Submitted by José Orlando Soares de Oliveira (orlando.soares@bol.com.br) on 2017-11-30T12:23:47Z No. of bitstreams: 1 2017_tese_acvmartins.pdf: 10270409 bytes, checksum: f2b0eb40db54875e0e40a6d040ce7336 (MD5) / Rejected by Weslayne Nunes de Sales (weslaynesales@ufc.br), reason: A aluna optou por publicar apenas os elementos pré-textuais. on 2017-12-01T12:36:51Z (GMT) / Submitted by José Orlando Soares de Oliveira (orlando.soares@bol.com.br) on 2017-12-01T13:50:35Z No. of bitstreams: 1 Tese corrigida - elementos pretextuais.pdf: 159585 bytes, checksum: 9531b29bc8c5a46f5ed5753442df383f (MD5) / Approved for entry into archive by Weslayne Nunes de Sales (weslaynesales@ufc.br) on 2017-12-01T13:57:30Z (GMT) No. of bitstreams: 1 Tese corrigida - elementos pretextuais.pdf: 159585 bytes, checksum: 9531b29bc8c5a46f5ed5753442df383f (MD5) / Made available in DSpace on 2017-12-01T13:57:30Z (GMT). No. of bitstreams: 1 Tese corrigida - elementos pretextuais.pdf: 159585 bytes, checksum: 9531b29bc8c5a46f5ed5753442df383f (MD5) Previous issue date: 2017-11-17 / Glutamate receptors are the mediators of most excitatory neurotransmission processes in the central nervous system, acting as prominent targets for the treatment of several neurological disorders such as Epilepsy, Amyotrophic Lateral Sclerosis, Parkinson’s disease and Alzheimer’s disease. Hence an improved understanding of how glutamate and other ligands interact with the binding domain, of these receptors, can bring relevant insights to the development of new ligands. Therefore, this work aims to study the GluA2–ligand interaction using the structure of GluA2 co-crystallized with the ligands glutamate, AMPA, kainate and DNQX applying a method based on the Density Functional Theory combined with the molecular fractionation with conjugate caps scheme. To address that the dielectric constant of the GluA2 receptor is not homogeneous, a novel molecular approach was proposed and it was applied to study the interaction between the GluA2 and the ligands glutamate, AMPA, kainate and DNQX. The results obtained, considering the inhomogeneous model, were compared with those obtained using an uniform dielectric function for the GluA2 receptor and with data published in the literature establishing a more detailed description of the relevant amino acid residues for the protein-ligand binding interaction. Molecular dynamics studies and protein DFT calculations usually consider a fixed value for the protein dielectric function. In this work when ε = 1 is considered, many amino acid residues seem important, but when the dielectric constant shield was considered, they lost their relevance. The results for the GluA2-ligand total interaction energy and the D1-ligand and D2-ligand total interaction energy also shed some light on the differentiation between full and partial agonists, and between agonists and antagonists. Additionally, the results allow a hypothesis on the correlation between the Glu705-ligand interaction energy and the ligand action, paving the way for the use of the inhomogeneous dielectric function to study glutamate receptors and other protein-ligand systems. Finally, the results also suggests that for different ligands, different homogeneous dielectric constant will be able to well represent the system GluA2-ligand, making it necessary the previous analyses with the inhomogeneous dielectric constant approach. / Os receptores de glutamato são os mediadores da maioria dos processos de neurotransmissão excitatória no sistema nervoso central, atuando como alvos proeminentes para o tratamento de vários distúrbios neurológicos, como Epilepsia, Esclerose Lateral Amiotrófica, Doença de Parkinson e Doença de Alzheimer. Assim, uma compreensão aprimorada de como o glutamato e outros ligantes interagem com o domínio de interação, desses receptores, pode trazer informações relevantes para o desenvolvimento de novos ligantes. Portanto, este trabalho teve por objetivo estudar a interação GluA2-ligante utilizando a estrutura de GluA2 co-cristalizada com os ligantes Glutamato, AMPA, Cainato e DNQX utilizando método baseado na Teoria do Funcional da Densidade combinado com o esquema de fracionamento molecular com capas conjugadas. Para abordar que a constante dielétrica do receptor GluA2 não é homogênea, foi proposta uma nova abordagem molecular, que foi aplicada para estudar a interação entre a GluA2 e os ligantes Glutamato, AMPA, Cainato e DNQX. Os resultados obtidos, considerando o modelo não-homogêneo, foram comparados com aqueles obtidos usando uma função dielétrica uniforme para o receptor GluA2 e com dados publicados na literatura, estabelecendo uma descrição mais detalhada dos resíduos de aminoácido mais relevantes para a interação proteína-ligante. Estudos de dinâmica molecular e cálculos DFT de sistemas proteicos normalmente consideram um valor fixo para a função dielétrica proteica. Nesse trabalho quando ε = 1 é considerado, muitos resíduos de aminoácido parecem relevantes, mas quando a blindagem da constante dielétrica foi considerada, eles perderam sua relevância. Os resultados apresentados para a energia de interação total GluA2-ligante e a energia de interação total D1-ligante e D2-ligante contribuiu com a diferenciação entre agonistas totais e agonistas parciais e entre agonistas e antagonistas. Além disso, os resultados permitem que seja feita hipótese sobre a correlação entre a energia de interação Glu705-ligante e a ação do ligante, abrindo caminho para o uso da função dielétrica não-homogênea para estudar receptores de glutamato e outros sistemas proteína-ligante. Por fim, os resultados também sugerem que para diferentes ligantes, diferentes constantes dielétricas homogêneas serão capazes de representar bem o sistema GluA2-ligante, tornando necessária a análise prévia com a abordagem da constante dielétrica não-homogênea.

AGUIAR, Acrísio Lins de. Estudo da interação da Benzonitrila com Nanoestruturas de Carbono (Nanotubos, Grafeno e Fulereno). 2008. 135 f. Dissertação (Mestrado em Física) - Programa de Pós-Graduação em Física, Departamento de Física, Centro de Ciências, Universidade Federal do Ceará, Fortaleza, 2008. / Submitted by Edvander Pires (edvanderpires@gmail.com) on 2015-05-29T19:16:59Z No. of bitstreams: 1 2008_dis_alaguiar.pdf: 6438622 bytes, checksum: 91506d6f271c3401e1e9063cd09af8fb (MD5) / Approved for entry into archive by Edvander Pires(edvanderpires@gmail.com) on 2015-05-29T19:29:20Z (GMT) No. of bitstreams: 1 2008_dis_alaguiar.pdf: 6438622 bytes, checksum: 91506d6f271c3401e1e9063cd09af8fb (MD5) / Made available in DSpace on 2015-05-29T19:29:20Z (GMT). No. of bitstreams: 1 2008_dis_alaguiar.pdf: 6438622 bytes, checksum: 91506d6f271c3401e1e9063cd09af8fb (MD5) Previous issue date: 2008 / Neste trabalho realizamos cálculos de primeiros princípios da interação da benzonitrila (uma típica base de Lewis) com várias nanoestruturas de carbono: Nanotubos de Carbono de Parede Simples, Grafeno e Fulerenos. Utilizamos de algumas modificações químicas tais como dopagens e modificações estruturais tais como a introdução de defeitos visando analisar possíveis modificações em nível eletrônico nestas estruturas de carbono. Os cálculos ab initio são baseados na teoria do funcional da densidade dentro das aproximações da densidade local (LDA) e do gradiente da densidade para o termo de troca e correlação. Os cálculos de energia total, com ou sem polarização de spin, foram realizados utilizando o código SIESTA, o qual têm se mostrado bastante eficiente nos cálculos de primeiros princípios. Os cálculos mostraram que a benzonitrila interage fracamente com nanotubos de carbono puros. A interação é relativamente mais forte via interação entre os anéis aromáticos ($pi-pi$) do que via o grupo nitrila ($pi$-CN). Este comportamento é praticamente o mesmo quando modificamos os nanotubos de carbono através de um defeito (retirada de um átomo de carbono) significando que os defeitos não promovem a interação com a benzonitrila. Os cálculos com grafeno mostraram uma interação relativamente mais forte via interação $pi-pi$ do que em nanotubos de carbono. Cálculos com o fulereno C60 puro também mostraram que a interação da benzonitrila é fraca com essas moléculas. A interação torna-se mais intensa no que diz respeito à transferência de carga e grandes modificações na estrutura eletrônica quando introduzimos um átomo de Ferro nas paredes dos Nanotubos de Carbono e dos Fulerenos. As previsões teóricas são suportadas por experimentos espectroscópios realizados em amostram de nanotubos de carbono colocadas em contato com a benzonitrila comfirmando que a benzonitrila não altera significativamente as propriedades dos nanotubos de carbono. Imagens de microscopia eletrônica revelam que a benzonitrila interage mais fortemente com partículas catalíticas e com nanopartículas de carbono do que propriamente com Nanotubos de Carbono. Experimentos óticos (Infravermelho, Raman, Absorção e Emissão) também revelam que a benzonitrila pouco interage com Nanotubos de Carbono purificados.

PIRES, Marcelo da Silva. Dinâmica molecular e cálculos ab initio em moléculas, nanocones de carbono e agregados de água. 2009. 95 f. Dissertação (Mestrado em Física) - Programa de Pós-Graduação em Física, Departamento de Física, Centro de Ciências, Universidade Federal do Ceará, Fortaleza, 2009. / Submitted by Edvander Pires (edvanderpires@gmail.com) on 2015-06-23T20:42:04Z No. of bitstreams: 1 2009_dis_mspires.pdf: 6865198 bytes, checksum: 5e8a1e933acef9d9453a7b24155a31de (MD5) / Approved for entry into archive by Edvander Pires(edvanderpires@gmail.com) on 2015-06-23T21:05:27Z (GMT) No. of bitstreams: 1 2009_dis_mspires.pdf: 6865198 bytes, checksum: 5e8a1e933acef9d9453a7b24155a31de (MD5) / Made available in DSpace on 2015-06-23T21:05:27Z (GMT). No. of bitstreams: 1 2009_dis_mspires.pdf: 6865198 bytes, checksum: 5e8a1e933acef9d9453a7b24155a31de (MD5) Previous issue date: 2009 / A presente dissertação insere-se no escopo da Nanociência e da Nanotecnologia, que têm como objeto de estudo são sistemas (nanoestruturas, nanopartículas, nanoagregados, etc.) com dimensões características no intervalo 1{100 nm (1nm = 10ºA). Nela sao investigadas: (a) propriedades estruturais de nanocestas moleculares de carbono e sua interação com o aminoácido L-alanina; (b) a interação entre nanocones de carbono anin- hados; e (c) a transição estrutural dependente da temperatura de agregados de água. Os nanosistemas foram estudados através de Dinâmica Molecular, que permite o estudo de sistemas com cerca até milhões de átomos, e da Teoria do Funcional da Densidade, que permite a obtenção das propriedades do estado fundamental de sistemas com até centenas de ¶atomos. No estudo das nanocestas de carbono C20-coranuleno, C30-hemifulereno, C35- hemifulereno e C36-triacenaftotrifenileno, obteve-se que as mesmas s~ao est¶aveis a temper- aturas elevadas, e demonstrou-se a capacidade das mesmas de servirem como armadilhas para o amino¶acido L-alanina, como efeito da mistura dos orbitais ¼ e ¾ nestas estruturas produzida pela curvatura. Nanocones de carbono s~ao estruturas c^onicas de carbono ob- servadas durante o processo de s¶³ntese de nanotubos de carbono, existindo com ^angulos de abertura 19:2 ±, 38:9 ±, 60:0 ±, 83:6 ±, e 112:9 ±. Experimentalmente estes nanocones encontram-se, em geral, aninhados. Para pares de nanocones de carbono aninhados, obteve-se a depend^encia do potencial de intera»c~ao entre os mesmos com o ^angulo ddas pontas e o n¶umero de ¶atomos de carbono. Finalmente, obteve-se que a intera»c~ao entre mol¶eculas de ¶agua atrav¶es de liga»c~oes de hidrog^enio d¶a origem a agregados estáveis de água: dímeros , trímeros, tetrâmeros, pentâmeros, hexâmeros, etc. quando formados por duas, três, quatro, cinco e seis moléculas de água, respectivamente. Para estes agregados, foi obtido o potencial de interação entre duas camadas empilhadas, e demonstrou-se uma surpreendente transição de fase de dois trímeros empilhados para um hexâmero, de quatro trímeros empilhados para dois hexâmeros, e também de três tetrâmeros empilhados para dois hexâmeros. As pesquisas realizadas enquadram-se na temática de atuação do In- stituto de NanoBioEstruturas & Simulação NanoBioMolecular [NANO(BIO)SIMES], um dos Institutos Nacionais de Ciência e Tecnologia financiados pelo CNPq a partir do início de 2009, que visa desenvolver atividades de pesquisa e formação de recursos humanos de alto nível em nanobioestruturas e simulação nanobiomolecular.

Le travail de cette thèse porte sur l’étude à l’échelle atomique des molécules de Cycloparaphénylènes ([n]CPPs) et leurs dérivés, par modélisation ab initio (calculs par DFT/LDA). La première étude a été de regarder la stabilité de ces anneaux lors de leurs fonctionnalisations par des halogènes et les changements structuraux induits. La notion importante d’énergie de courbure a été soulevée pour trouver de nouvelles routes de synthèse. L’encapsulation de fullerène C60 à l’intérieur des [10]CPPs est une part très importante de cette thèse, avec plus particulièrement l’interaction entre le dimère d’azafullerène (C59N)2 et deux [10]CPPs. Les interactions supramoléculaires et l’alignement de deux [10]CPPs sur ce dimère ont été regardés théoriquement mais aussi expérimentalement grâce à une collaboration avec deux équipes de recherches en Allemagne et en Grèce. La possibilité d’alignement des [10]CPPs a conduit à l’étude de la fonctionnalisation de ces molécules dans le but de les connecter avec différents ponts de type aromatique, polymère ou métallique pour former une nouvelle famille de pseudo-nanotubes composé de [10]CPPs connectés. Selon les connexions utilisées, les propriétés de conduction des pseudo-nanotubes varient de semi-conducteur à large gap jusqu’à des structures métalliques. Dans ce manuscrit, les interactions entre les [n]CPPs et les nanotubes de carbone ont été étudiés pour former des structures où le [n]CPP interagit à l’intérieur ou autour du nanotube de carbone. Dans ce cadre, l’étude de la rotation du [n]CPP montre une très faible force de frottement et permet ainsi de prévoir une rotation ultra rapide du CPP. / The work in this thesis concerns the study at the atomic scale of Cycloparaphenylene ([n]CPP) molecules and their complexes and derivatives, using ab initio modeling methods (DFT/LDA). I initially look at the stability of these molecular rings when functionalized by halogens, and the structural changes induced. The important notion of curvature energy is raised to find new synthesis routes. The encapsulation of C60 fullerene inside [10]CPPs is a very important part of this work and more particularly the interaction between the azafullerene dimer (C59N)2 and two [10]CPPs. This allowed us to look at supramolecular interactions and the alignment of two [10]CPPs on this dimer both theoretically and experimentally, through collaboration with research teams in Germany and Greece. The possibility of templated alignment of [10]CPPs leads to a study on the functionalization of these molecules with the aim of connecting them together with various connectors, for example with aromatic species, polymers or metals to form a new family of pseudo-nanotubes composed of multiply inter-linked [10]CPPs. Depending on the connections used, the conduction properties of the 'pseudo-nanotubes' can vary from wide-gap semiconductors to metallic structures. I also show in this manuscript, that [n]CPPs and carbon nanotubes can interact to form structures where the ring is encapsulated inside or around the carbon nanotube. In this context, the study of the rotation of cycloparaphenylene demonstrate a very low frictional force and thus predict ultra-rapid CPP rotation.

Submitted by ANA KARLA PEREIRA RODRIGUES (anakarla_@hotmail.com) on 2017-08-02T12:48:15Z No. of bitstreams: 1 arquivototal.pdf: 9118352 bytes, checksum: 10cb4965cf17b6691c55ca0de741b9d2 (MD5) / Made available in DSpace on 2017-08-02T12:48:15Z (GMT). No. of bitstreams: 1 arquivototal.pdf: 9118352 bytes, checksum: 10cb4965cf17b6691c55ca0de741b9d2 (MD5) Previous issue date: 2016-09-30 / Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq / This work deals with the computational quantum study of structural, electronic, vibrational, hyperconjugative and topological of hydrogen complexes with Cl3CH and F3CH donors, with the aceptor species proton, C2H2, C2H4, C3H4, C3H6 and C4H4, interacting with a region high electron density of the type π and pseudo-π. The computational methods used electronic structure were Density Functional Theory with functional hybrids B3LYP and X3LYP with Perturbative and Theory of many bodies of order 2, with a series of bases. The amounts of hydrogen bond energy suffered superposition error corrections of the Basic Feature Set and Vibrational Zero Point Energy. The complexes of hydrogen with the donor Cl3CH showed increases in the length of the C-H bond, while the present F3CH shortening of the C-H bond length due to formation of intermolecular bond. This trend is found for the deviation in the infrared spectrum, Chloroform has red shift while Fluoroform has blue shift deviations. The use of quantum theory of atoms in molecules shows the change in electron density of both interacting species, and in addition the density values are small and the Laplacian are positive. The methods followed the same trend for the properties of interest, suggesting the use of calculations via density functional theory, due to lower computational demand to study such systems. / Este trabalho trata do estudo quântico computacional de propriedades estruturais, eletrônicas, vibracionais, hiperconjugativas e topológicas dos complexos de hidrogênio com doadores Cl3CH e F3CH, com as espécies receptoras de próton, C2H2, C2H4, C3H4, C3H6 e C4H4, interagindo com uma região de alta densidade eletrônica do tipo π e pseudo- π. Os métodos computacionais de estrutura eletrônica empregados foram a Teoria do Funcional da Densidade com os funcionais híbridos B3LYP e X3LYP e a Teoria Perturbativa de Muitos Corpos de ordem 2, com uma série de bases. Os valores da energia da ligação de hidrogênio sofreram correções do Erro de Superposição do Conjunto de Funções de Base e da Energia Vibracional do Ponto Zero. Os complexos de hidrogênio com o doador Cl3CH apresentaram incrementos no comprimento da ligação C-H, enquanto o F3CH apresentam encurtamento do comprimento de ligação H-C, devido a formação da ligação intermolecular. Essa tendência é encontrada para o desvio no espectro infravermelho, o Clorofórmio apresenta red shift enquanto o Fluorfórmio tem desvios blue shift. O emprego da teoria quântica de átomos em moléculas evidencia a mudança na densidade eletrônica de ambas as espécies interagentes, e, além disso os valores da densidade são pequenos e do laplaciano da densidade são positivos. Os métodos empregados seguiram a mesma tendência para as propriedades de interesse, sugerindo o uso de cálculos via teoria do funcional da densidade, devido a menor demanda computacional, para estudar sistemas desse tipo. Palavras-Chave: Ligação de Hidrogênio Intermolecular, DFT/B3LYP, DFT/X3LYP, MP2 e QTAIM.

Conselho Nacional de Desenvolvimento CientÃfico e TecnolÃgico / A atividade citotÃxica e bactericida do extrato de alho, em trÃs linhagens de cÃlulas tumorais (HCT-166, SF-295 e OVCAR-8) e em quatro culturas de bactÃrias: duas gram-positivas (Staphylococcus aureus ATCC 25923 e Staphylococcus epidermidis ATCC 12228) e duas gram-negativas (Pseudomonas aeruginosa ATCC 9027 e Escherichia coli ATCC 11303), foi investigada neste trabalho. Visando melhorar a biodisponibilidade e o direcionamento destes nutracÃuticos para cÃlulas alvo (tumores ou bactÃrias), um sistema de liberaÃÃo de fÃrmacos baseado na adsorÃÃo do extrato de alho em micropartÃculas de carbonato de cÃlcio foi desenvolvido. Adicionalmente, simulaÃÃes computacionais no formalismo DFT (Density Functional Theory) foram realizadas para a determinaÃÃo das propriedades estruturais e vibracionais de duas molÃculas, alliina e metiina, presentes neste extrato aquoso. A molÃcula de alliina, espÃcie de maior concentraÃÃo no extrato aquoso utilizado, foi usada como modelo teÃrico para cÃlculos de potenciais de interaÃÃo do extrato de alho e das micropartÃculas de carbonato de cÃlcio. Os cÃdigos GAUSSIAN, Forcite e Dmol3, assim como o funcional meta-hÃbrido M06-2X e o funcional puro GGA na sua formulaÃÃo BPE foram usados nas simulaÃÃes. Os espectros vibracionais obtidos para a molÃcula de alliina revelaram intensas absorÃÃes em: 1637, 1592, 1519, 1430, 1397, 1390, 1357 1018, 544 cm-1 na regiÃo do infravermelho, principalmente associadas a vibraÃÃes dos grupos carboxila, amino e sulfÃxido, e em: 1643, 1429, 1404, 1316, 1297, 1207, 790, 744, 693, 588, 503 cm-1 no espectro Raman, associados a vibraÃÃes da cadeia carbÃnica. O espectro na regiÃo do infravermelho da molÃcula de metiina à semelhante ao da alliina, porÃm, seu espectro Raman revela bandas de absorÃÃo que podem diferenciar as duas espÃcies, principalmente a ausÃncia do pico observado em 1643 cm-1 reverente ao grupo alila. Os espectros vibracionais teÃricos calculados indicam uma Ãtima correlaÃÃo com os espectros experimentais obtidos, tanto paras molÃculas puras como para o extrato produzido em laboratÃrio. Os cÃlculos de potenciais de interaÃÃo sugerem a adsorÃÃo dos nutracÃuticos em pelo menos quatro camadas de solvataÃÃo em torno das micropartÃculas de carbonato de cÃlcio, o que promove sua lenta liberaÃÃo, elevando sua biodisponibilidade. Os testes de citotoxicidade revelaram inibiÃÃo do crescimento tumoral de cerca de 93%, nas as trÃs linhagens de cÃlulas tumorais, e atividade bactericida nas duas colÃnias de bactÃrias gram-positivas estudadas, o que comprovou o efeito sinergÃtico do extrato de alho com o carbonato de cÃlcio e sua eficÃcia como sistema de liberaÃÃo de nutracÃuticos. Estes resultados demonstram o potencial de aplicaÃÃo na prÃtica farmacÃutica do uso de micropartÃculas de carbonato de cÃlcio modificadas com extrato de alho para combate a cÃlulas tumorais e a aÃÃes bactericidas / The cytotoxic and bactericidal activities of garlic extract were tested in three tumor cell lines (HCT-166, SF-295 e OVCAR-8) and four bacteria cultures: two gram-positives (Staphylococcus aureus ATCC 25923 and Staphylococcus epidermidis ATCC 12228) and two gram-negatives (Pseudomonas aeruginosa ATCC 9027 e Escherichia coli ATCC 11303). Aiming to improve the bioavailability and cell targeting (tumor or bacteria) of these nutraceuticals, a drug delivery system based on the adsorption of garlic extract on calcium carbonate microparticles was developed. Additionally, computer simulations within the Density Functional Theory (DFT) formalism were accomplished to find the structural and vibrational properties of two molecules, alliin and methiin, present in garlic extract. alliin the highest concentration specie present in garlic extract was used as theoretical model to represent the garlic extract on the potential interaction calculations with calcium carbonate microparticles. The computer codes GAUSSIAN, Forcite and Dmol3, with the Meta hybrid M06-2X and the pure GGA-PBE Exchange-correlation functional were used to implement the computations. The vibrational spectra recorded for the alliin unveiled intense absorption peaks at: 1637, 1592, 1519, 1430, 1397, 1390, 1357 1018, 544 cm-1 on IR spectrum, mainly assigned to the carboxyl, amine and sulfoxide groups vibrations, and at 1643, 1429, 1404, 1316, 1297, 1207, 790, 744, 693, 588, 503 cm-1 on Raman spectrum, associated to the carbon chain vibrations. The methiin IR spectrum is similar to alliinâs, but, its Raman spectrum unveiled absorption bands which may differentiate both molecules, mainly for the absence of the absorption peak observed at 1643 cm-1 , ascribed to the allyl group vibration. The calculated theoretical vibrational spectra showed a good agreement with the experimental data. The interaction potential calculations suggests the adsorption of at least four solvation layers of the nutraceuticals around the calcium carbonate microparticles, this fact allow the slowly release of the species, preserving its bioavailability. The cytotoxicity tests showed tumor cells growth inhibition of 93% for the three tumor cell line studied, and bactericidal activity on gram-positives bacteria cell cultures, which proved the synergetic effect of garlic extract with calcium carbonate and its efficacy as drug delivery system. Those results shows the application potential of the calcium carbonate microparticles modified with garlic extract on the treatment of cancer and as antibacterial agent.

Nos travaux sont consacrés à la promotion du modèle de percolation phénoménologique en employant des méthodes indépendantes et libres de tout paramètre. Nous avons utilisé à cet effet des codes ab initio existants (PWscf et SIESTA) et développé une méthode semi-empirique pour étudier les propriétés vibrationnelles des alliages AxB1 xC. Les paramètres techniques du code PWscf ont été testés sur les composés binaires ZnSe, ZnTe et BeSe pour lesquels nous avons confronté nos résultats aux données expérimentales et théoriques disponibles. La validation du modèle de percolation a et e effectué sur l alliage Zn(Se,Te) appartenant à la catégorie des semi-conducteurs 1-liaison ! 2-modes. Nous avons confirmé le caractère général du comportement bimodal prévu par le modèle de percolation en montrant son existence pour chacune des liaisons Zn Se et Zn Te. Les propriétés vibrationnelles et structurales de Zn(Se,Te) ont et e calculées à différentes concentrations avec des cellules optimisées à 64 atomes. Les résultats obtenus sont en bon accord avec l expérience. Nous présentons en détail notre méthode semi-empirique de calcul de spectre de phonons, applicable en principe à tous les alliages sans restriction sur la taille des super-cellules. La mise au point a été réalisé sur les alliages (Zn,Be)Se et (In,Ga)As avec des cellules à64 atomes relaxées d une façon ab initio. L application de notre méthode à(In,Ga)As à 50% simulé par une super-cellule à 8.103 atomes relaxée avec un potentiel harmonique met en évidence que l étude des phonons demande des super-cellules qui reflètent fidèlement le désordre d un alliage / Our work is devoted to promoting the percolation model using phenomenological methods which are independent and free from any need of external parameters. We used for this purpose existing ab initio codes (PWscf and SIESTA) and developed a semiempirical method to study the vibrational properties of AxB1 xC alloys. The technical parameters of the PWscf code were tested on ZnSe, BeSe ZnTe binary compounds, for which we have confronted our results with theoretical and experimental data available. The percolation model validation was done on the alloy Zn(Se, Te) belonging to the category of 1-bond ! 2-modes semi-conductors. We have confirmed the general bimodal behavior provided by the percolation model showing its existence for each bond Zn Se and Zn Te. The vibrational and structural properties of Zn(Se, Te) were calculated for different concentration using optimized cells of 64 atoms. The results are in good agreement with experiments. We present in detail our semi empirical method of calculating the spectrum of phonons, in principle applicable to all alloys without restriction on the size of super-cells. The development was carried out on (Zn, Be)Se and (In, Ga)As alloys with cells of up to 64 atoms relaxed from first principles. The application of our method to (In, Ga)As at 50% simulated by a super-cell of 8.103 atoms with a harmonic relaxation potential underlines the fact that the study of phonons in alloys requires the use of supercells which adequately describe the alloy disorder

Concernant la recherche sur les semiconducteurs, la substitution isovalente sur un sous-réseau, qu’il soit cationique ou anionique, permet d’ajuster les paramètres de structure de maille et les propriétés électroniques ou élastiques. La pression hydrostatique externe peut augmenter ou inhiber les effets produits par cette substitution, et, en tout cas, offre un degré de liberté supplémentaire pour varier, ou sonder, les propriétés des semiconducteurs. Par ailleurs, la pression extérieure peut induire une s´séquence de transitions structurales de phase, qui à leur tour peuvent induire une modification de la structure de bande et des propriétés de dynamique du réseau inhabituelles. Puisque les énergies des phases en présence ainsi que les constantes de force sont des propriétés que relèvent de l’état fondamental, elles peuvent être obtenues de manière fiable à partir de calculs “premiers principes” effectués au sein de la théorie de la fonctionnelle de la densité (DFT). Le présent travail concerne de telles études d’ordre théorique, réalisées avec diverses méthodes de calcul, qui sont, en partie, complémentaires. L’analyse comparative des phases en compétition dans les composés purs ZnS et ZnSe sous pression hydrostatique, réalisée en utilisant la méthode de calcul de haute précision APW+lo (mise en oeuvre dans le logiciel WIEN2k), a permis de préciser la s´séquence des transitions de phase induites sous pression extérieure et de résoudre certaines controverses théoriques, liées à l’utilisation de schémas différents d’échange-corrélation. Le calcul des dispersions des phonons dans l’un des dits composés (ZnSe) sous pression, effectué dans le cadre du formalisme de la réponse linéaire via le code abinit, a permis d’identifier les instabilités dynamiques associées au “ramollissement” des modes acoustiques dans certaines parties de la zone de Brillouin, correspondant au pressentiment d’une transition de phase. Les spectres de vibration sous pression ont ensuite été simulés dans un système mixte, en l’occurrence (Zn,Be)Se, en utilisant la méthode des "phonons gelés" et le code Siesta. Enfin, la stabilité thermodynamique des phases en compétition, zincblende et wurtzite, du semiconducteur mixte Cd(S,Se) a été étudiée en utilisant le logiciel VASP selon la méthode du pseudopotentiel, en combinaison avec le formalisme des structures quasi aléatoires spéciales (SQS) permettant de représenter efficacement le caractère désordonné des phases considérées. Il a été possible, sur cette base, de réaliser la caractérisation structurale complète, et de discuter le diagramme de phase température–concentration / In semiconductor research, an isovalent substitution on a sublattice, either cationic or anionic one, is a convenient tool to tune lattice parameters, electronic or elastic properties. External hydrostatic pressure is another such tool, which may either enhance or inhibit the effects of alloying, and in any case offers an additional “coordinate” for scanning and probing the properties of semiconductors. Moreover, external pressure may induce a sequence of structural phase transitions, which in their turn may result in unusual band structures and lattice-dynamical properties. As energies of different phases (needed to construct phase diagrams) and force constants (responsible for vibrational spectra in crystals) are groundstate properties, they can be reliably obtained from first-principles calculations done within the density functional theory (DFT). The present work outlines such studies realized with different and, in part, complementary calculation methods. Comparative analysis of possible phases of pure ZnS and ZnSe compounds under hydrostatic pressure, done using a highly precision APW+lo method (realized in the WIEN2k code), helped to refine the sequence of pressure-induced phase transitions and to resolve some earlier controversies in theory works, related to the use of different exchange-correlation schemes. The calculation of phonon dispersions in the same compounds under pressure, done in linear-response formalism (abinit code), helped to identify dynamical instabilities associated with softening of acoustic modes in some parts of the Brillouin zone, indicating precursors of phase transition. The vibrational spectra under pressure were then subject to study under alloying, in the (Zn,Be)Se system; calculations done using the frozenphonon method as employed in Siesta code. The thermodynamic stability of the known competing phases (zincblende and wurtzite), in the alloy Cd(S,Se), is investigated using pseudopotential method (VASP), where the special quasirandom structures (SQS) formalism is employed to efficiently represent the disorder of the considered phases. On this basis, it became possible to give full structural characterization, and to discuss the temperature-concentration phase diagram

Iron containing metalloenzymes are an extremely important class of biocatalysts conserved throughout evolution because of their vital role in the biochemistry of life. Here we discuss a specific class of these enzymes that use molecular oxygen binding to enable there activity. We also attempt to describe synthetic analogues whose chemistry is based on that seen in those natural systems. This dissertation will highlight how computational research can illuminate specific aspects of the reaction mechanisms that these systems catalyse, which in many cases are unable to be understood purely experimentally. We report on two combined QM/MM and density functional theory (DFT) projects, which describe the AlkB demethylation enzyme and the SyrB2 halogenase; both highlight the strengths and weaknesses of each method. Our DFT work on an i-propyl-bis(imino)pyridine, an equatorial tridentate ligand, developed by one of the papers’ co-authors (Badiei, Siegler et al. 2011) exampifies superoxo chemistry based on the dioxygenases. Our other projects focus on monooxygenase catalysed chemistry one based on the biomimic [FeIV(O)(TPA)Cl]+ reports on a halogenase mimic that shows exciting chemoselectivity in halogenation vs. hydroxylation. I also report on publications examining two other biomimetic ligands. A imido-bridged diiron-oxo phtalocyanine complex capable of hydroxylating methane and a nonheme iron system which gives us a good deal of insight into the effects of secondary coordination sphere chemistry [FeII(N4Py2Ph)(NCCH3)](BF4)2. My computational studies have given insight into the chemical properties of metal-oxo oxidants and their reactivity patterns with substrate and have been utilized to explain experimentally observed data.

The diversity of transition metal complexes allows for a wide range of chemical processes to be mediated by the metal, from catalysis to surface chemistry. Investigations into the structure and electronic configuration of transition metal complexes allow for tuning of desired species by modifications to the ligands and/or metals to achieve more efficient thermodynamics and kinetics for the process of interest. Transition metals, often used in catalysts for a number of important processes, require detailed descriptions of intermediates, transition states and products to fully characterize a reaction mechanism(s) in order to design more active and efficient catalysts. Computational investigations into inorganic catalysts are explored with the aim of understanding the activity of each species and how modifications of supporting ligands, co-ligands and metals vary the interaction along the reaction pathway. Reported results give important insight into the development of the most active complexes in addition to determining the least active complexes to aid experimental development. This report first investigates the mechanisms of two unique transfer reactions: 1) formation of low coordinate nickel-nitrene ((P~P)Ni=NR; P~P = 1,2-bis(dihydrophosphino)-ethane or 1,2-bis(difluoromethylphosphino)-ethane) complexes as catalysts for nitrogen atom transfer and 2) oxidation of a triphosphorus niobium complex, [(η2-P3SnPh3)Nb(OMe)3], for the transfer of the phosphorus synthon, Ph3SnP3. These reactions have utility in the synthesis of nitrogen and phosphorus containing molecules, respectively, and the results presented provide mechanistic insight into the synthesis of the organometallic intermediates. Additionally, a computational approach towards rational catalyst design was performed on the ruthenium based hydroarylation catalyst TpRu(CO)(Ph) [Tp = hydrido-tris(pyrazolyl)borate]. Targeted modifications at the Tp, metal and co-ligand (CO) sites were studied in order to tune the electronics and sterics of the catalyst. Modifications, through computational methods, provided a more cost- and time-efficient way to study the impact of modifications, which provided direct input into attractive synthetic targets. The research described heir in highlights the use of computational chemistry methodologies, specifically DFT, in collaboration with experimental results, for the accurate description of reaction geometries and factors influencing the thermodynamics and kinetics of the systems. Valuable insight is gained by treating inorganic complexes with theoretical methods and additionally provides a fast, cheap way to predict and understand the chemistry of such complex systems.