Density-functional theory has become an indispensible tool for studying matter on the atomic level, being routinely applied across diverse disciplines from solid-state physics to chemistry and molecular biology. Its failure to account for dispersion interactions has spurred intensive research over the past decade. In this thesis, a semilocal density-functional approximation including dispersion is developed by combining standard functionals for exchange and correlation with the nonempirical “exchange-hole dipole moment“ (XDM) dispersion model of Becke and Johnson. With a minimum of empiricism, the method accurately describes all types of noncovalent interactions, from the extremely weak dispersion forces in rare-gas systems to the hydrogen bonding and stacking interactions responsible for the structure and function of biological macromolecules such as DNA and proteins. The method is compatible with a wide variety of standard Gaussian basis sets, and is easily applied to any system that can be modeled with density-functional theory.

Multiconfigurational quantum chemistry methods, and especially the multiconfigurational self-consistent field (MCSCF) and multireference perturbation theory (MRPT2), are powerful tools, particularly suited to the accurate modeling of photochemical processes and transition metal catalysis. However, they are limited by their high computational cost compared to other methods, especially density functional theory. Moreover, there are areas where they would be expected to perform well, but where they are not applied due to lack of experience. This thesis addresses those issues. First, the efficiency of the Cholesky decomposition approximation to reduce the cost of MCSCF and MRPT2 without sacrificing their accuracy is demonstrated. This then motivates the extension of the Cholesky approximation to the computation of MCSCF nuclear gradients, thus strongly improving the ability to perform MCSCF non-adiabatic molecular dynamics. Typically, a tenfold speed-up is observed allowing dynamic simulation of larger systems or over longer times. Finally, multiconfigurational methods are applied to the computation of X-ray spectra of transition metal complexes. The importance of the different parameters in the calculation is systematically investigated, laying the base for wider applications of those accurate methods in the modeling of X-ray spectroscopy. A tool to analyze the resulting spectrum in terms of molecular orbitals is also presented, strengthening the interplay between theory and experiments. With these developments and other significant ones that have happened in recent years, multiconfigurational methods can now reach new grounds and contribute to important new discoveries

This thesis aims at validating a theoretical protocol to develop global potential energy surfaces for use in the spectroscopy and dynamics of transition metal nitrosyl complexes. To get an insight into the homogeneous catalysis of NO with Cu and the chemical reaction dynamics, an accurate prediction of the nature of the interaction, as well as of the global potential energy surfaces (PES) is necessary in the gas phase. Experimental data are difficult to obtain, hence the importance of carrying out calculations of the lowest electronic states as accurate as possible to address the structure , spectroscopy and dynamics of this system. All ab initio calulations we report here were performed at the multi-reference configuration interaction (MRCI) and at the coupled cluster level of theory. We aslo investigate the importance of relativistic effects in the systems. For CuNO system, it is shown that a complete active space involving 18 valence electrons, 11 molecular orbitals and the prior determination of 12 roots in the MCSCF calculation is needed for overall qualitatively correct results from the MRCI calculations. The present calculations yield a bound singlet A' ground state for CuNO and comparared with previous results. We have obtained new, complete potential energy functions of the ground electronic states of CuO and CuN systems. Comparison of the term values for the lowest electronic states of CuO and CuN with those previously reported in the literature shows a quite good agreement. We derived a novel analytical representation of the adiabatic potential energy surface in the ground electronic state of the CuNO system as a sum of two-body and three-body terms. This compact and flexible representation enables us to make a physically correct interpolation of the ab initio data points at the MRCI level of theory. We use a modified Levenberg-Marquardt algorithm for fitting the potential, which has 19 adjustable parameters and which now enables us to do scattering dynamics of the CuNO system. We perform full dimensional quantum dynamical studies with this new potential. Convergence of the time dependent wavepacket calculation has been achieved. We find that the scattering in CuNO is highly inelastic. Intermediate, excited meta stable reaction products CuNO∗ live for about 0.5 to 1 ps and maybe more.

In the recent years, interest in TM oxides with 5d valence electrons has grown immensely due to the realization of novel spin-orbit coupled ground states. In these compounds, e.g., iridates and osmates, the intriguing situation arises where the spin-orbit and electron-electron interactions meet on the same energy scale. This has created a new window of interest in these compounds since the interplay of crystal field effects, local multiplet physics, spin-orbit couplings, and intersite hopping can offer novel types of correlated ground states and excitations. In 5d5 iridates, a spin-orbit entangled j = 1/2 Mott insulating state has been realized recently. A remarkable feature of such a ground state is that it gives rise to anisotropic magnetic interactions. The 2D honeycomb-lattice 213 iridium oxides, A2IrO3 (A=Li,Na), have been put forward to host highly anisotropic bond-dependent spin-spin interactions that resemble the Kitaev spin model, which supports various types of topological phases relevant in quantum computing. The 2D square-lattice 214 iridates Sr2IrO4 and Ba2IrO4 are, on the other hand, appealing because of their perceived structural and magnetic simi- larity to La2CuO4, the mother compound of the cuprate high-Tc superconductors. This has promoted the latter iridium oxide compounds as novel platforms for the search of high-Tc superconductivity. To put such considerations on a firm footing, it is essential to quantify the different coupling strengths and energy scales, as they for instance appear in effective Hamiltonian descriptions of these correlated systems. Moreover, it is important to correctly describe their effects. In this thesis, the electronic structure and magnetic properties of 5d5 (mainly 214 and 213) iridates are studied using wave-function-based quantum chemistry methods. These methods are fully ab initio and are capable of accurately treating the electron-electron interactions without using any ad hoc parameters. The spin-orbit entangled j = 1/2 ground state in 214, 213 and other lower symmetry Sr3CuIrO6 and Na4Ir3O8 iridates is first analyzed in detail, by studying the local electronic structure of the 5d5 Ir4+ ion. We establish that the longer-range crystal anisotropy, i.e., low-symmetry fields related to ionic sites beyond the nearest neighbor oxygen cage, strongly influence the energies of Ir d levels. The ground state in all the compounds studied is j = 1/2 like with admixture from j ≃ 3/2 states ranging from 1 – 15 %. Further, the average j ≃ 1/2 → j ≃ 3/2 excitation energy we find is around 0.6 eV. The NN magnetic exchange interactions we computed for 214 iridates are predominantly isotropic Heisenberg-like with J ~ 60 meV, 3 – 4 times smaller than found in isostructural copper oxides. However, the anisotropic interactions are an order of magnitude larger than those in cuprates. Our estimates are in excellent agreement with those extracted from experiments, e.g., resonant inelastic x-ray scattering measurements. For the 213 honeycomb-lattice Na2IrO3 our calculations show that the relevant spin Hamiltonian contains further anisotropic terms beyond the Kitaev-Heisenberg model. Nevertheless, we predict that the largest energy scale is the Kitaev interaction, 10 to 20 meV, while the Heisenberg superexchange and off-diagonal symmetric anisotropic couplings are significantly weaker. In the sister compound Li2IrO3, we find that the structural inequivalence between the two types of Ir-Ir links has a striking influence on the effective spin Hamiltonian, leading in particular to two very different NN superexchange pathways, one weakly AF (~ 1 meV) and another strongly FM (−19 meV). The latter gives rise to rigid spin-1 triplets on a triangular lattice.

This thesis consists of two parts. In the first part, the properties of excess electrons in water clusters are studied via a hybrid quantum and classical mechanics method. The existence of the solvated electron in water was experimentally demonstrated long ago, and it is among the most interesting charged species. However, a satisfactory characterization of the water clusters has always been a challenge. In our simulation, we treat a region of the cluster nearest to the centroid of the excess electron distribution quantum mechanically, while the rest of the water molecules are treated classically. The binding energies of a localized excess electron are calculated in clusters with sizes ranging from 16 to 300. The density distributions of the excess electrons verify the existence of both surface localization mode and interior localization model. We studied the energetically favored localization modes depending on the sizes of the clusters and the transition point. In the second part, the energy spectra, spin configurations, and entanglement characteristics of a system of four electrons in lateral double quantum dots are investigated using exact diagonalization (EXD), as a function of interdot separation, applied magnetic field, and strength of interelectron repulsion. As a function of the magnetic field, the energy spectra exhibit a low-energy band consisting of a group of six states, with the number six being a consequence of the conservation of the total spin of the four electrons and the ensuing spin degeneracies. These six states appear to cross at a single value of the magnetic field, with the crossing point becoming sharper for larger interdot distances. As the strength of the Coulomb repulsion increases, the six states tend to become degenerate and a well defined energy gap separates them from the higher-in-energy excited states. The appearance of the low-energy band is a consequence of the formation of a Wigner supermolecule. Using the spin-resolved pair-correlation functions, one can map the EXD many-body wave functions onto the spin functions associated with the four localized electrons. The ability to determine associated spin functions enables investigations concerning entanglement properties of the system of four electrons.

The electronic spectra of sulfide minerals can be complex, and their features difficult to assign. Often, therefore, they are interpreted using electronic-structure models obtained from quantum-chemical calculations. The aim of this study is to provide such models for the minerals sphalerite, wurtzite, pyrite, marcasite, and chalcopyrite. All are important minerals within a mining context, either as a source for their component metals or as a gangue mineral. They are also semiconductors. Each is the structural archetype for a particular class of semiconductors, and so a knowledge of their electronic structures has wider applicability. / PhD Doctorate

Thesis (M. Sc.)--Carleton University, 2004. / Includes bibliographical references (p. 127-130). Also available in electronic format on the Internet.

Orientador: Gustavo Troiano Feliciano / Banca: Eduardo Maffud Cilli / Banca: Maurício Domingues Coutinho Neto / Resumo: A pilina é um peptídeo produzido pela bactéria redutora de metais Geobacter sulfurreducens. Este peptídeo compõe um sistema biológico que tem atraído a atenção de pesquisadores, devido às suas propriedades condutoras interessantes. Estudos indicam que a pilina é a subunidade de uma estrutura filamentosa denominada pilus e que o conjunto desses filamentos formam uma proteína monolateral, a pili. Investigações revelaram processos de transferência eletrônica na faixa de micrômetros de comprimento, o que sugere, mais provavelmente, um regime de transporte por hopping. Além disso, correntes associadas à topografia referente ao filamento indicaram um comportamento ohmico, característica associada à metais. A ausência de cofatores e citocromo tornam essas propriedades ainda mais interessantes, indicando um transporte eletrônico ao longo da própria estrutura da proteína. Este trabalho apresenta a investigação de fatores que possam contribuir para um transporte de carga tão eficiente sem a presença de citocromo. Para isso, análises foram realizadas em aglomerados aromáticos dentro da estrutura de modelos que mimetizam a pilina e de modelos propostos para o pilus. O estudo é feito utilizando, primeiramente, métodos teóricos clássicos com os pacotes de simulação AMBER e GROMACS, e em seguida cálculos híbridos QM/MM, com tratamento quântico baseado na Teoria do Funcional da Densidade, implementada no código computacional CPMD, para a obtenção da estrutura eletrônica dos grupos aromáticos... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Pilin is a peptide produced by the metal reducing bacteria Geobacter sulfurreducens. This peptide is present in a biosystem that has been attracting attention due to its interesting conductive properties. Studies indicate that pilin is a subunit of a filamentous structure called pilus and the arrangement of these filaments form a unilateral protein called pili. Investigations revealed electronic transfer processes in the length range of micrometers, what suggests a hopping transport mechanism. Besides, currents associated with topography indicated an ohmic behavior along the filament, which is a metallic characteristic. The absence of cofactors and cytochrome is even more interesting because it indicates an electronic transport through the protein structure. This dissertation presents an investigation of factors that may contribute to a highly efficient charge transport without a cytochrome. Therefore, it was made an analysis in aromatic agglomerates within the structure of models that mimic pilin and within proposed models for pilus. Initially, it was used methods based on classical mechanics with the simulation packages AMBER and GROMACS, then hybrid calculations QM/MM were performed with a quantum approach based on the Density Functional Theory implemented in CPMD computer code. The mimetic peptides present a considerably high energetic gap for HOMO-LUMO in water. Nevertheless it was reduced in vacuum, mainly for groups of tyrosine where metal-like characteristics were ind... (Complete abstract click electronic access below) / Mestre

Dans cette thèse, nous avons optimisé avec succès tous les paramètres pour calculer l'état fondamental du systéme neutre [N,O, Cu]. L'étude de réactions impliquant NO et des métaux de transition est particulièrement intéressante pour le développement de catalyses efficaces pour la réduction de NO, en vue de sonder la possibilité d'une catalyse homogène impliquant les fragments Cu et NO; une prévision précise de la nature de l'interaction entre ces deux fragments est nécessaire en phase gaz. Il a été montré que les calculs MCSCF incluant 12 racines sont nécessaires pour avoir une convergence propre mais donnent des états inversés, l'asymptote. Pour décrire proprement l'état fondamental, nous utilisons les calculs MRCI sur 6 états par espèce de symétrie simultanément. Aussi nous montrons par calculs MRCI, que l'espace actif peut contenir tous les électrons 3d de Cu pour décrire précisément le système. Ici nous utilisons un CAS (22, 13) qui est proche de l'espace de valence complète du système. Nous avons développé une SEP analytique globale qui peut être utilisée pour modéliser les données ab initio obtenues. L'état lié est un état 1 A’ avec une énergie de rCu = 2.382 pm, rNO = 1.134 pm et tCu = 133.495. Nous avons également effectué des calculs précis sur l'état électronique fondamental et sur les états électroniques excités des diatomiques CuO et CuN et obtenu l'énergie de dissociation qui a ensuite été utilisée comme paramètre d'ajustement dans la représentation analytique. Les fondamentaux vibrationnels calculés se comparent bien avec les données expérimentales disponibles. Le potentiel analytique a été utilisé avec succès avec les meilleurs paramètres ajustés pour effectuer des calculs de dynamique quantique sur le complexe, dont les résultats indiquent une diffusion réactive avec un transfert de l'énergie translatoire vers l'énergie vibrationnelle dans le domaine de temps de la femtoseconde. Des résultats plus avancés non-inclus dans ce résumé impliquent des calculs CCSD(T), incluant des corrections relativistes, et une fusion originale entre les données MRCI et CCSD(T) et modélisées avec la SEP analytique, dont les résultats donnent un puit de potentiel plus profond et réduisent la distance de liaison rCu (distance Cu-NO). Nous avons aussi effectué des études de dynamique quantique avec un facteur d'impact variant (J > 0) et une diffusion des énergies de collision, toutes deux dans une approche soit isotrope, soit directionnelle du paquet d'onde initial. / This thesis aims at validating a theoretical protocol to develop global potential energy surfaces for use in the spectroscopy and dynamics of transition metal nitrosyl complexes. To get an insight into the homogeneous catalysis of NO with Cu and the chemical reaction dynamics, an accurate prediction of the nature of the interaction, as well as of the global potential energy surfaces (PES) is necessary in the gas phase. Experimental data are difficult to obtain, hence the importance of carrying out calculations of the lowest electronic states as accurate as possible to address the structure , spectroscopy and dynamics of this system. All ab initio calulations we report here were performed at the multi-reference configuration interaction (MRCI) and at the coupled cluster level of theory. We aslo investigate the importance of relativistic effects in the systems. For CuNO system, it is shown that a complete active space involving 18 valence electrons, 11 molecular orbitals and the prior determination of 12 roots in the MCSCF calculation is needed for overall qualitatively correct results from the MRCI calculations. The present calculations yield a bound singlet A' ground state for CuNO and comparared with previous results. We have obtained new, complete potential energy functions of the ground electronic states of CuO and CuN systems. Comparison of the term values for the lowest electronic states of CuO and CuN with those previously reported in the literature shows a quite good agreement. We derived a novel analytical representation of the adiabatic potential energy surface in the ground electronic state of the CuNO system as a sum of two-body and three-body terms. This compact and flexible representation enables us to make a physically correct interpolation of the ab initio data points at the MRCI level of theory. We use a modified Levenberg-Marquardt algorithm for fitting the potential, which has 19 adjustable parameters and which now enables us to do scattering dynamics of the CuNO system. We perform full dimensional quantum dynamical studies with this new potential. Convergence of the time dependent wavepacket calculation has been achieved. We find that the scattering in CuNO is highly inelastic. Intermediate, excited meta stable reaction products CuNO∗ live for about 0.5 to 1 ps and maybe more.

A escolha do catalisador no processo de reforma a vapor de etanol é de suma importância na determinação da eficiência de produção de hidrogênio, utilizado em células combustíveis. Superfícies de metais de transição (MT) são normalmente utilizadas como catalisadores, porém resultados experimentais têm apresentado que clusters MT suportados em óxidos são mais eficientes e mais seletivos que seus análogos macroscópicos. Assim, para se compreender o mecanismo de interação de etanol e água, e também do radical hidroxila (simples caracterização da ligação O-H), com clusters mágicos MT13 (MT = Ni, Cu, Pd, Ag, Pt e Au), foram utilizados cálculos ab initio baseados na teoria do funcional da densidade com o funcional proposto por Perdew-Burke-Ernzerhof (PBE) e a aproximação de Tkatchenko-Scheffler para as correções de van der Waals (vdW). Os orbitais de Kohn-Sham foram expandidos através de orbitais numéricos centrados nos átomos (NAOs), que estão implementados no pacote Fritz Haber Institute - ab initio molecular simulations (FHI-aims). Foi encontrado que clusters 3d e 4d apresentam configurações mais compactas, enquanto os sistemas de Pt13 e Au13 adotam geometrias mais abertas. Em particular, Au13 possui uma estrutura planar como configuração mais estável, enquanto o seu primeiro isômero mais energético possui uma estrutura 3D. Para os cálculos de adsorção foram selecionados os clusters de menor energia (LOW), e os clusters icosaédricos (ICO). Observou-se que a hidroxila (OH) não possui sítio preferencial ou dependência geométrica durante adsorção, enquanto água e etanol se ligam preferencialmente através do oxigênio no sítio top. Para o caso do etanol também é possível se encontrar isômeros com energias mais altas, na ordem de kT, que se ligam via hidrogênio do grupo CH e que são prováveis a temperatura ambiente. OH possui um elétron desemparelhado, o que favorece a formação de ligações químicas entre a molécula e MT13, de forma que a energia de adsorção varia entre -4.11 e -2.94 eV, condizente com a transferência de carga do cluster para a molécula. Quando se compara a adsorção de água (etanol) sobre superfícies MT(111) e MT13, nota-se que a energia de adsorção, que segue a ordem 3d > 4d > 5d para MT(111), é maior em relação aos clusters e varia entre -255 meV (-317 meV) < -Ead < -670 meV (-837 meV); porém a magnitude da interação ocorre na ordem 3d > 4d, mas 4d < 5d. A quebra da tendência pode ser explicada através dos efeitos de tamanho, que potencializam a atividade catalítica dos clusters de platina e ouro. É possível se observar ainda que as moléculas interagem mais fortemente com os MT13 dos metais com orbitais d semi-preenchidos, uma vez que esses proporcionam um maior rearranjo da densidade eletrônica. Ocorre uma pequena transferência de carga das moléculas de água e etanol para os clusters, apontando para a fraca interação. Cálculos vibracionais suportam as modificações estruturais e energéticas que ocorrem no sistema, onde νO-H aumenta para a hidroxila e diminui para água e etanol. / The choice of the catalyst in steam reforming of ethanol process has a central hole in determining the hydrogen production efficiency, used in fuel cells. Transition-metal (TM) surfaces are commonly used as catalysts, but experimental results have shown that TM clusters supported on oxides are more efficient and more selective than their macroscopic analogues. Therefore, to understand the mechanism of interaction between ethanol and water, and also the hydroxyl radical (simple characterization for the O-H bonding) with TM13 magic clusters (TM = Ni, Cu, Pd, Ag, Pt and Au), we performed ab initio calculations based on density functional theory within the functional proposed by Perdew-Burke-Ernzerhof (PBE) and Tkatchenko-Scheffler approach for van der Waals corrections (vdW). The Kohn-Sham orbitals were expanded by numerical atom-centered orbitals (NAOs), which are implemented at the Fritz Haber Institute - ab initio molecular simulations package (FHI-AIMS). We found that clusters 3d and 4d prefer more compact configurations, while Pt13 and Au13 systems adopt more open geometries. In particular case of Au13, our lowest energy configuration is a planar structure, while the first high energy isomer is a 3D configuration. For adsorption calculations, we selected the lowest energy configurations (LOW), and the icosahedral clusters (ICO). We observed that the hydroxyl (OH) has no adsorption site preference and also it does not show a geometric trend, while water and ethanol preferentially bind via oxygen at the top site. In the case of ethanol, it is also possible to find isomers with higher energies, which bind via hydrogen from CH group, and they are probable at room temperature. OH has an electron unpaired, which favors the formation of chemical bonds between the molecule and TM13, so that the adsorption energy varies from -4.11 to -2.94 eV, consistent with charge transfer from cluster to the molecule. When we compare the water and ethanol adsorption on surfaces TM(111) and on TM13, we note that the adsorption energy, that follows the order 3d > 4d > 5d for MT(111), is higher compared to the clusters energy. For water (ethanol), this property varies between -255 meV (-317 meV) < -Ead < -670 meV (-837 meV); however, the magnitude of the interaction occurs in the order 3d > 4d, but also 4d < 5d. The breaking of the trend can be explained by size effects, that enhances the catalytic activity of platinum and gold clusters. It is also observed that the stronger interaction between molecules and TM13 with d-orbitais partly occupied, since these metals provide a higher rearrangement of the electron density. There is a small charge transference from water and ethanol molecules to the clusters, pointing to the weak interaction. Vibrational calculations support the structural and energetic changes that occur in the system, where νO-H increases for the hydroxyl and decreases to water and ethanol.