Cette thèse s'articule autour de développements méthodologiques sur l'évaluation théorique des énergies quantiques et relativistes d'état électroniquement excité d'atome ou de molécule. La méthode basée sur la fonction d'onde "Coupled Cluster" (CC) est à l'heure actuelle, une des méthodes les plus précise pour calculer ces états pour les systèmes à N-corps. L'implémentation présentée est basée sur un Hamiltonien relativiste à N-corps: Dirac-Coulomb à 4 composantes et une fonction d'onde "Coupled Cluster" au rang d'excitation arbitraire. Les états excités sont évalués via la théorie de la réponse linéaire, en diagonalisant la matrice Jacobienne Coupled Cluster. L'accent des travaux se porte sur l'évaluation de ses éléments en seconde quantification via un nouvel algorithme basé sur les commutateurs, et sur son adaptation au formalisme relativiste de Dirac à 4 composantes. Enfin, des applications du code à des molécules diatomiques non triviales seront présentées.

This thesis describes a computational investigation of the mutagenicity of 5-bromouracil (BrU). In Chapter 1, three models of spontaneous and BrU-induced base mispairing (rare tautomer, wobble pair, and ion) are reviewed. Chapter 2 presents the computational techniques used: electronic structure methods (Hartree–Fock-based and density functional theory) and molecular dynamics. Chapter 3 presents optimisations of the keto and enol tautomers of BrU and uracil (U) in water clusters. The enol tautomer of BrU is found to be more stable than that of U. Chapter 4 is a molecular dynamics study of the keto-enol tautomerism of BrU and U in a periodic water box. The pKₐ of BrU at N3 is found to be lower than that of U. Chapter 5 is a study of stacked base dimers containing BrU, U, or thymine (T) stacking with natural bases. Some structures were taken from the Protein Data Bank, while others were generated using an in-house methodology. BrU is found to stack more strongly than T in vacuo, but solvation and thermal effects nullify this difference. Chapter 6 discusses the significance of the results in Chapters 3–5 in terms of BrU-induced mutagenesis. Appendices A and B–D provide supplementary material to Chapters 2 and 5, respectively. Appendix E is an investigation of the “base flipping” pathway of 2-aminopurine (2AP). Both 2AP/N and A/N dinucleosides (N = thymine or guanine) are found to adopt a wide range of energy-minimum conformations – not only stacked and “flipped”, but also intermediate – and the stacked are not the most favourable by free energy. Appendix F is a list of publications and papers in preparation. One publication concerns BrU stacking. The other is a conformational study of the dipeptide tyrosine-glycine: the theoretical results are shown to be consistent with experiment (R2PI spectra) if thermal effects are taken into account.

L'importance des effets relativistes dans la chimie a été reconnu depuis les années 1980. Par exemple, sans la relativité (a) l'or aurait la même couleur que l'argent (b) le mercure ne serait pas liquide à la température ambiante et (c) nos voitures ne démarrent pas avec une batterie de plomb. Pour une description théorique de la structure et la réactivité des éléments lourds, la relativité est un ingrédient essentiel. Le hamiltonien pour les calculs moléculaires relativistes à 4 composantes est construit en remplaçant la partie mono-électronique de l'hamiltonien électronique non-relativiste par le hamiltonien de Dirac. La partie bi-électronique est approchée par le terme de r Coulomb comme dans le cas non relativiste, ce qui donnel'hamiltonien de Dirac-Coulomb (DC). Pour réduire le coût de calcul, on peut utiliser des hamiltoniens relativistes à 2 composantes. Parmi eux, l'hamiltonien exact à 2 composantes (X2C) est le plus précise. La corrélation électronique est, cependant, une contribution très importante pour obtenir une description théorique à la fois qualitative et quantitative des spectroscopies moléculaires, réactions, etc. Dans cette thèse, nous avons étudié l'interaction entre la relativité et de la corrélation. à la fois par des développements méthodologiques et par des applications moléculaires. Dans la première partie de la thèse, nous avons calculé les constantes spectroscopiques dimères des gaz rares lourds. La liaison faible de ces dimères ne peut être décrit que par l'inclusion de la corrélation électronique. Les dimères des gaz rares les plus lourds, le radon et l'eka-radon, nécessite de plus un traitement adéquat de la relativité. Nos calculs sont basés sur l'hamiltonien X2Cmmf, à la fois avec des méthodes de corrélation basés sur une fonction d'onde et séparation de porte (srDFT). La deuxième partie de cette thèse concerne la simulation de la spectroscopie des rayons X, où l'on sonde la région du cœur d'une molécule, ou la relativité joue un rôle très important. Nous avons étudié la spectroscopie L-edge de la série isoélectronique: UO22 +, UNO+, et UN2, où le couplage spin-orbite joue un rôle majeur. Au niveau des méthodes, nous avons considéré MP2 à couches ouvertes et la théorie de la fonctionnelle de la densité dépendante de temps (TDDFT). Dans un autre étude, nous avons simulé la spectroscopie K-edge de la série H2X (X = O, S, Se, Te) et XH3 (X = N, P, As) ainsi que les molécules N2 et N2O2. Pour ces systèmes, l'interaction spin-orbite est moins important. Par conséquent, nous avons utilisé un hamiltonien DC sans spin (SF). Certains des systèmes pris en compte dans ce travail sont de caractère multi-référentielles ; nous avons utilisé la methode Coupled Cluster Multi-référentielle de type State Universal et adapté au groupe unitaire (UGA-SUMRCC) comme une méthode de corrélation. Dans la troisième et partie principale de la thèse, l'attention est de nouveau sur la relativité et de la corrélation, mais pour le calcul des propriétés électriques et magnétiques moléculaires. Nous avons développé et mis en œuvre un module pour le calcul des valeurs moyennes au niveau relativiste à 4-composantes coupled cluster monoréferentiel. Les propriétés qui sondent la densité électronique près de noyaux (lourds), telles que la résonance paramagnétique électronique (RPE), les paramètres des gradients de champ électrique et la non-conservation de la parité (NCP) des molécules chirales ,sont parfaitement adaptés pour l'application de cette méthode. Pour l'instant, nous avons étudié que la NCP. Ce module dans le logiciel DIRAC pour les calculs moléculaires relativistes fournit un cadre propice pour la mise en œuvre de méthodes de CC relativistes employant la symétrie de groupes doubles et de permutation de manière très efficace. En perspective, nous ciblons la mise en œuvre de la réponse linéaire CC pour le calcul des énergies d'excitation et propriétés moléculaires de second ordre tels que les paramètres de RMN. / The importance of relativistic effects in chemistry has been recognized since the 1980s. Without relativity (a) gold would have the same colour as silver (b) mercury would not be liquid at room temperature (c) our cars would not start (lead-battery). For a theoretical description of the structure and reactivity of heavy-elements, relativity is considered as an essential ingredient. The Hamiltonian for the 4-component relativistic molecular calculations is constructed by replacing the one-electronic part of the non-relativistic molecular Hamiltonian by the Dirac Hamiltonian. The two-electronic part of the Hamiltonian is approximated by the Coulombic repulsion term as in the non-relativistic case. The resulting Hamiltonian is called the Dirac-Coulomb (DC) Hamiltonian. For chemical applications there exist a class of relativistic Hamiltonians, where one-electronic part of the DC Hamiltonian is transformed to a 2-component one. Among them the eXcact 2-component (X2C) Hamiltonian is the most accurate one. Electron correlation, however, is a very important contribution to achieve a both qualitative and quantitative correct description of molecular spectroscopies, reactions etc. It is, therefore, essential to study the interplay between relativity and correlation. In this thesis, we have studied this interplay both in terms methodological developments and molecular applications. In the first part of the thesis we have studied the spectroscopic constants of the heavy rare gas dimers. The weak bonding of those dimers can only be described by the inclusion of electron correlation. The heavier analogues in the rare gas series i.e, Radon and eka-Radon, in addition require adequate treatment of relativity. Our calculations are based on the eXact 2-Component molecular-mean field (X2Cmmf) Hamiltonian both with wave function methods and range-separated DFT methods. The second part of this thesis simulates X-ray spectroscopy, where one probes the core region of a molecule. In the core region relativity plays a very significant role. Removal and excitation of electrons from that region involve various processes, which are beyond a mean-field description. We have studied L-edge spectroscopy of the isoelectronic series: UO22+, UNO+, and UN2, where spin-orbit coupling plays a major role. For the theory we have considered single reference open-shell MP2 and Time Dependent Density functional Theory (TDDFT). In another work, we have studied K-edge spectroscopy of the H2X (X= O, S, Se, Te) and XH3 (X= N, P, As) series as well as N2, N2O2 molecules. For this study spin-orbit coupling is less important, therefore, we have treated them with the Spin-Free (SF) DC Hamiltonian. Some of the systems considered in this work are Multi-Reference in nature; we have used Unitary Group Adapted (UGA) State Universal Multi-reference Coupled Cluster (UGA-SUMRCC) theory as a correlation method. In the third and major part of the thesis, the thrust is again on relativity and correlation, but for the calculation of molecular electric and magnetic properties. We have developed and implemented a module for the calculation of expectation values at the 4-component Relativistic Single Reference Coupled Cluster level. Properties that probe the electron density near (heavy) nuclei, such as Electron Paramagnetic Resonance (EPR) parameters, electric field gradients and parity non-conservation (PNC) in chiral molecules are ideally suited for the application of this method. However, we have only studied PNC so far. This module in the DIRAC software for relativstic molecular calculations provides a convenient framework for the implementation of relativistic CC methods employing double group and permutation symmetry very efficiently. In the near future we therefore target the implementation of Linear Response CC for the calculation of excitation energies and second-order molecular properties such as NMR parameters.

Porphyrins are an important class of biomolecules, which are heavily studied, both ex- perimentally and computationally. But, despite the intensive efforts, for many questions we still aren't able to consistently find an agreement between theory and experiment. One of the still unresolved issues is the character of the ground state of the Fe(II)-porphyrin molecule. We used a model of the Fe(II)-porphyrin molecule to study the effects of geometrical changes on the spin states. By carrying out extensive DMRG-CASSCF cal- culations topped with TCCSD correlation treatment we are able to link the effects of these geometrical changes to the experimental results, and predict a quintet ground state for the isolated Fe(II)-porphyrin molecule. Also, using a ligated porphyrin belonging to the iron porphyrin carbene class of molecules, we demonstrate by combining the CASSCF and AC0 methods that geometrical changes outside the porphyrin core cannot be over- looked. 1

Low dimensional semiconductor structures are modeled using techniques from the field of many-body atomic physics. B-splines are used to create a one-particle basis, used to solve the more complex many-body problems. Details on methods such as the Configuration Interaction (CI), Many-Body Perturbation Theory (MBPT) and Coupled Cluster (CC) are discussed. Results from the CC singles and doubles method are compared to other high-precision methods for the circular harmonic oscillator quantum dot. The results show a good agreement for the energy of many-body states of up to 12 electrons. Properties of elliptical quantum dots, circular quantum dots, quantum rings and concentric quantum rings are all reviewed. The effects of tilted external magnetic fields applied to the elliptical dot are discussed, and the energy splitting between the lowest singlet and triplet states is explored for varying geometrical properties. Results are compared to experimental energy splittings for the same system containing 2 electrons.

This dissertation describes the implementation of the molecular electronic structure calculations with an implicit solvent model using coupled-cluster theory. The theory for and the implementation of the solvent reaction field method (SCRF) and the reference interaction site model (RISM) at the coupled-cluster singles and doubles (CCSD) are presented. In the SCRF model a solute molecule is placed in a spherical cavity, and the outer solvent is represented by a dielectric continuum, which is characterized by the dielectric constant of the solvent. The reaction field is introduced to the system by using the multipole moment expansion of the electronic structure of the solute molecule and the dielectric constant. The SCRF method has been used to calculate the conformational equilibrium and the rotational barriers of 1,2-dichloroethane in vacuum and in different solvents. The calculated results are compared with experimental values. In addition, the solvent effects on the energetics of the mechanism of nitration of benzene are reported using the implemented CCSD-SCRF model. The idea of RISM is to replace the reaction field in continuum models by a microscopic expression in terms of the site-site radial distribution functions between solute and solvent, which can be calculated from the RISM integral equations. The statistical solvent distribution around the solute is determined based on the electronic structure of the solute, while the electronic structure of solute is influenced by the surrounding solvent distribution. Therefore, the wave function and the RISM equations are solved self-consistently with CCSD. Pair correlation functions, partial atomic charges, and solvation free energies of water and N-methylacetamide are calculated in liquid water using proposed theory. Both the CC-SCRF and CC-RISM methods have been implemented in a developmental version of the Q-Chem 3.2 quantum chemistry package.

In this thesis, the implementation of the incremental scheme for open-shell systems with unrestricted Hartree-Fock reference wave functions is described. The implemented scheme is tested within robustness and performance with respect to the accuracy in the energy and the computation times. New approaches are discussed to implement a fully automated incremental scheme in combination with the domain-specific basis set approximation. The alpha Domain Partitioning and Template Equalization are presented to handle unrestricted wave functions for the local correlation treatment. Both orbital schemes are analyzed with a test set of structures and reactions. As a further goal, the DSBSenv orbital basis sets and auxiliary basis sets are optimized to be used as environmental basis in the domain-specific basis set approach. The performance with respect to the accuracy and computation times is analyzed with a test set of structures and reactions. In another project, a scheme for the optimization of auxiliary basis sets for uranium is presented. This scheme was used to optimize the MP2Fit auxiliary basis sets for uranium. These auxiliary basis enable density fitting in quantum chemical methods and the application of the incremental scheme for systems containing uranium. Another project was the systematical analysis of the binding energies of four water dodecamers. The incremental scheme in combination with the CCSD(T) and CCSD(T)(F12*) method were used to calculate benchmark energies for these large clusters.

<p>Quantum chemical calculations have been performed to investigate radical cation rearrangement, radical carbonylation, and homolytic substitution reactions of organic molecules.</p><p>The rearrangement of the bicyclopropylidiene radical cation to the tetramethyleneethane radical cation is predicted to proceed with stepwise disrotatory opening of the two rings. Each ring opening is found to be combined with a striking pyramidalization of a carbon atom in the central bond.</p><p>The isomerization of the norbornadiene radical cation to the cycloheptatriene radical cation (<b>CHT</b><b>.+</b>), initialized by opening of a bridgehead–methylene bond, is investigated. The most favorable path involves concerted rearrangement to the norcaradiene radical cation followed by ring opening to <b>CHT</b><b>.+</b>. The barrier of this channel is found to be significantly reduced upon substitution of the methylene group with C(CH₃)₂.</p><p>Stepwise mechanisms are predicted to be favored over concerted isomerization for the McLafferty rearrangement of the radical cations of butanal and 3-fluorobutanal. The barrier for the concerted rearrangement is found to be lowered by 17.2 kcal/mol upon substitution, a result which is rationalized by the calculated dipole moments and atomic charges.</p><p>Recent experiments showed that photoinitiated carbonylation of alkyl iodides with [¹¹C]carbon monoxide may be significantly enhanced by using small amounts of ketones that have nπ* character of their excited triplet state. DFT calculations show the feasibility of an atom transfer type mechanism, proposed to explain these observations. Moreover, the computational results rationalize the observed differences in yield when using various alcohol solvents.</p><p>Finally, following photolysis of methyliodide, recent electron spin resonance spectroscopy experiments demonstrated that the S_H2 reaction ^•CD₃ + SiD₃CH₃ → CD₃SiD₃ + ^•CH₃ proceeds with high selectivity over the energetically more favorable D abstraction. The role of geometrical effects, especially the formation of prereactive complexes between methylsilane and methyliodide is studied, and a plausible explanation for the experimentally observed paradox is presented.</p>

Quantum chemical calculations have been performed to investigate radical cation rearrangement, radical carbonylation, and homolytic substitution reactions of organic molecules. The rearrangement of the bicyclopropylidiene radical cation to the tetramethyleneethane radical cation is predicted to proceed with stepwise disrotatory opening of the two rings. Each ring opening is found to be combined with a striking pyramidalization of a carbon atom in the central bond. The isomerization of the norbornadiene radical cation to the cycloheptatriene radical cation (CHT.+), initialized by opening of a bridgehead–methylene bond, is investigated. The most favorable path involves concerted rearrangement to the norcaradiene radical cation followed by ring opening to CHT.+. The barrier of this channel is found to be significantly reduced upon substitution of the methylene group with C(CH3)2. Stepwise mechanisms are predicted to be favored over concerted isomerization for the McLafferty rearrangement of the radical cations of butanal and 3-fluorobutanal. The barrier for the concerted rearrangement is found to be lowered by 17.2 kcal/mol upon substitution, a result which is rationalized by the calculated dipole moments and atomic charges. Recent experiments showed that photoinitiated carbonylation of alkyl iodides with [11C]carbon monoxide may be significantly enhanced by using small amounts of ketones that have nπ* character of their excited triplet state. DFT calculations show the feasibility of an atom transfer type mechanism, proposed to explain these observations. Moreover, the computational results rationalize the observed differences in yield when using various alcohol solvents. Finally, following photolysis of methyliodide, recent electron spin resonance spectroscopy experiments demonstrated that the SH2 reaction •CD3 + SiD3CH3 → CD3SiD3 + •CH3 proceeds with high selectivity over the energetically more favorable D abstraction. The role of geometrical effects, especially the formation of prereactive complexes between methylsilane and methyliodide is studied, and a plausible explanation for the experimentally observed paradox is presented.

The phenomenon of pairing in atomic and nuclear many-body systems gives rise to a great number of different physical properties of matter, from areas as seemingly diverse as the shape of stable nuclei to superconductivity in metals and superfluidity in neutron stars. With the experimental realisation of the long sought BCS-BEC crossover observed in trapped atomic gases - where it is possible to fine tune the s-wave scattering length a of a many-fermion system between a dilute, correlated BCS-like superfluid of Cooper pairs and a densely packed BEC of composite bosons - pairing problems in atomic physics have found renewed interest in recent years. Given the high precision techniques involved in producing these trapped gas condensates, we would like to employ a suitably accurate many-body method to study such systems, preferably one which goes beyond the simple mean-field picture.The Coupled Cluster Method (CCM) is a widely applied and highly successful ab initio method in the realm of quantum many-body physics and quantum chemistry, known to be capable of producing extremely accurate results for a wide variety of different many-body systems. It has not found many applications in pairing problems however, at least not in a general sense. Our aim, therefore, is to study various models of pairing using a variety of CCM techniques - we are interested in studying the generic features of pairing problems and in particular, we are especially interested in probing the collective modes of a system which exhibits the BCS-BEC crossover, in either the BCS or BEC limit. The CCM seems a rather good candidate for the job, given the high precision results it can produce.