Neste trabalho foram estudadas as moléculas conhecidas corno cetonas-gaiola de Cookson e seus derivados pelo uso de técnicas computacionais de modelagem molecular. Estas moléculas participam de cicloadições [2+2], urna classe de reações cujo mecanismo ainda é estudado. As técnicas usadas foram as do Conjunto Completo de Funções de Base (CBS-4), Hartree-Fock, métodos de Teoria do Funcional de Densidade pBP e B3LYP e semi-empírico PM3. As técnicas foram usadas com diferentes conjuntos de base para analisar as conformações das moléculas e avaliar a exatidão do método em reproduzir resultados experimentais de termodinâmica e ressonância magnética nuclear. Com base na concordância dos resultados e com as caraterísticas do método, procura-se inferir quais as características estruturais e interações atômicas que explicam os resultados experimentais e os calculados. Foi estudada também a solvatação das espécies. Os programas empregados foram o Gaussian 94, Spartan 5.0, MOPAC e Amsol 6.6. Os resultados mostraram as interações interatômicas mais relevantes para a determinação das estabilidades relativas das moléculas. Foi considerado o efeito da estrutura no resultado de cálculos de energias e avaliado o método de reações isodésmicas para moléculas de estrutura complexa. / In this work the molecules known as Cookson\'s cage ketones and similar adducts were studied with the use of computational molecular modelling techniques. These molecules participate in cycloadditions [2+2], a class of reactions whose mechanism is still being studied. Toe techniques used were the Complete Basis Set (CBS-4), Hartree-Fock, Density Functional Theory methods pBP and B3LYP and semi-emprical PM3. The techniques were used with some basis sets to analise the molecular conformations and evaluate the agreement of the calculated with the experimental results of thermodynamics and NMR spectroscopy. Based on the agreement between the results and on the characteristics of the methods, it is sought to determine the structural characteristics and atomic interactions that explain the results. The solvation of the species was also studied. The programs used were the Gaussian 94, Spartan 5.0, MOPAC and Amsol 6.6. The results show the more important interactions that determine the relative stabilities of the molecules. The effect of the molecular structure on the energy calculation was studied and the method of isodesmic reactions was evaluated for complex molecules.

O entendimento das propriedades de complexos metálicos é de fundamental importância para o desenvolvimento de fármacos. No entanto, tanto do ponto de vista experimental quanto no de modelagem teórica, ainda temos muitas dificuldades de simular e mensurar as mudanças que a complexação com um metal causa em um composto. Este trabalho apresenta estudos de simulacões ab initio de complexos de Epiisopiloturina com Cu e Zn. Foram realizadas otimizações de estrutura, simulaçoes de espectroscopia vibracional, NMR e EPR além de estudos de reatividade. Obtivemos uma geometria otimizada condizente com a da forma cristalizada. Além disso, os resultados espectroscópicos mostram que as estruturas dos com plexos permanecem intactas em solução. Por fim, os estudos de reatividade conrmam que o complexo de Cobre aumenta a reatividade da molécula. / Understanding the properties of metal complexes is fundamental goal in the development of drugs. However, both from the experimental point of view and theoretical modeling, many diculties in the simulation and evaluatio of the changes that the metal causes upon complexation still remains. This work presents ab initio computational simulations of Epiisopiloturin com plexes with Cu and Zn. We make structural optimizations, simulations of vibrational spectroscopy, NMR and EPR, as well as reactivity studies. We obtain an optimized geometry that corresponds to that of the crystallized form. In addition, the spectroscopic results conrm that the complexes remain intact in solution. Finally, the reactivity studies conrm that the copper complex increases the reactivity of the molecule.

Clusters sub-nanométricos de metais de transição (TM) têm atraído grande atenção devido às suas propriedades físicas e químicas singulares, muito diferentes dos homólogos na fase bulk. Estas propriedades incomuns podem variar de acordo com o tamanho, a composição e o estado de carga para clusters em fase gasosa. Uma compreensão aprofundada da evolução das propriedades em função de tais parâmetros é um pré-requisito necessário para potencializar diversas aplicações, desde catálise até armazenamento magnético, bem como para responder questões fundamentais relacionadas com a estabilidade intrínseca desses sistemas. Porém, esse entendimento ainda não é satisfatório. Neste projeto, usando cálculos de primeiros princípios baseados na teoria do funcional da densidade dentro da aproximação de gradiente generalizado na formulação proposta por Perdew-Burke-Ernzerhoff, investigamos as estruturas atômicas, as propriedades eletrônicas e a estabilidade de todos os TM (30 elementos) clusters unários em função do tamanho (2 – 15 átomos). Para estudar a influência da carga, consideramos clusters de Cun e Ptn (n = 2 – 14) nos estados catiônico, neutro e aniônico, enquanto os efeitos de composição foram considerados para clusters bimetálicos de PtnCum com m = 2,3, · · · ,14 e n = 0,1, · · &middot ;,m. Nossos resultados sugerem que: (i) Os mecanismos de estabilização para os TM clusters unários baseiam-se na natureza das ligações químicas, em que a ocupação dos orbitais d ligantes ou antiligantes e a hibridização s – d afetam fortemente as propriedades. Por exemplo, a maioria dos TM clusters mágicos são acompanhados por picos de hibridização s – d e momentos de dipolo elétrico nulos.(ii) Diferentes parâmetros afetam as estruturas de TM clusters nesse regime de tamanho, tais como, propriedades do átomo livre, interações magnéticas de troca e efeitos relativísticos. (iii) As propriedades são muito susceptíveis ao estado de carga; em particular, as estruturas tendem a diminuir a coordenação atômica quando um elétron é adicionado ao sistema, o que afeta fortemente a transição 2D-3D. (iv) Energia de excesso negativa foi obtida para a maioria dos Pt–Cu clusters, o que fornece uma forte evidência para a formação de clusters bimetálicos. Além disso, nossas análises sugerem que a formação de estruturas tipo caroço(Cu)-casca(Pt) começa neste regime de tamanho, afim de liberar energia de tensão. (v) O centro de gravidade dos estados d ocupados da liga Pt–Cu varia com a composição, e se aproxima do orbital mais alto ocupado para composições em torno de 50%-50%. Em particular, nossos cálculos sugerem um aumento na energia de adsorção de CO e NO sobre Pt7Cu6 em comparação com os clusters unários de Pt13 e Cu13. Consequentemente, estes resultados constituem uma base para compreender a formação de partículas maiores bem como para investigar sistemas mais complexos e realistas, como reações químicas de sistemas moleculares adsorvidos sobre TM clusters estabilizados por ligantes ou suportados. / Sub-nanometre sized transition metal (TM) clusters have attracted great attention due to their unique physical and chemical properties, very different from the bulk counterparts. These unusual properties can vary with size, composition and state of charge for gas-phase clusters. An in-depth understanding of the properties evolution in function of such parameters is a necessary prerequisite to leverage diverse applications, from catalysis to magnetic storage, as well as to answer fundamental questions related with the intrinsic stability of these systems. However, this understanding is not yet satisfactory. In this project, using first-principles calculations based on density functional theory within the generalized gradient approximation in the formulation proposed by Perdew-Burke-Ernzerhoff, we investigate the atomic structures, electronic properties and stability of all TM (30 elements) unary clusters in function of size (2 – 15 atoms). To study the influence of the charge we considered Cun and Ptn (n = 2 – 14) clusters in the cationic, neutral and anionic states, while compositional effects were considered for bimetallic PtnCum–n clusters with m = 2,3, · · · ,14 and n = 0,1, · · · ,m. Our results suggest that: (i) The stabilization mechanisms for unary clusters are based on the nature of chemical bondings, on which the occupation of the bonding or antibonding d orbitals and the s – d hybridization strongly affect the properties. For example, most magic TM clusters are accompanied by peaks in s – d hybridization and null electric dipole moments.(ii) Different parameters affect TM cluster structures in that size regime, such as, free-atom properties, magnetic exchange interactions and relativistic effects. (iii) The properties are very susceptible to the charge state; in particular, the structures tend to decrease the atomic coordination when one electron is added to the system, which strongly affects the 2D-3D transition. (iv) Negative excess energy was obtained for the most PtCu clusters, which provides a strong evidence for the formation of these bimetallic clusters. Moreover, our analyzes suggest that the formation of core(Cu)-shell(Pt) like structures starts at this size regime, in order to release strain energy. (v) The center of gravity of the occupied d states of the Pt–Cu alloy vary with composition and approaches to the highest occupied molecular orbital for compositions around 50%-50%. In particular, our calculations suggest an increase in the adsorption energy of CO and NO on Pt7Cu6 in comparison with Pt13 and Cu13 unary clusters. Thus, these results form a basis to understand the formation of greater particles as well as to investigate more complex and realistic systems, such as chemical reactions of molecular systems adsorbed on ligand stabilized or supported TM clusters.

O objetivo deste trabalho é descrever a estrutura eletrônica da espécie diatôrnica BeMg, utilizando métodos ab initio multiconfiguracionais. A primeira descrição teórica da espécie BeMg foi feita por Chiles e Dykstra em 1982, empregando os métodos SCF, CCD e CEPA. Naquele trabalho, os autores propuseram que a estrutura eletrônica do BeMg seria intermediária entre a apresentada pelas espécies Be2 e Mg2. Em 1994, Boldyrev et al. empregaram o método QCISD e conjuntos de bases atômicas do tipo 6 - 311 + G* para calcular a distância de equilíbrio do BeMg. Até onde sabemos, não existe nenhum outro estudo téorico, nem experimental, sobre esta espécie. Apesar dos esforços anteriores, devido à natureza dos átomos envolvidos, para descrever com maiores detalhes e precisão não somente o estado fundamental, mas também diferentes estados eletrônicos excitados, é necessário empregar métodos ab initio multiconfiguracionais, fato explicitamente reconhecido por Boldyrev et al. Em 1994. No presente trabalho, as curvas de energia potencial para os estados eletrônicos energeticamente mais baixos, que correlacionam com os primeiros quatro canais de dissociação, da espécie BeMg foram descritas teoricamente empregando conjunto de bases atômicas do tipo cc-pVQZ e funções de onda do tipo CASSCF/MRCI. Todos os orbitais de valência, além de um conjunto adicional de funções de correlação do tipo s e p foram incluídos no espaço ativo. Diversas constantes espectroscópicas também foram calculadas para os estados eletrônicos selecionados. O estado fundamental foi caracterizado como de simetria 1Σ+ e fracamente ligado (De = 0,05 eV), possuindo consequentemente uma distância internuclear de equihbrio relativamente longa (3, 30 Å, ωe = 44, 2 cm-1). É interessante notar que nos trabalhos anteriores a distância internuclear de equilíbrio do estado fundamental foi calculada com sendo 4, 5 Å e 5,1 Å, por Chiles e Dykstra e Boldyrev et al., respectivamente. Os dois primeiros estados excitados são o a3II (Re = 2,416 Å, Te = 11029 cm-1) e o b3 Σ+ (Re = 2,578 Å, Te = 11058 cm-1), ambos com energia de dissociação igual a 1,28 eV. / The first theoretical description of BeMg (using the SCF, CCD, and CEPA methods) was done by Chiles and Dykstra in 1982, when it was proposed that its electronic structure would be intermediate to Be2 and Mg2. In 1994, Boldyrev et al., using the QCISD method and 6 - 311+G* basis sets, presented other results on this diatomic species. To the best of our knowledge, there are no other study about this diatomic species. However, due to the nature of the atoms involved, it is necessary to employ more sophisticated theoretical methods to describe BeMg accurately. In this study, potential energy curves for the lowest-lying electronic states correlating with the first four dissociation channels were determined using the cc-p VQZ basis sets and CASSCF /MRCI wave functions. All valence orbitals plus one set of s and p correlating functions were included in the active space. A whole set of spectroscopic constants completes the characterization of each state. In its ground state (X1Σ+) BeMg is weakly bond (De = 0.05 eV), and consequently has a long internuclear equilibrium distance (Re = 3.30 Å, we = 44.2cm-1). It is interesting to note that in previous theoretical works, the internuclear equilibrium distance was calculated to be around 4.5 Å and 5.1 Å. The first two excited states are an a3II (Re = 2.416 Å, Te= 11029 cm-1) and a b3Σ+ (Re = 2.578 Å, Te= 11058 cm-1), with the same dissociation energy, 1.28 eV.

Protein pK(a)s and metalloprotein reduction potentials are studied with computational methodologies based on an ab initio quantum mechanics (QM) description of the protein and a linearized Poisson-Boltzmann Equation (LPBE) description of the solvent. The practical applicability of the QM/LPBE method is extended to proteins by using a QM description of the ionizable residue and a molecular mechanics (MM) description of the rest of the protein. This QM/MM/LPBE method is used to predict the pKa of Lys55 in the serine protease inhibitor turkey ovomucoid third domain (OMTKY3) and the prediction of 11.0 is in good agreement with the experimental value of 11.1. This is the first time a protein pKa value has been predicted with QM/MM methods. The QM/LPBE method is used to predict and interpret the pKa values of the five carboxyl residues (Asp7, Glu10, Glu19, Asp27, and Glu43) in OMTKY3. All the predicted pKa values are within 0.5 pH units of experiment, with a root mean square deviation of 0.31 pH units. We find that the decreased pKa values observed for some of the residues are primarily due to hydrogen bonds to the carboxyl oxygens. Hydrophobic effects are also shown to be important in raising the pKa. Interactions with charged residues are shown to have relatively little effect on the carboxyl pKa values in this protein, in general agreement with experiment. The relative Cu2+/Cu+ reduction potentials of six type-1 copper sites (cucumber stellacyanin, P. aeruginosa azurin, poplar plastocyanin, C. cinereus laccase, T. ferrooxidans rusticyanin and human ceruloplasmin), which lie in a reduction potential range from 260 mV to over 1000 mV, have been studied with the QM/LPBE method. For the first time, the range and relative orderings of the reduction potentials are reproduced well compared to experimental values. The study suggests that the main interactions determing the relative reduction potentials of blue copper sites are located within 6 Å of the Cu atoms. Further analysis suggests that the reduction potential differences of type-1 copper sites are caused by axial ligand interactions, hydrogen bonding to the S(Cys), and protein constraints on the inner sphere ligand orientations.

<p>Possibly the most fascinating biochemical mechanism remaining to be solved is the formation of oxygen from water in photosystem II. This is a critical part of the photosynthetic reaction that makes solar energy accessible to living organisms.</p><p>The present thesis uses quantum chemistry, more specifically the density functional B3LYP, to investigate a mechanism where an oxyl radical bound to manganese is the active species in O-O bond formation. Benchmark calculations on manganese systems confirm that B3LYP can be expected to give accurate results. The effect of the self-interaction error is shown to be limited. Studies of synthetic manganese complexes support the idea of a radical mechanism. A manganese complex with an oxyl radical is active in oxygen formation while manganese-oxo complexes remain inactive. Formation of the O-O bond requires a spin transition but there should be no effect on the rate. Spin transitions are also required in many short-range electron-transfer reactions.</p><p>Investigations of the superproficient enzyme orotidine decarboxylase support a mechanism that involves an invariant network of charged amino acids, acting together with at least two mobile water molecules.</p>

<p>Oscillator strengths and transition energies are calculated for several mono-substitutes of benzene and naphthalene molecules. The substituents investigated are chlorine, bromine and iodine. Calculations for these molecules are presented, at the Hartree-Fock and DFT level of theory. The functional used in DFT is CAM-B3LYP.</p>

<p>Smaller cellular telephones and more energy-efficient windows are just two examples of technological advances which call for new materials. Materials chemists seek to develop new materials, both out of pure curiosity to see which combination of elements and structures can be obtained and in efforts to produce materials, with specific properties. The starting materials (in solid, liquid or gaseous form) can then be combined and prepared in various ways. A chemical method that is gaining more attention for thin-film growth is Atomic Layer Deposition (ALD). This is a sophisticated type of vapor deposition in which the precursor gases are introduced separately into the reaction chamber.</p><p>Silicon carbide (SiC) and cubic boron nitride (c-BN) are extremely hard diamond-like materials, both with a high potential for application within the modern microelectronics and tool industry. Hexagonal boron nitride (h-BN), with its graphite-like layered structure, is a promising ceramics material.</p><p>Deposition of thin SiC and BN films from gaseous precursors has been studied by theoretical and experimental methods. The chemical composition and atomic arrangement of a growing surface is important for vapor growth. The surface may be terminated (e.g., by hydrogen atoms) and adopt various geometrical structures. Reconstruction of unterminated SiC(0001) surfaces, as well as H abstraction from the corresponding H-terminated surfaces, were studied using quantum mechanical calculations. Elementary reactions for vapor growth of SiC and BN, and <i>in situ</i> incorporation of dopant and contaminant species into these surfaces were also investigated theoretically. Moreover, thin films of BN were deposited by means of laser-assisted ALD. The general goal has been to predict and/or explain experimental results by investigating growth mechanisms.</p>

Les réactions de transfert de charge entre molécules sont des processus fondamentaux dans de nombreux domaines scientifiques. En particulier, elles sont responsables de la conversion de la lumière en énergie chimique (photosynthèse) ou en énergie électrique dans les cellules solaires organiques (domaine du photovoltaïque). Ces dernières visent à produire de l’électricité à coût réduit afin de contribuer aux besoins en énergie renouvelable. Leur rendement reste toutefois faible (environ 5-6% contre 25% pour les cellules à base de silicium) et leur amélioration requiert l’optimisation de chaque étape du processus de transformation de l’énergie lumineuse en courant électrique : absorption de la lumière ; dissociation des excitations ; séparation des charges ; transport des charges. Les processus de dissociation d’excitations, de transport de charge, ainsi que de recombinaison de charges (diminuant le rendement de la cellule solaire) impliquent tous des réactions de transfert d’électron. Les transistors à effet de champ sont des composants fondamentaux en électronique, utilisés comme interrupteurs, déterminant si le courant passe ou non. Les transistors organiques se posent comme alternative moins couteuse aux transistors à base de silicium. Comme dans les cellules solaires, les processus de transfert de charge sont d’une importance primordiale, gouvernant ici la mobilité des charges au sein du dispositif. Rendre les dispositifs d’électroniques organiques concurrentiels par rapport aux dispositifs inorganiques nécessite de les rendre plus performants. Cette amélioration des performances passe, entre autres, par une optimisation des processus de transfert de charge. Dans ce contexte, cette thèse porte sur une étude théorique, basée sur des méthodes de chimie quantique et de mécanique moléculaire, de systèmes donneur-pont-accepteur, dans le but de mieux comprendre les processus de transfert de charge au sein de ces systèmes, en vue de leur utilisation en électronique organique. Ces systèmes présentent plusieurs avantages pour les cellules solaires : le fait de lier chimiquement le donneur et l’accepteur réduit la ségrégation de phase et la séparation des charges est facilitée lorsque les charges sont formées loin l’une de l’autre (grâce à la présence du pont) car l’attraction de Coulomb entre charges générées est réduite. Des molécules pontées peuvent également avoir d’autres applications, comme par exemple l’amélioration de la mobilité des charges dans un transistor organique à effet de champ en permettant un transport entre couches moléculaires. Nous nous sommes intéressés dans un premier temps à des structures modèles afin de mieux comprendre les mécanismes fondamentaux associés aux processus à transfert de charge. Nous avons ensuite appliqué cette méthode à trois types de systèmes réels, synthétisés et caractérisés expérimentalement. La première étude concerne le transport de charge au sein d’un copolymère conjugué donneur/accepteur, F8BT. La seconde concerne l’utilisation de systèmes pontés en vue d’une utilisation dans des transistors à effets de champs organiques. La dernière concerne l’injection de charges dans un matériau organique conjugué via une couche mono-moléculaire auto-assemblée. Pour terminer, nous nous sommes intéressés à l’influence de la dynamique structurale (vibrations moléculaires) sur les vitesses des réactions de transfert de charge dans des systèmes donneur-pont-accepteur.

In this thesis I concentrate on the description of electron transport properties of microscopic objects, including molecular junctions and nano junctions, in particular, inelastic electron tunneling in surface-adsorbate systems are examined with more contemplations. Boosted by the rapid advance in experimental techniques at the microscopic scale, various electric experiments and measurements sprung up in the last decade. Electric devices, such as transistors, switches, wires, etc. are expected to be integrated into circuit and performing like traditional semiconductor integrated circuit (IC). On the other hand, detailed information about transport properties also provides new physical observable quantities to characterize the systems. For molecular electronics, which is in the state of growing up, its further applications demands more thorough understanding of the underlying mechanism, for instance, the effects of molecular configuration and conformation, inter- or intra-molecular interactions, molecular-substrate interactions, and so on. Inelastic electron tunneling spectroscopy (IETS), which reflects vibration features of the system, is also a finger print property, and can thus be employed to afford the responsibility of single molecular identification with the help of other experimental techniques and theoretical simulations.There are two parts of work presented in this thesis, the first one is devoted to the calculation of electron transport properties of molecular or nano junctions: we have designed a negative differential resistance (NDR) device based on graphene nanoribbons (GNRs), where the latter is a star material in scientific committee since its birth;The transport properties of DNA base-pair junctions are also examined by theoretical calculation, relevant experimental results on DNA sequencing have been explained and detailed issues are suggested.The second part focused on the simulation of scanning tunneling microscope mediated IETS (STM-IETS). We have implemented a numerical scheme to calculate the inelastic tunneling intensity based on Tersoff-Hamann approximation and finite difference method, benchmark results agree well with experimental and previous theoretical ones; Two applications of single molecular chemical identification are also presented following benchmarking. / QC20100630