers d'indicateurs dynamiques tels que la fréquence de transfert du proton en excès. La dernière partie de cette thèse est consacrée à l'étude de l'influence de petits agrégats d'eau (allant de 1 à 10 molécules d'eau) sur la réaction de recombinaison entre l'atome H et la molécule CO. Cette réaction est la première étape de formation des molécules organiques oxygénées simples dans le milieu interstellaire. Elle présente donc un intérêt particulier. Grâce à l'analyse de dynamiques collisionnelles entre H et CO ainsi qu'au calcul de sections efficaces de réaction, nous avons montré que la présence des molécules d'eau joue un rôle important dans le processus de formation du radical HCO. / Water clusters constitute an important class of chemical species due to their central role in many physico-chemical and biological processes, in particular, atmospheric processes. Their physical and chemical properties are particularly sensitive to size and finite-temperature effects, which makes them particularly difficult to characterize experimentally. This thesis focused on the theoretical investigation of the structural, dynamical and thermodynamical properties as well as on the reactivity of various water clusters with the aim to implement appropriate modeling tools to enable a more detailed description of these systems. To do so, we used the paralleltempering molecular dynamics approach that was coupled with calculations of energies and gradients carried out by the Self-Consistent-Charge Density-Functional based Tight-Binding (SCC-DFTB) method.Three main areas were addressed during the work. In the first part, a detailed analysis of the structure of water clusters (H2O)nSO24- and (H2O)nH2SO4 with n=1-20 is performed. This study highlights the influence of the nature of the sulfur impurity on the hydrogen bond network of these species.The second part of this thesis focuses on the study of the "solid-liquid" phase transition in various water clusters. In addition to the sulfur-containing water clusters mentioned above, we also investigated protonated water clusters containing from 19 to 23 water molecules. To better understand the phase transition mechanism, we considered various structural changes associated with the transition, such as the evolution of the distributions of intermolecular angles and the evolution of the number of molecular rings in the cluster. We also characterized the phase transition through dynamical indicators such as the crossover frequency of the excess proton. The last part of this thesis is devoted to the study of the influence of small water clusters (from 1 to 10 water molecules) on the recombination reaction between the H atom and the CO molecule. This reaction is the first step in the formation of simple oxygenated organic molecules in the interstellar medium. It is therefore of particular interest. Due to the analysis of collisional dynamics between H and CO and the calculation of effective reaction cross sections we showed that the presence of water molecules plays an important role in the HCO radical formation.

Kovalente organische Frameworks (COFs) haben in den letzten Jahren aufgrund ihrer potenziellen Anwendungen in verschiedenen Bereichen großes Interesse hervorgerufen. Obwohl die Eigenschaften der synthetisierten Materialien empfindlich von den Eigenschaften der entsprechenden organischen Liganden abhängen, ist der Beitrag der einzelnen Bausteine zu den Kristalleigenschaften nicht eindeutig definiert. In dieser Arbeit werden die elektronischen und mechanischen Eigenschaften von einschichtigen zweidimensionalen (2D) COFs untersucht, wobei der Schwerpunkt auf den molekularen Bausteinen liegt. Zunächst wurde die Kristallstruktur als Hooke'sches Federnetzwerk angenommen, und analytische Formeln für 2D-COFs mit quadratischer und hexagonaler Gittertopologie wurden abgeleitet, wobei eine Vorhersage des Kompressionsmoduls aus der Berechnung der Monomer-Federkonstante angestrebt wurde. Alle geschätzten Werte für Moleküle und periodische Strukturen wurden mit der DFTB-Methode (Density Functional based Tight-Binding) berechnet. Benchmarking-Berechnungen mit der Dichtefunktionaltheorie (DFT) wurden eingesetzt, um die Anwendbarkeit der semiempirischen Methode zu überprüfen. In einem zweiten Schritt wurden Methoden vorgeschlagen, um die elektronische Bandstruktur und die elektronischen Eigenschaften von COFs zu verändern, wie z.B. die Änderung von Bindungen oder Linkern, Seitengruppen oder Funktionalisierung und die Erhöhung der Massendichte. Die verschiedenen Methoden ergeben unterschiedliche Eigenschaften der resultierenden Strukturen. Darüber hinaus wurden mehrere Polymere durch periodische Fortsetzung in einer oder zwei Dimensionen auf der Grundlage derselben molekularen Bausteine modelliert. Es wurde ein zweistufiges System auf der Grundlage des Tight-Binding-Ansatzes vorgeschlagen, und dessen Parameter wurden mit Hilfe der Bandoberkante des Valenzbandes und der Bundunterkante des Leitungsbandes abgeschätzt. Ein maschinelles Lernverfahren wurde eingesetzt, um die elektronische Bandlücke auf der Grundlage der gleichen Kernmonomere vorherzusagen. Interessanterweise erbt das 2D-COF die elektronische Lücke von der monomeren Einheit mit der niedrigeren elektronischen Energiedifferenz zwischen besetztem und unbesetztem Band. Schließlich wurde die Protonentautomerisierung in zwei sehr häufig verwendeten Kernmonomeren für 2D-COFs, Porphyrin und Phthalocyanin, und ihren Derivaten untersucht. Die Freie-Energie-Oberfläche wurde mit Quanten-Molekulardynamik-Simulationen durch Kombination von DFTB und Metadynamik berechnet. Durch die Analyse der Potenzialporträts werden die strukturellen Symmetrien des Moleküls in Protonentransferreaktionen widergespiegelt. Ich erwarte, dass die Ergebnisse dieser Arbeit Einsichten für die Synthese von 2D COFs geben werden, welche auf optimierte elektronische Eigenschaften mit hoher struktureller Stabilität abzielt.:ABSTRACT ZUSAMMENFASSUNG 1. INTRODUCTION Motivation Nomenclatures Experimental characterization and computational studies Objectives and outline 2. THEORETICAL AND COMPUTATIONAL BACKGROUND Many-body system Density Functional Theory (DFT) Kohn-Sham auxilary approach and the computational application of DFT Exchange-correlation functional Hybrid functionals Basis-set Pseudo-potentials Tight-binding model Density Functional based Tight-binding model (DFTB) Slater-Koster approach Slater-Koster sets in DFTB Molecular Dynamics and Metadynamics Classical Molecular Dynamics (MD) Quantum Molecular Dynamics (QMD) Metadynamics(MTD) 3. PREDICTING THE BULK MODULUS Conceptualization Equivalent spring constant Two dimensional bulk modulus Computational details COFs with square lattice type Models Molecular Spring constant Single layer 2D COFs COFs with hexagonal lattice type Models Single layer 2D COFs Synopsis 4. ENGINEERING THE ELECTRONIC PROPERTIES Computational details COFs with square lattice type Models Benchmarking of different methods π -conjugated COFs COFs with hexagonal topology Models π -conjugated COFs Synopsis PREDICTING THE ELECTRONIC BAND GAP Conceptualization Models Computational protocol 1D- and 2D-polymer Comparing the cores Predicting the gap Synopsis 6 SIMULATING THE PROTON TAUTOMERIZATION Models Collective variables (CVs) Computational protocol FES portraits and energy barriers Synopsis 7 CONCLUSIONS AND OUTLOOK APPENDIX A APPENDIX B APPENDIX C BIBLIOGRAPHY SCIENTIFIC OUTPUT ACKNOWLEDGEMENTS

The nature and role of defects is of primary importance to understand the physical properties of C and BN single walled nanotubes. Transmission electron microscopy (TEM) is a well known powerful tool to study the structure of defects in materials. However, in the case of SWNTs, the electron irradiation of the TEM may knock out atoms. This effect may alter the native structure of the tube, and has also been proposed as a potential tool for nanoengineering of nanotubular structures. Here we develop a theoretical description of the irradiation mechanism. First, the anisotropy of the emission energy threshold is obtained via density functional based calculations. Then, we numerically derive the total Mott cross section for different emission sites of carbon and boron nitride nanotubes with different chiralities. Using a dedicated STEM microscope with experimental conditions optimised on the basis of derived cross-sections, we are able to control the generation of defects in nanotubular systems. Either point or line defects can be obtained with a spatial resolution of a few nanometers. The structure, energetics and electronics of point and line defects in BN systems have been investigated. Stability of mono- and di- vacancy defects in hexagonal boron nitride layers is investigated, and their activation energies and reaction paths for diffusion have been derived using the nudged elastic band method (NEB) combined with density functional based techniques. We demonstrate that the appearance of extended linear defects under electron irradiation is more favorable than a random distribution of point defects and this is due to the existence of preferential sites for atom emission in the presence of pre-existing defects, rather than thermal vacancy nucleation and migration.

The calculation of the electron–phonon coupling from first principles is computationally very challenging and remains mostly out of reach for systems with a large number of atoms. Semi-empirical methods, like density functional tight binding (DFTB), provide a framework for obtaining quantitative results at moderate computational costs. Herein, we present a new method based on the DFTB approach for computing electron–phonon couplings and relaxation times. It interfaces with PHONOPY for vibrational modes and DFTB+ to calculate transport properties. We derive the electron–phonon coupling within a non-orthogonal tight-binding framework and apply them to graphene as a test case.

Cette thèse présente le développement et les applications d'un formalisme hybride quantique-classique pour décrire la structure électronique d'un système actif avec un environnement cryogénique (agrégat ou matrice d'atomes de gaz rare). La description quantique de la structure électronique du système actif est faite dans le cadre d'une approximation de type Liaisons Fortes de la Théorie de la Fonctionnelle de la Densité, avec charges atomiques autocohérentes (SCC-DFTB). L'environnement de gaz rare est décrit par des potentiels classiques atome-atome (FF). L'interaction entre le sytème actif et les atomes de l'environnement cryogénique est représentée par des opérateurs matriciels locaux anisotropes électron-atome, ainsi que par des contributions de polarisation et de dispersion. La détermination des opérateurs et des paramètres d'interaction est extraite de calculs ab initio post Hartree-Fock (CCSD-T) sur les paires atome actif/atome d'argon. Les applications concernent les interactions entre hydrocarbures, agrégats d'eau isolés ou complexes hydrocarbures/eau avec des agrégats et ou des matrices d'argon. Le modèle est validé sur de petits systèmes (molécule C6H6 , molécule H2O) en interaction avec des atomes et agrégats d'argon. Nous avons ainsi déterminé les données structurales et énergétiques pour les agrégats (C6H6)Arn (n < 55) qui ont été comparées à des données ab initio (DFT, CCSD-T) pour les plus petits agrégats, ou à des calculs de champ de force publiés dans la littérature pour les agrégats de plus grande taille. Le modèle permet également un traitement unifié de différentes situations électroniques permettant ainsi la détermination de l'évolution des potentiels d'ionisation du système actif en fonction de la taille n de l'agrégat solvatant. Le modèle DFTB/FF a ensuite été appliqué à des molécules et nano-agrégats d'eau (H2O)n (n=2-6) insérés dans des matrices d'argon, représentées par des sous-ensembles finis du réseau cristallin cubique faces centrées. Des données structurales et énergétiques ont été obtenues. Des études de dynamique moléculaire ont permis la détermination de spectres infrarouges (IR) à température finie. La comparaison des spectres IR théoriques caractérisant une molécule d'eau en matrice avec les données expérimentales nous a permis de valider l'approche DFTB/FF. Le cas de l'hexamère (H2O)6, plus petit agrégat présentant une structure tri-dimensionnelle et caractérisé par plusieurs isomères stables, a été étudié de façon exhaustive : l'effet de la matrice sur les structures de certains de ces isomères a été mis en évidence, ainsi que des effets différentiels sur leur stabilités respectives. Une influence sur les positions des bandes IR des agrégats a également été montrée. Les résultats obtenus permettent une interprétation satisfaisante des données expérimentales existantes pour les plus petits agrégats. L'assignation des spectres expérimentaux de l'hexamère demeure incertaine. Enfin, des résultats préliminaires sur les structures, l'énergétique et les spectres IR à température finie ont été obtenus pour des complexes d'Hydrocarbures Aromatiques Polycycliques avec l'eau (HAP-H2O) en matrices d'argon. L'ensemble des données obtenues pour ces complexes est discuté en relation avec les résultats expérimentaux en environnement cryogénique obtenus dans l'équipe de Joëlle Mascetti de l'Institut des Sciences Moléculaires de l'Université Bordeaux I, dans le cadre d'une collaboration ANR (ANR PARCS no 13-BS08-0005). Ce travail a bénéficié d'une allocation de thèse co-financée par l'Institut de Physique du CNRS et le Conseil Régional de la région Midi-Pyrénées. / This thesis presents the development and applications of an hybrid quantum-classical formalism in order to describe the electronic structure of an active system in a cryogenic environment (cluster or rare gas matrix). The quantum description of the electronical structure of the active system is based on a a tight-binding approximation of the density functional theory, with self-consistency regarding the charges (SCC-DFTB). The rare gaz environment is described via classical atom-atom potential (FF). The interaction between the active system and the atoms of the cryogenic environment is represented by local anisotropic matricial electron-atom operators, as well as by polarisation and dispersion contributions. Operators and interaction parameters are extracted from post Hartree-Fock \textit{ab initio} calculations (CCSD-T) of active atom/argon atom pairs. The applications involve hydrocarbons, isolated water clusters or hydrocarbon/water complexes in interaction with argon clusters or matrices. The model has been validated on small systems (C6H6 molecule, H2O molecule) in interaction with argon atoms and clusters. We have been able to determine structural and energetic data for (C6H6)Arn (n < 55) clusters which are benchmarked against ab initio results (DFT,CCSD-T) for the smaller sizes, or with respect to FF calculations, available in the literature, for larger sized clusters. The model enables to treat various electronic situations, allows in particular to determine the evolution of the ionization potentials of the active system as a function of the inert cluster size. The SCC-DFTB/FF model has then been applied to water molecules and water nano-clusters (H2O)n (n=2-6) embedded in argon matrices, represented by finite size cristal pieces of the face centered cubic lattice. Structural and energetical data have been obtained. Molecular dynamics studies have enabled the determination of finite temperature infrared (IR) spectra. Comparison between the theoretical and experimental spectra of the water monomer embedded in the matrix validates the SCC-DFTB/FF approach. The case of the water hexamer (H2O)6, the smallest cluster presenting a three-dimensional structure and caracterized by several low-energy isomers, has been investigated exhaustively : the effect of the matrix on the structures of some isomers has been shown as well as differential effects on their respective stabilities. An influence on IR lines positions has also been highlighted. Our theoretical study allows for a satisfactory interpretation of the experimental data for the smallest clusters (n<4). The assignment of the experimental spectra of the hexamer remains in discussion. Finally, preliminary results on structures, energetics and finite temperature IR spectra have been obtained for Polycyclic Aromatic Hydrocarbons (PAH) /water complexes. The results for the complexes are discussed in relation with experimental data obtained in the team of Joëlle Mascetti at the Institute of Molecular Sciences (University of Bordeaux I), in the context of an ANR collaborative project (ANR PARCS no 13-BS08-0005). The thesis has been co-financed by the CNRS Institute of Physics and Conseil Regional of Region Midi-Pyrénées.