Neste trabalho, a reação O(3P) + HBr → OH + Br, que se insere no contexto da química atmosférica, mais especificamente nos ciclos de destruição catalítica do ozônio, foi estudada empregando superfícies de energia potencial ab initio de alta qualidade. Construímos superfícies para os estados eletrônicos 3A\" e 3A\', baseadas na expansão de muitos corpos, com potenciais de dois corpos ajustados por funções \"switched-MLJ\" e potenciais de três corpos interpolados utilizando o método RKHS. Os pontos ab initio utilizados foram obtidos no nível de teoria MRCISD+Q/CBS+SO. A superfície final para o estado eletrônico 3A\" foi corrigida por um fator multiplicativo de modo que reproduzisse cálculos benchmark para a altura de barreira, em que foram considerados efeitos relativísticos (escalares e spin-órbita), correlação caroço-valência e correlação de ordem alta (excitações triplas e quádruplas). As principais características da SEP 3A\" são dois mínimos de van der Walls no canal de entrada e saída e um estado de transição com uma barreira energética de 5,01 kcal mol-1. A SEP 3A\' tem um estado de transição linear em 6,45 kcal mol-1. O valor obtido para a entalpia de reação, a 0 K, foi de -15,7 kcal mol-1, muito próximo do valor experimental de -15,14 kcal mol-1. Calculamos constantes de velocidade, no intervalo de 200 a 1000 K, utilizando a teoria do estado de transição variacional com contribuições de tunelamento multidimensional (ICVT/µOMT) e com uma aproximação de espalhamento reativo quântico (QM/JS). Estes valores estão em ótima concordância com os dados experimentais da literatura, em todo intervalo de temperatura em que estão disponíveis: de 221 a 554 K para reação O + HBr e de 295 a 419 K para reação O + DBr. As constantes de velocidade, a 298 K e em cm3 molécula-1 s-1, obtidas para a reação O + HBr são: 3,62·10-14 (ICVT/µOMT) e 3,35·10-14 (QM/JS), enquanto que o valor experimental é 3,78·10-14. A qualidade destes resultados reforça nossa confiança nos procedimentos e aproximações utilizadas, abrindo caminho para a caracterização, em alto nível, de uma grande variedade de reações em fase gasosa. / In this work, the O(3P) + HBr → OH + Br reaction, which is relevant to atmospheric chemistry, specially for the catalytic ozone depletion, was studied using high-level ab initio potential energy surfaces. We constructed surfaces for the 3A\" and 3A\' electronic states, based on the many-body expansion, with the two-body potentials adjusted by the switched-MLJ function and the three-body potentials interpolated using the RKHS method. The ab initio points were calculated at the MRCISD+Q/CBS+SO level of theory. The main features of the 3A\" are the presence of two van der Waals minima, at the entrance and exit channels, and a transition state with a barrier height of 5.01 kcal mol-1. The 3A\' PES has a linear transition state at 6.45 kcal mol-1. We obtained the enthalpy of reaction, at 0 K, of -15.7 kcal mol-1, in close agreement with the experimental value of -15.14 kcal mol-1. Rate constants, in the temperature range from 200 to 1000 K, were calculated using the variational transition state theory with contributions of multidimensional tunneling (ICVT/µOMT) and also a quantum reactive scattering approach (QM/JS). Their values are in fair agreement with the experimental data in the literature in the whole temperature range available: from 221 to 554 K for the O + HBr reaction, and from 295 to 419 K for the O + DBr reaction. At 298 K, the calculated rate constants, in cm3 molecule-1 s-1, for the O + HBr reaction are 3.62·10-14 (ICVT/µOMT) and 3.35·10-14 (QM/JS); and the experimental value is 3.78·10-14. The quality of these results reinforces our confidence in the procedures and approximations used, leading to the possibility of high-level characterization of a variety of gas phase reactions.

L’obtention, dans des conditions douces, sélectives et de chimie durable de molécules ciblées est aujourd’hui un enjeu majeur. Les métalloenzymesartificielles représentent une voie d’investigation importante, car en jouant, par exemple, sur la seconde sphère de coordination,il est possible de modifier fortement la réactivité de ces systèmes bio-inspirés. Le développement de cette chimie suppose une connaissanceapprofondie des différentes étapes du mécanisme de la réaction envisagée. Pour cela, la chimie théorique est essentielle à la rationalisation dela réactivité chimique mais elle souffre encore de nombreuses insuffisances pour les systèmes que nous nous proposons d’étudier.Dans ce travail, nous avons choisi d’étudier la superoxyde réductase, enzyme détoxifiante du radical superoxyde. Si de nombreuses expérimentalessont disponibles détaillant certains intermédiaires, le mécanisme précis est peu documenté. Le but a été de mettre en place uneméthodologie complète allant du développement de paramètres MM spécifiques à l’étude de la réactivité par métadynamiques QM/MM.Le développement de paramètres MM pour le site actif à fer a permis son étude en dynamique MM donnant des informations sur la conformationsdu squelette peptidique ainsi que l’interaction avec les molécules de solvant. De part la nature du fer, une description QM du site actifà été nécessaire via l’utilisation de DFT hybride. Les métadynamiques QM/MM ont permis quant à elles d’explorer les chemins réactionnelset de caractériser les espèces ainsi formées et les énergies d’activations.Cette méthodologie a permis la compréhension en premier lieu de la réactivité native de la forme sauvage et elle a aussi permis d’explorer lesréactivités nouvelles des mutations de la SOR permettant ainsi de définir le rôle crucial de la seconde sphère de coordination. / Obtaining targeted molecules under gentle, selective and sustainable conditions is still a major challenge. Artificial metalloenzymes are animportant line of enquiry, because by playing, for example, with the second sphere of coordination, it is possible to strongly modify thereactivity of these bio-inspired systems. The development of this chemistry presupposes a thorough knowledge of the different stages of themechanism of the reaction under study. For this reason, theoretical chemistry is essential to rationalize chemical reactivity, but it still suffersfrom many shortcomings for the systems we propose to study.In this work, we study the superoxide reductase, a detoxifying enzyme of the superoxide radical. While many experiments are available detailingsome intermediates, the precise mechanism is not well documented. The aim was to implement a complete methodology ranging from thedevelopment of specific MM parameters to the study of reactivity by QM/MM metadynamics.The development of MM parameters for the iron active site allowed its study by MM dynamics giving informations on the conformation ofthe peptide backbone as well as on the interaction with solvent molecules. Due to the nature of the iron, a QM description of the active sitewas required using hybrid DFT. QM/MM metadynamics have allowed us to explore reaction pathways and to characterize the compoundsformed to obtain the needed activation energies. This methodology made it possible to understand the native reactivity of the wild form ofthe SOR, but also to explore the new reactivity of the mutations of the SOR and thus to define the crucial role of the second coordination sphere.

L'objectif de cette thèse est de fournir des bornes d'erreur pour des problèmes aux valeurs propres linéaires et non linéaires issus du calcul de structure électronique, en particulier celui de l'état fondamental avec la théorie de la fonctionnelle de la densité. Ces bornes d'erreur reposent principalement sur des estimations a posteriori. D'abord, nous étudions un phénomène de compensation d'erreur de discrétisation pour un problème linéaire aux valeurs propres, grâce à une analyse a priori de l'erreur sur l'énergie. Ensuite, nous présentons une analyse a posteriori pour le problème du laplacien aux valeurs propres discrétisé par une large classe d'éléments finis. Les bornes d'erreur proposées pour les valeurs propres simples et leurs vecteurs propres associés sont garanties, calculables et efficaces. Nous nous concentrons alors sur des problèmes aux valeurs propres non linéaires. Nous proposons des bornes d'erreur pour l'équation de Gross-Pitaevskii, valables sous des hypothèses vérifiables numériquement, et pouvant être séparées en deux composantes venant respectivement de la discrétisation et de l'algorithme itératif utilisé pour résoudre le problème non linéaire aux valeurs propres. L'équilibrage de ces composantes d'erreur permet d'optimiser les ressources numériques. Enfin, nous présentons une méthode de post-traitement pour le problème de Kohn-Sham discrétisé en ondes planes, améliorant la précision des résultats à un faible coût de calcul. Les solutions post-traitées peuvent être utilisées soit comme solutions plus précises du problème, soit pour calculer une estimation de l'erreur de discrétisation, qui n'est plus garantie, mais néanmoins proche de l'erreur. / The objective of this thesis is to provide error bounds for linear and nonlinear eigenvalue problems arising from electronic structure calculation. We focus on ground-state calculations based on Density Functional Theory, including Kohn-Sham models. Our bounds mostly rely on a posteriori error analysis. More precisely, we start by studying a phenomenon of discretization error cancellation for a simple linear eigenvalue problem, for which analytical solutions are available. The mathematical study is based on an a priori analysis for the energy error. Then, we present an a posteriori analysis for the Laplace eigenvalue problem discretized with finite elements. For simple eigenvalues of the Laplace operator and their corresponding eigenvectors , we provide guaranteed, fully computable and efficient error bounds. Thereafter, we focus on nonlinear eigenvalue problems. First, we provide an a posteriori analysis for the Gross-Pitaevskii equation. The error bounds are valid under assumptions that can be numerically checked, and can be separated in two components coming respectively from the discretization and the iterative algorithm used to solve the nonlinear eigenvalue problem. Balancing these error components allows to optimize the computational resources. Second, we present a post-processing method for the Kohn-Sham problem, which improves the accuracy of planewave computations of ground state orbitals at a low computational cost. The post-processed solutions can be used either as a more precise solution of the problem, or used for computing an estimation of the discretization error. This estimation is not guaranteed, but in practice close to the real error.

This work outlines the numerical strategies for two sets of problems of great importance in correlated materials research. First, we analyze the electronic structure and magnetic properties of 3d transition metals with linear coordination. Second, we study the mutiplet structure of 4f ions arranged on the 2D triangular-lattice.

Le comportement des actinides dans l’environnement (site miniers, sites de stockagedes déchets et sites contaminés) dépend de l’interaction de ces éléments avec des ligandsprésents dans les différents milieux (air, sol, eaux superficielles et souterraines). Lesinteractions des actinides avec des ligands organiques polyfonctionnels peuvent piéger ceséléments ou au contraire favoriser leur migration.Dans ce travail, le comportement d’actinides aux degrés d’oxydation III, V et VI ensolution aqueuse a été étudié en présence de deux ligands polyaminocarboxyliques : l’acidenitrilotriacétique (NTA) et l’acide iminodiacétique (IDA).L’étude de la complexation du protactinium pentavalent par NTA et IDA a été conduiteselon une double approche : une étude thermodynamique réalisée par extraction par solvant,avec le protactinium à l’échelle des traces (C233Pa < 10-10 M) et une étude structurale, avecle protactinium en quantité pondérable (C231Pa ≈ 10-3 M), réalisée par Spectroscopied’Absorption des rayons X (SAX) et complétée par des calculs de chimie quantique.Les variations du coefficient de distribution de Pa(V) dans le systèmeTTA/Toluène/ HClO4 / NaClO4 /Pa(V)/ligand en fonction de la concentration de ligands àplusieurs températures et/ou acidités ont permis de déterminer la stœchiométrie maximale et lacharge moyenne des complexes Pa(V)-NTA et Pa(V)-IDA ainsi que les constantes de formationassociées à chaque espèce. Une stœchiométrie maximale de 2 a été observée pour les deuxsystèmes. Pour le système Pa-NTA, les deux complexes successifs prédominants dans la phaseaqueuse sont une espèce neutre PaO(NTA) pour le complexe (1:1) et une espèce de charge -3pour le complexe (1:2) qui pourrait correspondre à PaO(NTA) -:R. Une étude complémentairepar Electrophorèse Capillaire couplé à un spectromètre de masse (EC-ICP-MS) a permis deconfirmer la charge (-3) du complexe Pa − (NTA)-. Pour le système Pa-IDA, les résultats ontmontré la formation successive de deux complexes positifs PaO(IDA)3+ et PaO(IDA)+2.Lagéométrie de coordination et les distances interatomiques des complexes de stœchiométriemaximale ont été déterminés à partir de calculs DFT ou de dynamique moléculaire.L’étude de la complexation d’actinides trivalents (Am et Cf) et hexavalents (Np et Pu)par IDA a été réalisée par EC-ICP-MS. Les variations de la mobilité électrophorétique globaleen fonction de la concentration en IDA-R ont permis de déterminer les constantes de formationdes actinides avec IDA. Les constantes de formation des complexes de stœchiométrie (1:1)sont rapportées pour Am (III) et Cf (III). Concernant les complexes Np (VI) et Pu (VI) avecl'acide iminodiacétique, les constantes de formation des complexes de stœchiométriques (1:1)et (1:2) ont été déterminées. / The behaviour of actinides in the environment (in the surroundings of uranium miningsites, waste storage or contaminated sites) depends on the interaction of these elements with theorganic ligands present in these different systems. The interactions of actinides withpolyfunctional organic ligands could trap the element or inversely, favour their migration.In this work, the behaviour of actinides (III, V and VI) in aqueous solution was studied in thepresence of two polyaminocarboxylic ligands: nitrilotriacetic acid (NTA) and iminodiaceticacid (IDA).The study of the complexation of pentavalent protactinium by NTA and IDA was conductedaccording to a dual approach. A thermodynamic study carried out by liquid-liquid extraction inthe system TTA/Toluene/HClO4/NaClO4/Pa(V)/ligand, with protactinium at tracer scale (C233Pa< 10−10 M), has been implemented in order to determine the stoichiometry, the mean charge ofcomplexes and the associated formation constants. A structural approach with protactiniumin weighable quantity (C231Pa≈ 10−3 M) was conducted in order to determine the coordination geometry of complexes and interatomic distances.The variations of the distribution coefficient D of Pa(V) as a function of nitrilotriacetateconcentration enabled to determine that the maximum stoichiometry for the Pa-NTA and Pa-IDA systems is 2. For the Pa-NTA system, the two successive complexes predominant in theaqueous phase are a neutral species for (1:1) complex PaO(NTA) and charge -3 for the (1:2)which may correspond to PaO(NTA) -:R. In addition, Capillary Electrophoresis InductivelyCoupled Plasma Mass Spectrometry experiments have been performed to confirm the charge (-3) for the maximum stoichiometry complex. For the Pa-IDA system, the results have shownthe successive formation of two positive complexes PaO(IDA)3+ and PaO(IDA)+2. Optimized structures of Pa-NTA and Pa-IDA complexes were established using DFT or molecular dynamics calculations.The complexation of trivalent (Am and Cf) and hexavalent (Np and Pu) actinides with IDA was performed by Capillary Electrophoresis coupled with Inductively Coupled Mass Spectrometry(CE-ICP-MS). The variations of overall electrophoresis mobility of actinides species as function of CIDA2 allow the determination of the formation constants of actinides IDAcomplexes. The formation constants of complexes with (1:1) stoichiometry are reported forAm(III) and Cf(III). Concerning the complexes Np(VI) and Pu(VI) with iminodiacetic acid,formation constants of (1:1) and (1:2) stoichiometry complexes were determined

The effect of inclusion of explicit polarization is investigated through several theoret- ical studies of crystalline porous materials herein. In addition to the use of Monte Carlo simulation for such studies, a robust molecular dynamics software is presented which is suitable for analyzing time dependent properties of gases or other molecules in porous materials and other condensed phase systems. Metal-organic frameworks (MOFs) are the main focus of the work included here, a relatively young class of materials originally in- troduced in the early 1990s. These are usually three dimensional crystalline nanoporous materials that exhibit unique properties such as gas separation, storage and catalysis. They are synthesized by the combination of a metal ion e.g. Cu2+ with an organic linker e.g. benzene dicarboxylate. They are a very popular topic of scientific research due to the diversity in possible structures and manifold utility – finding applications in electron transfer, sensing, drug release etc. Industrially, MOFs like HKUST-1 and others are on the global market for use in gas storage and separation in fuel cell and raw materials processing. These materials are often ideal candidates for computer simulation owing to their crystalline nature – a very large atomic system (that is, moles of particles) can be under- stood by only evaluating one or a few unit cells of the MOF, usually less than 5,000 atoms, and macroscopic properties such as gas sorption capacity and diffusion coefficients can be calculated through extrapolation of atomistic interactions in a mathematically infinite lattice. The software developed by the space group as of 2005, Massively Parallel Monte Carlo (MPMC), allows for sophisticated calculation of repulsion dispersion, electrostatic and polarization energies. In this work, Monte Carlo Molecular Dynamics (MCMD) is in- troduced, which can hybridize both methods to explore the phase space of a system with ease and better efficiency, as well as explore the effects of MOF flexibility and dynamic properties which to-date are rarely studied. Studies involving primarily CO2, H2 and CH4 will be presented, but other gases investigated include C2 H2 , C2 H4 , C2 H6 , N2 , H2 O and others. Metal-organic materials with a wide variety of composition and structure will also be presented. Finally, features of the software MCMD will be presented for use by future studies.

This thesis concerns with 4 basic aspects of the charge carrier transport: (1) depth of the potential well formed around the charge carrier when localized on a polymer chain; i.e. so called polaron binding energy. (2) Extent of the charge carrier delocalization over the polymer chain and influence of steric effects on this value. (3) Intrachain mobility of the charge carrier. (4) Effect of charge carrier transfer on the chain stability. Polysilanes, which are well known for their semi-conducting properties, were chosen as model material for investigation. Outlined properties were studied by means of quantum chemistry and molecular dynamics, which allowed us to investigate the process of the charge carrier transfer in great detail. Theoretical results were then compared to the experiments with very good agreement.

Title: Optimizing quantum simulations and the DMRG method Author: Jan Brandejs Department: Department of Chemical Physics and Optics Supervisor: doc. Dr. rer. nat. Jiří Pittner, DSc., J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences Abstract: In this work, we explore the quantum information theoretical aspects of simulation of quantum systems on classical computers, in particular the many- electron strongly correlated wave functions. We describe a way how to reduce the amount of data required for storing the wavefunction by a lossy compression of quantum information. For this purpose, we describe the measures of quantum entanglement for the density matrix renormalization group method. We imple- ment the computation of multi-site generalization of mutual information within the DMRG method and investigate entanglement patterns of strongly correlated chemical systems. We present several ways how to optimize the ground state calculation in the DMRG method. The theoretical conclusions are supported by numerical simulations of the diborane molecule, exhibiting chemically interest- ing electronic structure, like the 3-centered 2-electron bonds. In the theoretical part, we give a brief introduction to the principles of the DMRG method. Then we explain the quantum informational...

Two dimensional (2D) materials, such as graphene, phosphorene and transition metal chalcogenides, have received a great attention in recent years due to their unique physical and chemical properties. A majority of 2D materials is intrinsically non-magnetic, therefore, their applications in spintronics are limited. The design and synthesis of new 2D materials with intrinsic magnetism and high spin-polarization remains a challenge. Computational discovery of new 2D materials with desired magnetic and electronic properties is the subject of this thesis. Using density functional theory with PBE, PBE+U and HSE06 functionals, we have systematically investigated the structure, electronic, magnetic and topological properties of novel 2D materials. Investigated materials include MXenes and layered transition-metal trihalides, both with great potential applications in spintronic devices. Four different classes of materials showing unique magnetic properties were investigated and reported in this thesis. (1) Asymmetrically functionalized MXenes were studied. The coexistence of the fully compensated antiferromagnetic order (zero magnetization) and completely spin-polarized semiconductivity was found for the first time. Moreover, the spin carrier orientation and induced transition from bipolar antiferromagnetic...

Electron confinement due to the two-dimensional (2D) nature of layered materials accounts for their fascinating electronic properties and for their applications in new-generation electronic devices. Moreover, the large specific surface area of 2D materials also enables their use in surface-related applications, such as catalysis and adsorption. In addition, these 2D materials are promising photocatalysts thanks to the shorter migration distance of photogenerated electrons and of electron holes. The research reported in this thesis aimed to provide atomistic insight into 2D layered materials, particularly into their structures, electronic properties and potential applications in the field of catalysis, photocatalysis and alkali metal ion batteries. Our findings are not only theoretically relevant but also open new research avenues for our experimental collaborators to improve specific properties and activities of their materials. The main results from this thesis, for five different classes of 2D materials, are summarized below. 2D covalent organic frameworks (COFs). CTF-type COFs with similar topology but different nitrogen-to-carbon ratios were investigated for their potential in photocatalytic water splitting. More specifically, torsion and bending effects on structure stability were investigated in...