The emerging 2D materials are potential solutions to the scaling of electronic devices to smaller sizes with lower energy cost and faster computing speed. Unlike traditional semiconductors e.g. Si, Ge, 2D materials do not have surface dangling bonds and the short-channel effect. A wide variety of band structure is available for different functions. The aim of the thesis is to calculate the electronic structures of several important 2D materials and study their application in particular devices, using density functional theory (DFT) which provides robust results. The Schottky barrier height (SBH) is calculated for hexagonal nitrides. The SBH has a linear relationship with metal work function but the slope does not always equal because Fermi level pinning (FLP) arises. The chemical trend of FLP is investigated. Then we show that the pinning factor of Si can be tuned by inserting an oxide interlayer, which is important in the application to dopant-free Si solar cells. Apart from contact resistance, we want to improve the conductivity of the electrode. This can be done by using a physisorbed contact layer like FeCl3, AuCl3, and SbF5 etc. to dope the graphene without making the graphene pucker so these dopants do not degrade the graphene's carrier mobility. Then we consider the defect formation of 2D HfS2 and SnS2 which are candidates in the n-type part of a tunnel FET. We found that these two materials have high mobility but there are also intrinsic defects including the S vacancy, S interstitial, and Hf/Sn interstitial. Finally, we study how to make defect states chemically inactive, namely passivation. The S vacancy is the most important defect in mechanically exfoliated 2D MoS2. We found that in the most successful superacid bis(trifluoromethane) sulfonamide (TFSI) treatment, H is the passivation agent. A symmetric adsorption geometry of 3H in the -1 charge state can remove all gap states and return the Fermi level to the midgap.

Direct hydrocarbon fuel cells are fuel cells than use hydrocarbons directly as fuel instead of the most commonly used fuel in a fuel cell, hydrogen. Studies are being done on direct hydrocarbon fuel cells because they have the potential to be energetically more efficient than hydrogen fuel cells. There are many different hydrocarbons that are available to use as a feed stock and each one reacts at different reaction rates. As the current density of a fuel cell is linked to the reaction rate, it is important to know the energetics of an oxidation reaction that is occurring. Density Functional Theory (DFT) is a technique that can be used to predict the energy states of intermediate reaction steps in a given mechanism. The focus of this study is the using DFT to explore the energetics of the oxidation of ethane to ethylene in a nickel-anode catalyst fuel cell. DFT was used in adsorption runs to optimize the geometries beginning (adsorbed ethane) and end (adsorbed ethylene) of the oxidation reaction. DFT was then used to calculate the energy of transition states by varying bond lengths. It was determined the removal of the second hydrogen from the ethyl radical is the most energy intensive step and, thus, the rate limiting step. Hydrogen, ethane, and ethylene were all explored in this study. The heats of adsorption varied from largest to smallest in the order of ethylene, hydrogen, and ethane. It was determined that the heat of adsorption of hydrogen is sufficient to meet the energy requirements for the dissociation reaction. This may help explain why hydrogen reacts so readily in fuel cells. Conversely, the heats of adsorption for the hydrocarbons did not meet the energy requirements for the dissociation reactions. This may help explain why ethane and ethylene react more slowly in a fuel cell as compared to hydrogen. Also, the oxidation of ethane to ethylene requires two large activation energies. These two additional activation energies may help explain why ethylene reacts more readily than ethane in a fuel cell.

Submitted by Julio Henrique Hartmann (juliohenrique@msn.com) on 2018-04-16T06:15:34Z No. of bitstreams: 1 Dissertação_final Julio Henrique Hartmann.pdf: 2243165 bytes, checksum: dd94af85066e93f95365876d2a3c7e82 (MD5) / Approved for entry into archive by Raphael Vilas Boas (raphaelboas@ibict.br) on 2018-04-25T18:45:57Z (GMT) No. of bitstreams: 1 Dissertação_final Julio Henrique Hartmann.pdf: 2243165 bytes, checksum: dd94af85066e93f95365876d2a3c7e82 (MD5) / Made available in DSpace on 2018-04-25T18:45:57Z (GMT). No. of bitstreams: 1 Dissertação_final Julio Henrique Hartmann.pdf: 2243165 bytes, checksum: dd94af85066e93f95365876d2a3c7e82 (MD5) Previous issue date: 2014 / In this work we examined theoretically via computer simulation of first principles, the interaction of graphene with the molecules of resveratrol and quercetin. To do this, use the Density Functional Theory and the pseudopotential method as implemented in the SIESTA computer code. Resveratrol is an antioxidant drug and several studies have highlighted and proven the benefits of resveratrol health. This has been shown flavonoid chemopreventive, antioxidant, antiplatelet, antifungal, anti-inflammatory, cardioprotective, among others. Quercetin is the main flavonoid present in the human diet and its therapeutic properties have been studied in recent decades, highlighting the potential antioxidant, anticarcinogenic and its protective effects on renal, cardiovascular and hepatic systems, and also has antimicrobial activity. However, these two drugs are very unstable. In this regard, the main motivation is to use graphene with these two drug molecules to overcome the instability of the same, because of the properties of graphene Its primary is exactly be electrochemically stable. Our results show that the most stable configuration for the binding energy of quercetin with graphene was 0.93 eV and resveratrol value found for the binding energy was 0.53 eV indicating the occurrence of weak interaction through physical adsorption. Analyzing the band structure of the interacting systems, we found that no significant changes occur in the electronic properties compared to pure graphene. The stability of the molecules was improved due to charge transfer and the decrease of the total energy of the molecules. / Neste trabalho analisamos, teoricamente, via simulação computacional de primeiros princípios, a interação do grafeno com as moléculas de resveratrol e quercetina. Para isso, utilizamos a Teoria do Funcional da Densidade e o método de pseudopotenciais conforme implementados no código computacional SIESTA. O resveratrol é um fármaco antioxidante e vários estudos têm destacado e comprovado os benefícios do resveratrol à saúde. Este flavonóide tem demonstrado propriedades quimiopreventivas, antioxidantes, antiplaquetárias, antifúngicas, anti-inflamatórias, cardioprotetoras, entre outras. A quercetina é o principal flavonóide presente na dieta humana e suas propriedades terapêuticas têm sido estudadas nas últimas décadas, destacando-se o potencial antioxidante, anticarcinogênico e seus efeitos protetores aos sistemas renal, cardiovascular e hepático, sendo que possui também atividade antimicrobiana. Entretanto, estes dois fármacos são bastante instáveis. Neste sentido, a principal motivação do trabalho é utilizar o grafeno com estas duas moléculas de fármacos para suprir a instabilidade das mesmas, pois uma das propriedades precípuas do grafeno é justamente ser eletroquimicamente estável. Nossos resultados mostram que para as configurações mais estáveis, a energia de ligação da quercetina com o grafeno foi de 0,93 eV e para o resveratrol o valor encontrado para a energia de ligação foi de 0,53 eV indicando a ocorrência de interação fraca por meio de adsorção física. Analisando a estrutura de bandas dos sistemas interagentes, observamos que não ocorrem alterações significativas nas propriedades eletrônicas quando comparadas com o grafeno puro. Em relação à estabilidade das moléculas houve uma melhora devido à transferência de carga, à diminuição da energia total das moléculas e ao fato de que não houve alteração significativa na geometria dos sistemas.

Neste trabalho é introduzido e avaliado um conjunto de novas ideias para aumentar a eficiência do método Basin-Hopping Monte Carlo (BHMC) aplicado à otimização global de clusters e nanopartículas, que resultou no método BHMC revisado. Dentro deste método, tomou-se o cuidado de manter as características fundamentais do método BHMC padrão, que consistem na transformação da superfície de energia potencial em um conjunto de basins de atração, e no emprego de amostragem de Monte Carlo utilizando o critério de Metropolis. As ideias por trás do método BHMC revisado incluem um grande conjunto de operadores locais e não locais construídos especificamente para clusters e nanopartículas e que permitem maior mobilidade sobre a superfície de energia potencial durante a busca pelo mínimo global, duas estratégias de seleção de operadores, e um operador de filtro estrutural para remover soluções não físicas. A eficiência do método apresentado foi avaliada através da sua aplicação a um grande número de clusters e nanopartículas de tamanhos variados, compreendendo sistemas descritos tanto por potenciais empíricos, quanto por primeiros princípios dentro do formalismo da teoria do funcional da densidade (DFT). Os sistemas investigados foram clusters de Lennard-Jones e Sutton-Chen contendo até 148 átomos, um conjunto de nanopartículas de Lennard-Jones com tamanhos variando entre 200 e 1500 átomos, clusters binários de Lennard-Jones com até 100 átomos, clusters binários de metais de transição (AgPd)55 descritos pelo potencial de Sutton-Chen, clusters de alumínio puros com até 30 átomos descritos por DFT, e clusters de alumínio com até 15 átomos dopados com um átomo de cobre, também descritos por DFT. Através da otimização global sem bias de todas essas partículas, o método BHMC revisado foi capaz de reproduzir com sucesso os mínimos globais putativos mais recentes disponíveis na literatura obtidos por diversas técnicas de otimização global, e também foi capaz de identificar mínimos globais previamente desconhecidos. Além disso, em comparação com o método BHMC padrão, o método RBHMC mostrou maior eficiência para muitos dos sistemas investigados. As ideias contidas na metodologia apresentada constituem uma ferramenta valiosa para auxiliar investigações teóricas visando uma melhor compreensão da estrutura atômica de clusters e nanopartículas. / In this work it is introduced and evaluated a set of new ideas to increase the efficiency of the Basin-Hopping Monte Carlo (BHMC) method applied to the global optimization of clusters and nanoparticles, which resulted in the revised BHMC method. Within this method, care was taken to keep the main features of the standard BHMC method, which are the transformation of the potential energy surface into a set of basins of attraction, and the use of Monte Carlo sampling employing the Metropolis criterion. The ideas behind the revised BHMC method include a large set of local and non-local operators built specifically for clusters and nanoparticles which allow a greater mobility over the potential energy surface along of the search for the global minimum, two strategies for selecting the operators, and a structural filter operator to remove unphysical solutions. The efficiency of the presented method was evaluated by applying it to a large number of clusters and nanoparticles of various sizes, comprising systems described both by empirical potentials and by first-principles within the formalism of density functional theory (DFT). The systems that were investigated were Lennard-Jones and Sutton-Chen clusters with up to 148 atoms, a set of Lennard-Jones nanoparticles with sizes from 200 to 1500 atoms, binary Lennard-Jones clusters with up to 100 atoms, binary transition metal clusters (AgPd)55 described by the Sutton-Chen potential, pure aluminum clusters with up to 30 atoms described by DFT, and aluminum clusters with up to 15 atoms doped with a copper atom, also described by DFT. Through the unbiased global optimization of all those particles, the revised BHMC method was able to successfully reproduce the most recent putative global minima available in the literature obtained by several different global optimization techniques, and moreover, it was able to identify previously unkown global minima. Furthermore, in comparison with the standard BHMC method, the RBHMC method proved to be more efficient for many of the systems that were investigated. The ideas comprised within the presented methodology characterize a valuable tool for aiding theoretical investigations leading to a better understanding of the atomic structure of clusters and nanoparticles.

Desde a identificação do vírus da imunodeficiência humana (HIV, do inglês Human Immunodeficiency Virus) como agente causador da Síndrome da Imunodeficiência Adquirida (AIDS ? do inglês Acquired Immunodeficiency Syndrome), a busca para tratamentos seguros e eficazes contra o HIV transformou-se no principal foco para a descoberta de uma nova droga em todo o mundo. A AIDS aparece como um dos principais problemas de saúde pública para as próximas décadas, onde será o maior determinante de mortalidade na faixa etária entre 20 e 50 anos em praticamente todos os países do mundo. Tendo como objetivo relacionar a atividade de compostos biflavonóides anti-HIV-1 com algumas de suas propriedades moleculares, serão utilizados métodos de Mecânica Molecular e Química Quântica. O método de cálculo semi-empírico AM1 foi empregado para calcular um conjunto de propriedades moleculares dos 14 compostos biflavonóides com atividade anti-HIV-1. A seguir utilizar-se-á métodos estatísticos com a finalidade de separar os 14 compostos em duas classes, ativos e não ativos, de forma que se relacione qual as propriedades, dentre as calculadas, são responsáveis pela atividade dos compostos biflavonóides estudados. As técnicas estatísticas utilizadas foram a Análise de Componentes Principais (PCA: Principal Components Analysis), Análise Hierárquica de Agrupamentos (HCA: Hierarquical Clusters Analysis) e Análise de Discriminates por Passos (SDA: Stepwise Discriminant Analysis). Os estudos com PCA, HCA, e SDA mostraram que as variáveis HOMO (Highest Occupied Molecular Orbital - Orbital Molecular Ocupado de Maior Energia), LUMO (Lowest Unoccupied Molecular Orbital ? Orbital Molecular Desocupado de Menor Energia), e Área superficial são responsáveis pela separação dos compostos com alta e baixa atividade anti-HIV-1. O comportamento destas três propriedades pode ser útil na tentativa de se obter outros compostos biflavonóides com elevada atividade inibidora anti-HIV-1. / A set of 25 quinone compounds with anti-trypanocidal activity was studied by using the Density Functional Theory (DFT) method in order to calculate electronic atomic and molecular properties to be correlated with the biological activity. The chemometric methods Principal Component Analysis (PCA), Hierarchical Cluster Analysis (HCA), Stepwise Discriminant Analysis (SDA), Kth nearest neighbor (KNN) and Soft Independent Modeling of Class Analogy (SIMCA) were used to obtain possible relationships between the calculated descriptors and the biological activity studied and predict the anti-trypanocidal activity of new quinone compounds from a test set. Four descriptors were responsible for the separation between the active and inactive compounds: T5 (torsion angle), HOMO-1 (energy of the first molecular orbital below HOMO), QTS1 (sum of absolute values of the atomic charges) and VOLS2 (volume of the substituent at region B). These descriptors give information on the kind of interaction that occurs between the compounds and the biological receptor. The prediction study was done with a set of three new quinone compounds by using the PCA, HCA, SDA, KNN and SIMCA. Beside the five chemometric methods, the neural network method was used by employing the backpropagation algorithm. The four variables (T5, QTS1, VOLS2 and HOMO-1) were employed to validate the models constructed previously. The architecture of networks consisting of four neurons at input layers, ten neurons at intermediary layers and two neurons at output layers was adopted to observe the root mean square error between the true and desired output over the entire training set. The percentage of correct classification was 87.5%, and only one compound was predicted wrong in the test set, which indicates that the model is robust and could be able to make predictions. The docking studies were carried out with two different programs in the approach of ligands: the Autodock and FlexX. The docking results on trypanothione reductase enzyme showed that all studied compounds stay at second hydrophobic pocket in the outer region of the active site called the Z-site. The residues that could be specifically involved in the binding of ligands are Lys62, Thr66, Thr397, Thr463, Leu399, Ser464, Glu466 and Glu467, where the residues Thr66, Thr463 and Leu399 are conserved in different trypanothiones and could be used for the development of selective inhibitors against to the parasite enzyme.

Simulações computacionais são ferramentas essenciais para a compreensão num nível microscópico de diversos fenômenos que ocorrem na natureza. Em particular, simulações ab initio, isto é, de primeiros princípios, podem predizer novas propriedades e auxiliar na interpretação de resultados experimentais, sem a necessidade de potenciais empíricos os quais são ajustados para uma específica configuração do sistema. No entanto, mesmo para simulações ab initio são necessárias aproximações tanto para o cálculo de estrutura eletrônica quanto para a descrição dos movimentos nucleares. Nesta tese, novas aproximações para o funcional de energia de troca e correlação da Teoria do Funcional da Densidade (DFT) são propostas e testadas no cálculo de estrutura eletrônica de átomos, moléculas e sólidos. Para a descrição dos movimentos nucleares a técnica de Monte Carlo é utilizada, porém as energias totais são obtidas com a DFT. Propomos também uma nova metodologia que permite descrever movimentos intramoleculares de sistemas cujas frequências de vibração não podem ser tratadas classicamente. Como aplicações estudamos aglomerados de água e água líquida, mostrando a relevância dessa nova metodologia na descrição de propriedades estruturais, vibracionais e de momento de dipolo desses sistemas. / Computer simulations are essential tools for a microscopic understanding of many processes that occur in nature. In particular, ab initio simulations, i.e., first principles simulations, can predict new properties and support experimental results, without the need to use empirical potentials which are fitted for a specific configuration of the system. However, even in ab initio simulations it is necessary to do approximations for the electronic structure calculations and for the description of the nuclear movements. In this thesis, new approximations for the exchange-correlation energy functional of Density Functional Theory (DFT) are proposed and tested for atoms, molecules and solids. The description of the nuclear movements was done using the Monte Carlo technique, however the total energy calculations were obtained by DFT. We also propose a new methodology which allows the description of intramolecular movements whose vibrational frequencies can not be treated classically. As an illustration, we have studied water clusters and liquid water, showing the relevance of this new methodology on the description of structural, vibrational and of the dipole moment of these systems.

Os calcogenetos têm atraído atenção devido à variedade de propriedades físicas e químicas que exibem, apontando para sua utilização em muitas aplicações tecnológicas, incluindo a possibilidade de se obter novos materiais bidimensionais. Os calcogenetos quaternários A2MIIMIV3Q8, onde A = K, Cs; MII = Mg, Zn, Cd, Hg; MIV = Ge, Sn; Q = S, Se, Te, possuem uma grande variabilidade de band gaps e portanto eles podem ser estudados para engenharia de band gap através de mudanças na composição química. Além disso, dois tipos de estruturas cristalinas são observados nessa família, um formado por empilhamento de camadas, e outro definido por uma rede tridimensional fechada. Assim, é importante entender os fatores que afetam a estabilidade de estruturas em camadas desses compostos complexos. Nesse trabalho, os materiais A2MIIMIV3Q8 são estudados com cálculos de teoria do funcional da densidade, usando funcionais de troca e correlação semi-local e híbrido, e correções de van der Waals. Os parâmetros de rede variam com a composição conforme o esperado com base no raio atômico. A redução do número atômico de um dos componentes, principalmente Q, aumenta a energia de coesão, devido à intensificação das interações iônicas. Os resultados de energia de ligação entre camadas demonstram a importância das interações de van der Waals, e os valores são similares aos reportados na literatura para vários materiais. Seguindo a tendência de funcionais semi-locais, os band gaps são subestimados, mas cálculos com o funcional híbrido fornecem valores mais apropriados. Os resultados mostram a diversidade de band gaps e uma correlação aproximadamente linear entre band gap e volume da célula unitária. O band gap é principalmente afetado pela mudança do calcogênio, em que o aumento do número atômico diminui o band gap, devido ao aumento da energia dos estados p de Q. As análises dos coeficientes de absorção óptica e elementos de matriz de transição mostram que não existe diferença significativa entre band gap fundamental e óptico nesses materiais. O estudo de estabilidade relativa das estruturas em 9 compostos, com diferentes A e Q, mostra que os raios atômicos têm um importante papel. A estrutura sem formação de camadas é favorecida comparada com as estruturas em camadas apenas na região de raios intermediários, o que é explicado com base na diminuição das tensões na estrutura e em interações coulombianas entre íons da rede. / Chalcogenides have attracted attention due to the variety of physical and chemical properties which they display, pointing to their use in many technological applications, including the possibility to obtain new bidimensional materials. The quaternary chalcogenides A2MIIMIV3Q8, where A = K, Cs; MII = Mg, Zn, Cd, Hg; MIV = Ge, Sn; Q = S, Se, Te, have a large variability of band gaps and therefore they can be studied for band gap engineering through changes in the chemical composition. Futhermore, two types of crystal structure are observed in this family, one formed by the stacking of layers, and the other defined by a closed three dimensional framework. Thus, it is important to understand the factors that affect the stability of layered structures of these complex compounds. Here, the materials A2MIIMIV3Q8 are studied with density functional theory calculations, using semi-local and hybrid exchange-correlation functionals, and van der Waals corrections. Lattice parameters vary with composition according to expected based on the atomic radius. The reduction of the atomic number of one of the components, mainly Q, increases the cohesive energy, due to the intensification of the ionic interactions. The results of interlayer binding energies demonstrate the importance of van der Waals interactions, and the values are simillar to those reported in the literature for several materials. Following the trend of semi-local functionals, band gaps are underestimated, but hybrid functional calculations provide more accurate values. The results show the diversity of band gaps and an approximate linear correlation between band gap and unit cell volume. The band gap is mainly affected by changing the chalcogen, in which the increase of the atomic number decreases the band gap, due to the increase in the energy of Q p states. The analysis of optical absorption coefficients and transition matrix elements show that there is no significative difference between fundamental and optical band gap in these materials. The study of relative stability of the structures in 9 compounds, with different A and Q, shows that the atomic radii have an important role. The structure without layer formation is favored compared with the layered structures only in the region of intermediate radii, which is explained based on the reduction of strain in the structure and coulomb interactions between ions in the framework.

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.

Dirhodium complexes such as carboxylates and carboxylamidates are very efficient metal catalysts used in the synthesis of pharmaceuticals and agrochemicals. Recent experimental work has indicated that there are significant differences in the isomeric ratios obtained among the possible products when synthesizing these complexes. The relative stabilities of the Rh2(NPhCOCH3)4 tolunitrile complexes, Rh2(NPhCOCH3)4(NCC6H4CH3)2, were determined at the HF/LANL2DZ ECP, 6-31G and DFT/B3LYP/LANL2DZ ECP, 6-31G levels of theory using NWChem 6.3. The LANL2DZ ECP (effective core potential) basis set was used for the rhodium atoms and 6-31G basis set was used for all other atoms. Specifically, the o-tolunitrile, m-tolunitrile, and p-tolunitrile complexes of the 2,2-trans and the 4,0- isomers of Rh2(NPhCOCH3)4 were compared.

Heteroaryl nitrone spin traps have been suggested to act as free radical scavengers. The geometry optimizations and the single-point energies of the spin trapping reactions of the heteroaryl nitrones, 5,5-dimethylpyrroline-N-oxide (DMPO) and α-phenyl-N-t-butylnitrone (PBN) have been computationally studied using ab initio (Hartree-Fock (HF) and second-order Møller-Plesset (MP2)) methods and Density Functional Theory (DFT) methods. The effects of new heteroaryl substituents on a parent nitrone spin trap have been examined at the HF and MP2 levels with the 6-31G*, and cc-pVnZ (n=D, T, Q) basis sets. The thermodynamics of the spin trapping at the C-site and O-site with •H, •CH3 and •OH radicals were studied at the HF/6-31G* and DFT/m06/6-31G* levels. The addition reactions favor at the C-sites and the double adducts are thermodynamically more stable than the mono adducts. The spin trapping of DMPO, PBN and α(Z)-(3-methylfuroxan-4-yl)-N-tert-butylnitrone (FxBN) with •OH have also been studied.