Estudos pioneiros na década de 1970 com cálculos ab initio inauguraram o campo da química quântica relativística computacional. Desde então, também devido ao crescimento exponencial da capacidade computacional, a aplicação de Hamiltonianos relativísticos em cálculos de química teórica tem se tornado cada vez mais frequente. No entanto, o desenvolvimento de conjuntos de funções de base para estes cálculos não seguiu no mesmo ritmo. Após décadas, as melhores opções disponíveis ainda apresentam certas limitações técnicas, como sinais de prolapso variacional. Desta forma, o objetivo deste trabalho foi a geração de eficientes conjuntos relativísticos de funções de base Gaussianas para aplicação em cálculos ab initio correlacionados. Usou-se então de uma versão polinomial do método da coordenada geradora Dirac-Fock para elaboração de um conjunto primitivo de funções otimizadas variacionalmente livres de prolapso. Funções de correlação/polarização e funções difusas foram adicionadas em acordo com uma incrementação do tipo quadruple-ζ. Estas funções foram escolhidas através do tratamento multi-referencial de interação de configurações com o Hamiltoniano Dirac-Coulomb. Cálculos moleculares de propriedades fundamentais atestaram a qualidade destes conjuntos, denominados RPF-4Z, em comparação com outras bases relativísticas bastante utilizadas na literatura. Adicionalmente, momentos de quadrupolo nuclear de isótopos de bismuto e potássio e uma curva de energia potencial do dímero de rádio foram obtidos com estes conjuntos. Ao prover funções de base que retornam resultados comparáveis a outros conjuntos relativísticos disponíveis de qualidade quadruple-ζ, mas com uma significativa redução na demanda computacional, espera-se que as bases RPF-4Z se traduzam em um grande avanço na área. / Pioneering studies with ab initio calculations from the 1970s gave rise to the computational relativistic quantum chemistry field. Since then, also due to the exponential growth in computational resources, the application of relativistic Hamiltonians in theoretical chemistry calculations has become more common. However, the development of basis sets to be used in such calculations have presented its struggles. After decades, technical limitations, such as the variational prolapse issue still persist. Hence, the aim of the present thesis was the development of efficient relativistic Gaussian basis sets to be applied in correlated ab initio calculations. In order to do that, a polynomial version of the generator coordinate Dirac-Fock method has been applied to obtain variationally optimized primitive sets that are free of prolapse. Correlating/polarization functions, as well as diffuse ones, were added to these sets in a quadruple-ζ type of increment. Such functions were chosen by means of the Dirac-Coulomb multi-reference configuration interaction treatment. Molecular calculations of fundamental properties have attested the high quality of the designated RPF-4Z sets in comparison with other well-known relativistic sets. Furthermore, nuclear electric quadrupole moments of bismuth and potassium isotopes and a potential energy curve of the radium dimer were also analyzed. Since these generated sets are as accurate as commonly used relativistic quadruple-ζ sets already available, but with the advantage of a reduced computational demand, the RPF-4Z sets are expected to represent a great advance in the field.

A química do selênio é um assunto de crescente interesse devido a sua presença em diversos ambientes químicos, em particular, na atmosfera terrestre. A ausência de estudos sobre espécies relativamente simples contendo 2-4 átomos motivou este projeto, que se concentrou na investigação teórica rigorosa de uma serie de espécies moleculares: SeF, SeCl, SeBr, HSeF, HFSe, HSeCl, HClSe, HSeBr, HBrSe e de vários isômeros na superfície de energia potencial 1[H, S, Se, Cl]. Propriedades espectroscópicas de um conjunto de estados eletrônicos e o calor de formação das moléculas SeF, SeCl e SeBr foram determinados. Juntamente com os novos resultados desta investigação, sugerimos uma revisão e correção de alguns dados teóricos e experimentais da literatura. Aspectos energéticos, estruturais e espectroscópicos associados aos pontos estacionários nas superfícies de energia potencial singleto [H, Se, X], X = F, Cl e Br, e [H, S, Se, Cl] também foram caracterizados, assim como determinados os calores de formação dos isômeros mais estáveis. Barreiras energéticas para os vários processos de isomerização foram estimadas bem como o gasto energético envolvido nas diferentes possibilidades de dissociação dos isômeros mais estáveis. No caso dos sistemas triatômicos ainda estimamos as constantes de velocidade para as reações de isomerizações direta e reversa. Nesse contexto, esperamos que este trabalho possa servir como uma referência para estudos teóricos e experimentais futuros desses sistemas e/ou de outros de complexidade idêntica. / The chemistry of selenium is a subject of increasing interest due to its presence in many chemical enviroments, specially in the Earth\'s atmosphere. The lack of studies of relatively simple species containing 2-4 atoms has motivated this project which was focused on a rigorous theoretical investigation of a series of molecular especies: SeF, SeCl, SeBr, HSeF, HFSe, HSeCl, HClSe, HSeBr, HBrSe, and the isomers on the 1[H, S, Se, Cl] potential energy surface. Spectroscopic properties of a set of electronic states and the heat of formation of SeF, SeCl, and SeBr were determined. Along with the new results from this investigation, we showed that some theoretical and experimental data reported in the literature be revised and corrected. Energetic, structural, and spectroscopic aspects associated with the stationary points on the singlet potential energy surfaces [H, Se, X], X = F, Cl e Br, and [H, S, Se, Cl] were also characterized, and the heats of formation of the most stable isomers evaluated. Energetic barriers for the various processes of isomerization were estimated, as well as the energy involved in the dierent possibilities of dissociation of the most stable isomers. In the case of triatomic systems, we still estimated the rate constants for the direct and reverse reactions. In this context, we expect that this work should serve as reference in future theoretical and experimental studies on these systems and/or others of similar complexity

O triptofano é um aminoácido essencial, sendo o precursor do neurotransmissor serotonina. Esse composto é suscetível a oxidação por ação do oxigênio singleto, o que atrai interesse acadêmico devido a sua associação com doenças como a catarata. Nesse sentido, o presente trabalho se dedicou a investigar as propriedades estruturais e espectroscópicas de quatro moléculas envolvidas nessa oxidação: triptofano, triptofano hidroperóxido, tautômero anelar do triptofano hidroperóxido (WOOH) e álcool (WOH) reduzido dessa última molécula, através da aplicação de técnicas de Química Quântica: Teoria de Pertubação e Teoria do Funcional de Densidade Dependente do Tempo, e de simulação computacional: Método de Monte Carlo e Dinâmica Molecular. Foram analisadas as formas estruturais preferenciais do triptofano (neutra ou zwiteriônica) dependendo do meio (vácuo ou água), investigou-se a formação de ligações de hidrogênio e se obteve teoricamente os espectros UV-vis e de Ressonância Magnética Nuclear para esse aminoácido. Esses dois espectros também foram calculados para as moléculas de WOOH e WOH. Para o triptofano hidroperóxido, que é uma molécula postulada, se avaliou a plausibilidade de sua existência, assim como uma possível razão para sua não observação experimental. / Tryptophan is an essential amino acid, being the precursor of neurotransmitter Serotonin. This compound is susceptible to oxidation by singlet molecular oxygen, which has attracted academic interest due to its association with disorders like cataract. In this sense, this work was dedicated to investigate the structural and spectroscopic properties of four molecules involved in this oxidation: tryptophan, tryptophan hydroperoxide, ring chain tautomer of tryptophan hydroperoxide (WOOH) and an alcohol (WOH) reduced from this latter molecule, by means of Quantum Chemistry techniques: Pertubation Theory and Time- Dependent Density Functional Theory, as well as computer simulation: Monte Carlo method and Molecular Dynamics. The preferential conformations of tryptophan (neutral or zwitterionic) depending upon the medium (vacuum or water) were analyzed, in addition it was investigated the formation of hydrogen bonds and obtained the theoretical UV-vis and Nuclear Magnetic Ressonance spectra of this amino acid. These spectra were also calculated for the WOOH and WOH molecules. Regarding tryptophan hydroperoxide, a postulated molecule, it was evaluated the plausibility of its existence, as well as the reason for its non-experimental observation.

Ce document traite des aspects différents de la modélisation moléculaire d'une protéine de la matrice extracellulaire. Le domaine de signature des thrombospondines est étudié en détail dans ce document en faisant appel aux champs variés de la science. La complexité de ce domaine nécessite l'utilisation des approches de la mécanique quantique moléculaire en plus de la dynamique moléculaire classique. En reliant les deux approches un nouveau algorithme a été développé afin d'attribuer des charges partielles à partir des résultats obtenus par des méthodes ab-initio. Pour implémenter cet algorithme d'une façon efficace, les nouvelles méthodes de la programmation massivement parallèle ont été utilisées qui nous permettent entre autres de faire tourner cet algorithme sur les procsesseurs graphiques. Nous avons également utilisé et développé des nouvelles méthodes de la visualisation moléculaire rapprochant l'art à la science. En plus, de ces développements nous avons obtenus des résultats intéressants sur la dynamique du domaine de signature. Nous avons pu identifier les ions échangeables de ce domaine. Nous avons vérifié et élargie les modèles existants de la thrombospondine dans des concentrations faibles de calcium. En utilisant la dynamique moléculaire nous avons également évalué des sites importants de fixations pour le développement de nouveaux médicaments contre le cancer. / This document deals with the various aspects of molecular modeling of a protein in the extracellular matrix. In this work the thrombospondin signature domain is studied in detail, using various methods from different fields of science. Due to the complexity of the protein, a classical molecular dynamics and a quantum molecular approach is chosen to gain insights into the thrombospondin signature domain. During this process a new algorithm that allows to derive partial charges from ab-initio calculations has been developed. In order to run this algorithm in an efficient way new programming techniques, such as massive multiparallel programming on graphics processors has been used. Further new visualization methods have been either tried or developed effectively generating a new kind of art from the scientific results that have been obtained in this project. Besides these developments several interesting insights into the dynamics of thrombospondins have been revealed. We were able to identify the exchangeable ions within the thrombospondin signature domain, and were further capable to verify and extend existing models for a low calcium signature domain structure. Binding sites important for cancer drug design have also been evaluated using the molecular dynamics simulations.

In this thesis, we present a theoretical investigation of reactive processes involving the HeH$^+$ molecular ion, with applications in laboratory and astrophysical plasma physics. We consider in particular two processes, which are the charge transfer in H + He$^+$ collisions at low energy from a molecular approach and the photodissociation of HeH$^+$.<p><p>At the molecular level, the cross section is the basic quantity that has to be determined in order to achieve an understanding of reactive processes. Its calculation will be based on the description of the reactions using an emph{ab initio}, quantum mechanical approach. In this work, we will rely on the Born-Oppenheimer approximation, which allows the molecular motion to be separated into an electronic and a nuclear motion. The evaluation of cross sections then follows two steps.<p>The first is the determination of the electronic structure of the molecule. We will calculate the adiabatic potential energy curves of the excited electronic states as well as the dipole matrix elements between these states. The non-adiabatic radial and rotational couplings, which result from the breakdown of the Born-Oppenheimer approximation, are also estimated. The second step is to solve the nuclear motion, which we achieve using a time-dependent method based on the propagation of wave packets on the coupled electronic states. <p><p>A particular emphasis will be put on the importance of the excited states and of the non-adiabatic couplings in the description of reactive processes. <p>In the treatment of the charge transfer reaction between H and He$^+$ in excited states, it is well known that the non-adiabatic radial couplings cannot be neglected. However, we will show that the inclusion of the non-adiabatic rotational couplings is also necessary in order to obtain accurate state-to-state cross sections.<p>In the description of the photodissociation of HeH$^+$ from its ground state, we will show the influence of the excited states on the rate constant and the role of the non-adiabatic radial couplings in the determination of partial cross sections.<p>We will also consider the possible astrophysical applications of the first triplet state of HeH$^+$. We will show that this state is metastable by evaluating its lifetime, and calculate the cross sections and rate constants for the photodissociation and radiative association of HeH$^+$ in this state.<p> / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

The TiO2-catalyzed synthesis of nucleosides in non-aqueous formamide environ- ment via so-called acyclonucleoside intermediates represents an alternative way for the emergence of nucleic acids monomeric units, which could address the the fundamental problem associated with the formation of a --glycosidic bond between a nucleobase and a sugar moiety. In this computational contribution we present a plausible reaction route for the prebiotic TiO2-catalyzed synthesis of purine C2- and C3-acyclonucleosides in formamide, which does not require photocatalytic or radical chain mechanisms. The maximum computed activation energy along the proposed reaction channel is ≥ 32 kcal·mol≠1 , which is clearly feasible under the experimental conditions of the Saladino synthesis. We show that the rate determining step of the entire reaction path is the deprotonation of the formaldehyde hydrate methylene carbon occurring likely on defective binding sites of an anatase surface. Our calculations thus support the view of Saladino et al. about the catalytic role of the TiO2 surface in the one-pot synthesis of purine acyclonucleosides in heat formamide solution.

It has been proven that platinum and ruthenium complexes are active in anti- cancer treatment. Nowadays, the common chemotherapeutica have a lot of side effects, therefore, drugs with fewer negative impacts are intensively searched for. The first part of the thesis focuses on the study of cis-[Pt(NH3)2Cl2] (cisplatin, DDP) and four platinum potential anticancer agents PtCl2(diaminocyclohexane), PtCl2(NH3)(cyclohexylamine) (JM118), cis-[PtCl2(NH3)(piperidine)] and trans-[PtCl2(NH3)(thiazole)]. Thermodynamic and kinetic parameters of reac- tions of these complexes in semi-hydrated and fully-hydrated form with guanine were studied using QM methods. The reaction with guanine is the key process ini- tiating the anticancer activity. Analyses of electron density were performed at the B3LYP/6-311++G(2df,2pd) level of theory in IEF-PCM model. The second part of the thesis studies the reaction of the so-called 'piano stool' Ru(II) transition metal complex, [Ru(II)(η6 -p-cymene(nalidixic acid)(H2O)]2+ , first with guanine using QM methods and second with ds-DNA model using QM/MM methods. The reaction site, which is described by QM method, is two consecutive guanines and the Ru(II) complex. Analyses of thermodynamic and kinetic parameters, and electron density were performed at the B97D/6-31G* level of theory. All the...

L’hélium, deuxième élément le plus abondant de l’univers après l’hydrogène (He/H ~ 1/10), n’a étonnamment jamais été observé sous une autre forme que celle d'atomes neutres ou ionisés dans le milieu interstellaire (MIS). L’hélium étant un gaz noble peu réactif, sa non-observation au sein d’un édifice moléculaire neutre est compréhensible mais cela est plus surprenant pour des espèces chargées positivement comme HeH+, [HeH3]+ ou CHe2+. La première partie de cette thèse a pour but de proposer des raisons chimiques à cette non-observation à l’aide de calculs de chimie quantique de haut niveau (CASPT2) couplés à des calculs d’association radiative. Au vu des résultats sur les mécanismes de destruction de HeH+, nous suggérons une zone du MIS où il serait envisageable de le détecter.La seconde partie de ce travail porte sur la possibilité de détection de variations temporelles des constantes fondamentales de la physique. En 1999, Webb et al., après analyse de la lumière issue de quasars lointains, affirmèrent que la constante de structure fine α pouvait avoir été plus faible par le passé. Aucune étude postérieure ne vint confirmer ce résultat. Il était donc important de déterminer théoriquement dans quelle mesure une telle variation affecterait le spectre électronique de petites molécules primordiales afin d’en évaluer la détectabilité par les instruments actuels. Nous avons pour cela mis au point un protocole ab initio qui évalue le décalage spectral induit par une variation d’α. Les calculs (niveau MRCI) montrent qu’une variation d’α de l’ordre de grandeur de ce que Webb et al. auraient détecté induirait des déplacements de raies non décelables par les télescopes actuels. / Despite Helium is the second most abundant element in the Universe (He/H ~ 1/10), it has never been observed in any other forms than that of an atom or an ion in the InterStellar Medium (ISM). Since He is a noble gas, its non-observation as part of neutral molecular systems is understandable, but it is quite surprising for positively charged species like HeH+, [HeH3]+ or CHe2+. The first part of this study aims at finding a chemical reason for such a non-observation and in particular for the three ions mentioned above. For that purpose, we have computed high level quality (CASPT2) energy hyper-surfaces and performed radiative association calculations. Finally, we are able to suggest a region of the ISM where the detection of HeH+ might be achieved.The second part of this work deals with the possibility that the fundamental constants could be time-dependent. In 1999, Webb et al., analyzing the quasar emissions, claimed that the fine structure constant α could have been smaller in the past, but this result has not been confirmed. Thus it seemed necessary to determine theoretically how much such a variation could affect the electronic spectra of some primordial molecules in order to determine whether such variations might be detectable or not with the current observational instrumentation. For that purpose, we have developed an ab initio protocol to evaluate the shift induced by a variation of α. High level quantum chemistry calculations (MRCI) show that a variation of α of the same order of magnitude than that reported by Webb et al., would induce shifts that are not detectable by the current telescopes.

No description available.

L'objectif de ce travail de thèse est double : - Le développement et application de méthodes originales pour la chimie quantique ; - La mise au point de stratégies informatiques variées permettant la réalisation de simulations à grande échelle. Dans la première partie, les méthodes d'integration de configuration (IC) et monte carlo quantique (QMC) utilisées dans ce travail pour le calcul des propriétés quantiques sont présentées. Nous détaillerons en particulier la méthode d'\IC sélectionnée perturbativement (CISPI) que nous avons utilisée pour construire des fonctions d'onde d'essai pour le QMC. La première application concerne le calcul des énergies totales non-relativistes des atomes de transition de la série 3d ; ceci a nécessité l'implémentation de fonctions de base de type Slater et a permis d'obtenir les meilleures valeurs publiées à ce jour. La deuxième application concerne l'implémentation de pseudo-potentiels adaptés à notre approche QMC, avec pour application une étude concernant le calcul des énergies d'atomisation d'un ensemble de 55 molécules. La seconde partie traite des aspects calcule haute performance (HPC) avec pour objectif l'aide au déploiement des simulations à très grande échelle, aussi bien sous l'aspect informatique proprement dit - utilisation de paradigmes de programmation originaux, optimisation des processus monocœurs, calculs massivement parallèles sur grilles de calcul (supercalculateur et Cloud), outils d'aide au développement collaboratif \textit{et cætera} -, que sous l'aspect \emph{utilisateur} - installation, gestion des paramètres d'entrée et de sortie, interface graphique, interfaçage avec d'autres codes. L'implémentation de ces différents aspects dans nos codes-maison quantum pakcage et qmc=chem est également présentée. / This thesis work has two main objectives: 1. To develop and apply original electronic structure methods for quantum chemistry 2. To implement several computational strategies to achieve efficient large-scale computer simulations. In the first part, both the Configuration Interaction (CI) and the Quantum Monte Carlo (QMC) methods used in this work for calculating quantum properties are presented. We then describe more specifically the selected CI approach (so-called CIPSI approach, Configuration Interaction using a Perturbative Selection done Iteratively) that we used for building trial wavefunctions for QMC simulations. As a first application, we present the QMC calculation of the total non-relativistic energies of transition metal atoms of the 3d series. This work, which has required the implementation of Slater type basis functions in our codes, has led to the best values ever published for these atoms. We then present our original implementation of the pseudo-potentials for QMC and discuss the calculation of atomization energies for a benchmark set of 55 organic molecules. The second part is devoted to the Hight Performance Computing (HPC) aspects. The objective is to make possible and/or facilitate the deployment of very large-scale simulations. From the point of view of the developer it includes: The use of original programming paradigms, single-core optimization process, massively parallel calculations on grids (supercomputer and Cloud), development of collaborative tools , etc - and from the user's point of view: Improved code installation, management of the input/output parameters, GUI, interfacing with other codes, etc.