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In order to understand the behaviour and function of proteins, their three dimensional structure needs to be known. Determination of macro-molecules’ structures is done using X-ray diffraction or electron microscopy, where the resulting diffraction pattern is used for molecular reconstruction. These methods are however limited by radiation damage.The aim of this work is to study radiation damage of peptides in proteins using computer simulations. Increased understanding of the atomic and molecular dynamics can contribute to an improvement of the method ofimaging biological molecules. To be able to describe the processes that take place as accurately as possible, the problem must treated quantum mechanically.Thus, the simulations are performed with molecular dynamics based on first principles. In order to capture the dynamics of the excited states of the molecule when exposed to X-rays, time-dependent density functional theory with delta self-consistent field is used. These simulations are compared to ground state simulations. The results of the thesis conclude that the excited and ground state simulations result in differences in the dynamics, which are most pronounced for lager molecules.

Nesta tese de doutorado apresentamos os resultados de quatro tópicos referentes a estudos de propriedades elétricas que são interpretados com o auxílio da Teoria Quântica de Átomos em Moléculas (QTAIM). No primeiro deles, foram calculados momentos de dipolo e suas derivadas através de um novo formalismo de divisão de átomos em moléculas, baseado em campos de forças de Ehrenfest (CFE), sendo que estes dados são comparados com aqueles advindos da QTAIM. Desta forma, um modelo alternativo de partição em carga - fluxo de carga - fluxo de dipolo (CFCFD) é discutido para derivadas do momento dipolar. Os resultados gerais obtidos pelo formalismo CFE foram satisfatórios em termos quantitativos, embora QTAIM ainda fornece uma descrição mais apropriada destes fenômenos das polarizações atômicas e de suas variações durante vibrações. Na sequência, investigamos os Atratores Não Nucleares (NNAs), que são identificados através de uma análise QTAIM da densidade eletrônica. O nosso intuito foi descobrir novas moléculas que apresentam essa peculiaridade, bem como encontrar padrões entre os casos encontrados que permitam contribuir para o entendimento dos fatores que levam ao seu aparecimento. Para isso trabalhamos com moléculas diatômicas homonucleares de elementos representativos com números atômicos que variavam de Z=1 até Z=38 e moléculas heteronucleares formadas pela combinação dos mesmos. Os nossos dados mostram que NNAs podem ser encontrados em alguns pontos dentro da faixa de distâncias internucleares investigada para quase todos os sistemas diatômicos homonucleares, exceto para as moléculas de Hidrogênio, Hélio e Estrôncio. Por sua vez, encontramos trinta casos de NNAs em sistemas heteronucleares, muitos dos quais ainda inéditos na literatura. Descobrimos também que a polarizabilidade atômica aparentemente tem um papel importante na explicação dos casos encontrados. Tratamos também de moléculas contendo interações fracas como as de Van der Waals (moléculas tri-atômicas contendo um gás nobre ligado a um composto diatômico iônico) de modo a investigar os valores de dipolos atômicos QTAIM de uma maneira mais direta, ou seja, via comparação com um modelo simples para estes compostos. Por fim, estudamos moléculas em estados excitados, sendo que nossa análise focou em dois casos peculiares (CO e de CF2N2) que apresentam momento de dipolo nulo no estado fundamental, enquanto valores significativos desta propriedade são observados em seus primeiros estados excitados. Desta forma, QTAIM foi fundamental para compreender como o processo de excitação pode levar à mudanças tão significativas em tais propriedades elétricas. / In this PhD thesis we present the results of four different topics that refer to a study of electric properties interpreted with The Quantum Theory of Atoms and Molecules (QTAIM). First, dipole moments and their derivatives were calculated from a new formalism based on Ehrenfest Force Fields (EFF) and a comparison with data from QTAIM is carried out. Therefore, the Charge-Charge Flux-Dipole Flux (CCFDF) model was discussed for the dipole moment derivatives. The results from EFF were satisfactory in quantitative terms although QTAIM still seems to be better for the description of atomic polarization and its variations during vibrations. In the sequence, we investigated the Non-Nuclear Attractors (NNAs) that could be identified with the QTAIM formalism. Our intention was to discover new molecules that present this peculiarity, as well as to find trends among these cases that allow contributing for the understanding of the factors that lead to their appearance. For this purpose, we selected homonuclear diatomic molecules of elements presenting atomic numbers ranging from Z=1 to Z=38 and heteronuclear diatomic molecules containing these same elements. Our data shows that NNAs could be found in almost every homonuclear molecule expect by the systems formed by Hydrogen, Helium, and Strontium. On other hand, we have found 30 cases of NNAs in heteronuclear molecules, many of them seen for the first time. We also have noticed that the atomic polarizabilities play a main role in the understanding of these cases. We also treated molecules containing weak Van der Waals interactions (triatomic complexes presenting a noble gas bonded to a diatomic ionic molecule) in order to investigate the atomic dipole values obtained with QTAIM in a direct way, that is, by means of a comparison using a simple model for this kind of bonding. Finally, we studied molecules in excited states. Our focus was in two peculiar cases (CO and CF2N2), which present null dipole moments in their ground states but exhibit significant dipole moment values in their first excited states. Therefore, QTAIM was fundamental to understand how the excitation process can lead to important changes in electric properties.

Cette thèse s'intéresse à la rationalisation du mécanisme de transfert d'excitation dans des polyphénylènes éthynylènes (PPE). Une étude statique approfondie a été réalisée en utilisant la TDDFT, permettant de confirmer la localisation des états excités de méta-PPE sur des fragments para, ainsi que la hiérarchie des interactions régissant les propriétés photochimiques des PPE. Des intersections coniques ont été identifiées, de même que les principales composantes de l'espace de branchement. Leur étude a soutenu l'hypothèse d'un transfert d'énergie par conversion interne entre états excités localisés sur des fragments para.D'autre part, nous avons proposé un modèle vibronique multiéchelles pour l'énergie des états électroniques. En particulier, nous avons exprimé les énergies des orbitales frontières de PPE en fonction des énergies des orbitales frontières du benzène et de l'acetylène via un Hamiltonien effectif de type Hückel. Un travail de mapping et d'optimisation nous a permis d'aboutir à une expression pour l'énergie de transition électronique en fonction d'un nombre réduit de coordonnées nucléaires locales. / The present work is focused on the rationalization of the excitation transfer mechanism in polyphenylene ethynylenes (PPEs). A static study was performed using TDDFT, allowing to confirm both the localization of the excited states of meta-PPEs on para building blocks and the hierarchy in the interactions governing the photochemical properties of PPEs. Conical intersections were identified, along with few components of their branching spaces. Studying those supported the assumption of an energy transfer proceeding through internal conversion between excited states localized on different building blocks.In addition, we proposed a multiscale vibronic model for the energy of the eletronic states. In particular, we expressed the energies of the frontier orbitals of PPEs in terms of the energies of the frontier orbitals of benzene and acetylene, using an effective Hückel-type Hamiltonian. Perfoming different optimizations, we achieved to propose an expression for the energy of the electronic transition in terms of a reduced number of local nuclear coordinates.

<p>Quantum chemical methods have been used to provide a better understanding of the photochemistry of astaxanthin and phytochromobilin; the photoenzymic repair of UV-light induced DNA damages; and the formation of lignin. </p><p>The carotenoid astaxanthin (AXT) is responsible for the colouration of lobster shell. In solution, the electronic absorption spectra of AXT peak in the 470-490 nm region, corresponding to an orange-red colouration. Upon binding to the lobster-shell protein-complex α-crustacyanin, the absorption maximum is shifted to 632 nm, yielding a slate-blue colouration. Herein, the structural origin of this bathochromic shift is investigated on the basis of recent experimental work.</p><p>The tetrapyrrole phytochromobilin (PΦB) underlies the photoactivation of the plant photoreceptor phytochrome. Upon absorption of 660-nm light, PΦB isomerizes from a C15-<i>Z,syn</i> configuration (in the inactive form of the protein) to C15-<i>E,anti</i> (in the active form). In this work, a reaction mechanism for this isomerization is proposed. </p><p>DNA photolyases are enzymes that repair DNA damages resulting from far-UV-light induced [2+2] cycloaddition reactions involving pyrimidine nucleobases. The catalytic activity of these enzymes is initiated by near-UV and visible light, and is governed by electron transfer processes between a catalytic cofactor of the enzyme and the DNA lesions. Herein, an explanation for the experimental observation that the repair of cyclobutane pyrimidine dimers (CPD) – the major type of lesion – proceeds by electron transfer from the enzyme to the dimer is presented. Furthermore, the formation of CPD is studied.</p><p>Lignin is formed by dehydrogenative polymerization of hydroxycinnamyl alcohols. A detailed understanding of the polymerization mechanism and the factors controlling the outcome of the polymerization is, however, largely missing. Quantum chemical calculations on the initial dimerization step have been performed in order to gain some insight into these issues.</p>

Quantum chemical methods have been used to provide a better understanding of the photochemistry of astaxanthin and phytochromobilin; the photoenzymic repair of UV-light induced DNA damages; and the formation of lignin. The carotenoid astaxanthin (AXT) is responsible for the colouration of lobster shell. In solution, the electronic absorption spectra of AXT peak in the 470-490 nm region, corresponding to an orange-red colouration. Upon binding to the lobster-shell protein-complex α-crustacyanin, the absorption maximum is shifted to 632 nm, yielding a slate-blue colouration. Herein, the structural origin of this bathochromic shift is investigated on the basis of recent experimental work. The tetrapyrrole phytochromobilin (PΦB) underlies the photoactivation of the plant photoreceptor phytochrome. Upon absorption of 660-nm light, PΦB isomerizes from a C15-Z,syn configuration (in the inactive form of the protein) to C15-E,anti (in the active form). In this work, a reaction mechanism for this isomerization is proposed. DNA photolyases are enzymes that repair DNA damages resulting from far-UV-light induced [2+2] cycloaddition reactions involving pyrimidine nucleobases. The catalytic activity of these enzymes is initiated by near-UV and visible light, and is governed by electron transfer processes between a catalytic cofactor of the enzyme and the DNA lesions. Herein, an explanation for the experimental observation that the repair of cyclobutane pyrimidine dimers (CPD) – the major type of lesion – proceeds by electron transfer from the enzyme to the dimer is presented. Furthermore, the formation of CPD is studied. Lignin is formed by dehydrogenative polymerization of hydroxycinnamyl alcohols. A detailed understanding of the polymerization mechanism and the factors controlling the outcome of the polymerization is, however, largely missing. Quantum chemical calculations on the initial dimerization step have been performed in order to gain some insight into these issues.

Thesis (Ph.D.); Submitted to Univ. of California, Berkeley, CA (US); 1 Jun 2003. / Published through the Information Bridge: DOE Scientific and Technical Information. "LBNL--54350" Scielzo, Nicholas David. USDOE Director. Office of Science. Nuclear Physics (US) 06/01/2003. Report is also available in paper and microfiche from NTIS.

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Le but de cette thèse est la compréhension de pourquoi certains complexes de ruthénium sont soit pasluminescents soit avec un temps de vie très courte de l’état excité. Des calculs de type théorie de lafonctionnelle de la densité (DFT) ou DFT dépendante du temps (TD-DFT) étaient effectués pour cinqcomplexes existants et aussi pour un complexe hypothétique. Selon la théorie de champs de ligand (LFT),la plus proche sont les énergies des états de type transfert de charge métal-ligand (MLCT) à un état de typemétal centré (MC), alors le plus facile est-ce à peupler l’état MC ainsi menant à une dèsexcitation nonradiative de l’état MLCT. Les calculs DFT/TD-DFT s’avéraient suffisants pour reproduire les géométrieset spectres d’absorption expérimentales. Ceci, ensemble avec la technique de densité d’états partielle,permettaient une validation de l’idée fondamentale issue du modèle LFT en confrontant les résultats denos calculs avec les temps de vie mesurés. / Density-functional theory (DFT) and time-dependent DFT (TD-DFT) were carried out for 5 rutheniumcomplexes and one hypothetical one. The goal was to understand the lack of luminescence or very shortexcited state lifetimes at room temperature in some of them. According to ligand-field theory (LFT), thecloser the energies of the metal-to-ligand charge transfer (MLCT ) and the metal-centred (MC) states,the easier it is to populate the MC state, leading to radiationless disactivation of the luminescent MLCT.DFT/TD-DFT calculations proved adequate in reproducing experimental geometries and absorption spectra.Verification of LFT explanation was done by use of partial density of states whose results agreedreasonably well with the usual hypothesis.