This study addresses the structure and the bonding in the family of tetrahedral boranes. The specific molecules studied are the series B4X4 (X=H, F, Br, Cl, I), the series B4BrCl3, B4Br2Cl2, and B4Br3Cl and tetra-tert-butyl-tetraborane, t-Bu4B4. The research presented herein employs the Hartree-Fock Self Consistent Field (HFSCF), the Moller-Plesset second-order perturbation theory (MP2), and the Density Function Theory (DFT). A variety of basis sets was employed. Our calculations are the first theoretical studies of B4Br4, B4I4, B4BrCl3, B4Br2Cl2, and B4Br3Cl, and are also the first calculations for the D4h structures of any of these molecules, except for B4H4. These results were compared with experimental results, where such comparisons can be made. The most energetically stable structure for all the B4X4 and B4BrnClm molecules has symmetry Td.

A descoberta da magnetoresistência (GMR) em materiais granulares gerou um grande interesse no estudo destes materiais, havendo um empenho particular no estudo de grãos de CO em CU e AG. Como as propriedades de transporte estão ligadas intimamente às estruturais, o entendimento da GMR nestes materiais requer uma descrição acurada destas características. Neste trabalho, procurando determinar algumas características magnéticas locais, usamos o método RS-LMTO-ASA para realizar um estudo sistemático dos momentos magnéticos locais e campos hiperfinos com respeito ao tamanho de grãos de CI com até 135 átomos em matrizes de CU e AG fcc. Além disso, estudamos FE e CO nas configurações espaciais seguintes em hospedeiro AG: impurezas isoladas, dímeros FE-FE e FE-CO e precipitados com 13, 19 e 43 átomos. Calculamos o FE enquanto impureza central nos grãos de CO e, para os clusters com 13 e 19 átomos, também consideramos a impureza em posições de interface. Encontramos para os grãos em AG momentos magnéticos bastante estáveis e, para o CU, obtivemos uma ligeira dependência do momento magnético médio com o tamanho do grão. Nossos resultados mostram que há uma diferença significativa no comportamento de grãos e clusters livres. Para os campos hiperfinos, mostramos que este segue comportamentos semelhantes em todos os casos, tendo uma dependência sistemática com relação ao sítio / The discovery of giant magnetoresistance (GMR) in granular materiais generated a great interest in the study of these systems. Special attention has been devoted to Co grains inside Cu and Ag medium. As the transport properties are closely related to structural characteristics, an accurate description is required in order to understand the GMR behavior in these materiais. Here we use the Real Space-LMTO-ASA method to perform a systematic study of the site and grain size dependence of local magnetic moments and hyperfine fields at Co grains ( up to 135 atoms) in fcc Ag and Cu hosts. We have also studied Fe and Co atoms in different spatial configurations in Ag hosts: isolated impurities, Fe-Fe and Fe-Co dimmers and precipitates containing 13, 19 and 43 atoms. Special attention is given to the differences between central and interface positions of Fe atoms in the two smallest Co clusters. We found a very stable value for the local moment at Co atoms in Ag hosts whereas the average local moments for Co grains in Cu tend to be slight ly larger for larger grains. we show that free and embedded Co clusters have very different magnetic behavior. The hyperfine fields present similar values in both matrices and exhibit a systematic site dependence.

O estudo da polarização eletrostática em líquidos homogêneos é crucial para compreender as propriedades termodinâmicas e de solvatação. Estes efeitos de polarização são também importantes para estudar a dinâmica molecular de reações químicas, conformações (tais como proteínas), e do meio solvente (solvatocromismo e RMN). Nesta dissertação, estudou-se a variação do momento de dipolo da fase gasosa para a fase líquida das moléculas: acetona, acetonitrila, amônia e água. Os momentos de dipolo em fase gasosa foram obtidos com cálculos quânticos ab initio para a molécula isolada. Para a fase líquida, cálculos equivalentes foram feitos sobre estruturas geradas de simulação computacional clássica (Monte Carlo). Tal procedimento foi feito segundo a metodologia \"Monte Carlo / Mecânica Quântica - Seqüencial\". Este método foi aplicado iterativamente, tornando possível estudar a variação do momento de dipolo e das propriedades termodinâmicas devido à mútua polarização das moléculas do solvente. Usando os resultados calculados, uma discussão foi realizada sobre a polarização eletrostática e o dipolo induzido em fase líquida. / The study of the electrostatic polarization in homogeneous liquids is crucial to the understanding of thermodynamic and solvation properties. These polarization effects are also important to study molecular dynamics of chemical reactions, conformations (such as proteins), and solvent environment (solvatocromism and NMR). In this dissertation, the variation of dipole moments from the gas phase to the liquid phase of acetone, acetonitrile, ammonia and water, were studied. The dipole moments in the gas phase were obtained with quantum mechanical ab initio calculation on the isolated molecule. For the liquid phase, equivalent quantum mechanical calculations were made on structures generated from classical computer simulations (Monte Carlo). Such procedure was made according to the methodology \"Sequential - Monte Carlo/Quantum Mechanics\". This method was applied iteratively, becoming possible to study the variation of the dipole moment and the thermodynamic properties due to the mutual polarization of the solvent molecules. Using the calculated results, a discussion was made of the electrostatic polarization and the induced dipole moment in the liquid phase.

Nesta tese estudamos o espectro de absorção da Merocianina de Brooker (MB) e três derivados em solventes com diferentes polaridades. O interesse no estudo desses sistemas se dá pela presença de algumas propriedades particulares das merocianinas, por exemplo, apresentam um grande deslocamento solvatocrômico devido à mudança na polaridade do meio. Nós apresentamos os resultados teóricos obtidos para o espectro de absorção das moléculas considerando diferentes estruturas para o estado fundamental: formas trans, cis, zwiteriônica (zw), protonada (MBH+) e dímero(MB2). O efeito do solvente foi considerado utilizando diferentes modelos de solvatação: (i) modelo contínuo polarizável (PCM), (ii) através de uma configuração eletrostática média do solvente (ASEC), (iii) incluindo algumas moléculas explícitas do solvente juntamente com um ambiente eletrostático gerado pelas demais moléculas do solvente. Como uma investigação adicional, apresentamos nossos resultados de medidas experimentais para o espectro de absorção da MB em vários solventes variando acidez e concentração. Vimos, através de cálculos quânticos, que as formas cis/trans apresentam a excitação eletrônica na mesma região, e que a deformação estrutural gerada pela forma zw provoca um deslocamento para o vermelho na excitação eletrônica. Os nossos resultados teóricos e experimentais mostram que a forma MBH+ apresenta um solvatocromismo pequeno, com deslocamento de 20 nm provocado pela mudança água-clorofórmio. Realizando medidas experimentais através da titulação espectroscópica nós obtivemos o pKa associado ao processo de desprotonação/protonação da MB em água e metanol. Em água obtivemos um valor de 8.7, em boa concordância com valores da literatura. Apresentamos um valor inédito do pKap da MB em metanol, 9.9. Conseguimos uma boa descrição teórica para a excitação eletrônica da MB em solventes com alta polaridade, na região entre 430-500 nm, utilizando o método quântico TD-DFT com funcionais B3LYP e CAM-B3LYP e conjunto de funções base 6-311+G**, porém a excitação em solventes de baixa polaridade, que ocorre na região entre 550-650 nm, não é corretamente descrita considerando a MB nos solventes. Nós vimos, através de estudos experimentais, que a sonda MB pode agregar em solventes de baixa polaridade. Os cáculos teóricos para dímeros em solução mostraram a existência de uma excitação eletrônica de baixa intensidade nesta região. Adicionalmente, os espectros experimentais em solventes de baixa polaridade mostraram 2 bandas, onde a segunda se assemelha com a banda observada para a forma MBH+. Para explicar essas 2 bandas experimentais para a MB, apresentamos uma proposta teórica onde ocorre uma transferência de prótons (H+) entre os monômeros do dímero formado, gerando uma estrutura desprotonada (MBH-) e uma protonada (MBH+). Cálculos teóricos para a forma MBH- mostram que essa forma apresenta uma excitação eletrônica de intensidade moderada na região entre 550-650 nm. Com essa hipótese nós conseguimos descrever, através de cálculos teóricos, o solvatocromismo anômalo observado experimentalmente para o espectro eletrônico de absorção da MB nas duas regiões de polaridade dos solventes: alta polaridade, sendo descrita pela forma MB, e baixa polaridade, descrita pela forma MBH-. / In this thesis we studied the absorption spectrum of merocyanine Brooker (MB) and three derivatives in solvents with different polarities.The interest in this system is given by the presence of some particular properties of this molecule, for example, it presents a large solvatochromic shift due to the change in the polarity of the medium. We present the results for the absorption spectrum of the molecules considering different structures to the ground state: forms trans, cis, zwitterionic (zw), protonated MBH+ and dimer (MB2). The solvent effect was treaty by different ways: (i) continuous model using the PCM polarizable, (ii) by an average electrostatic configuration of solvent, ASEC, (iii) including some explicit solvent molecules with an electrostatic environment generated by other solvent molecules. As an additional investigation, we present results of experimental measurements in the thesis. We have seen, through quantum calculations, that the forms cis/trans have the electronic excitation in the same region and the structural deformation generated in the zw form causes a red shift. Our theoretical and experimental results show that the MBH+ form has a small solvatochromism, with displacement of 20 nm caused by water-chloroform change. Performing spectroscopic titration we got the pKa associated with the process of deprotonation/protonation of MB in water and methanol. In water we obtained a value of 8.7, in good agreement with the values reported in the literature. We present a unpublished pKap for the MB in methanol, 9.9. We got a good theoretical description for electronic excitation of MB in solvents with high polarity, in the region between 430-500 nm, using a method quantum TD-DFT B3LYP and CAM-B3LYP functional whit basic functions set 6-311+G** but the excitation in low polarity solvents, which occurs in the region between 550-650 nm, is not properly described considering the MB form in the solvents. We have seen, through experimental studies that the MB probe can aggregate in low polarity solvents. Theoretical calculations for dimer in solution showed the existence of a low intensity electron excitation in this region. Additionally, the experimental spectra in low polarity solvents showed 2 bands, where in the second band is similar to the observed to MBH+ form. To explain these two experimental bands for MB, we present a theoretical proposal where there is a proton transfer (H+) between the monomers of the dimer, generating a deprotonated structure (MBH-) and a protonated (MBH+). Theoretical calculations for the MBH- show that this form presents an electronic excitation of moderate intensity in the region between 550-650 nm. With this assumption we can describe, through theoretical calculations, the anomalous solvatochromism for the electronic absorption spectrum of MB in the two polarity regions of solvents: high polarity is described by the MB form, and low polarity, described by the MBH- form.

In the present work we performed electronic structure calculations within the Kohn-Sham scheme of the density functional theory (DFT). We studied two molecules with potential applications in life sciences and medicine: ferrioxamine B and 5,10,15,20-tetrakis(1-methyl-4-pyridyl)-21H,23H (TMPyP) porphyrin. We used different methods and different exchange and correlation functionals, analyzing optical and vibrational properties and hyperfine interactions. In the case of ferrioxamine B, results in the crystalline phase (molecular crystal), and gas phase were compared with experimental results obtained using Mössbauer spectroscopy from the literature. We analyzed hyperfine parameters such as the electric quadrupole splitting, asymmetry parameter, hyperfine field and isomer shift. In the case of TMPyP porphyrin we analyzed vibrational properties in the gas phase and optical properties. For the electronic absorption, solvent effects and electronic charges states were analyzed. / In the present work we performed electronic structure calculations within the Kohn-Sham scheme of the density functional theory (DFT). We studied two molecules with potential applications in life sciences and medicine: ferrioxamine B and 5,10,15,20-tetrakis(1-methyl-4-pyridyl)-21H,23H (TMPyP) porphyrin. We used different methods and different exchange and correlation functionals, analyzing optical and vibrational properties and hyperfine interactions. In the case of ferrioxamine B, results in the crystalline phase (molecular crystal), and gas phase were compared with experimental results obtained using Mössbauer spectroscopy from the literature. We analyzed hyperfine parameters such as the electric quadrupole splitting, asymmetry parameter, hyperfine field and isomer shift. In the case of TMPyP porphyrin we analyzed vibrational properties in the gas phase and optical properties. For the electronic absorption, solvent effects and electronic charges states were analyzed.

Two dimensional (2D) materials with interesting fundamental physics and potential applications attract tremendous efforts to study. The versatile properties of 2D materials can be further tailored by tuning the electronic structure with the layer-stacking arrangement, of which the main adjustable parameters include the thickness and the in-plane twist angle between layers. The Angle-Resolved Photoemission Spectroscopy (ARPES) has become a canonical tool to study the electronic structure of crystalline materials. The recent development of ARPES with sub-micrometre spatial resolution (micro-ARPES) has made it possible to study the electronic structure of materials with mesoscopic domains. In this thesis, we use micro-ARPES to investigate the spatially-resolved electronic structure of a series of few-layer materials: 1. We explore the electronic structure of the domains with different number of layers in few-layer graphene on copper substrate. We observe a layer- dependent substrate doping effect in which the Fermi surface of graphene shifts with the increase of number of layers, which is then explained by a multilayer effective capacitor model. 2. We systematically study the twist angle evolution of the energy band of twisted few-layer graphene over a wide range of twist angles (from 5° to 31°). We directly observe van Hove Singularities (vHSs) in twisted bilayer graphene with wide tunable energy range over 2 eV. In addition, the formation of multiple vHSs (at different binding energies) is observed in trilayer graphene. The large tuning range of vHS binding energy in twisted few-layer graphene provides a promising material base for optoelectrical applications with broad-band wavelength selectivity. 3. To better extract the energy band features from ARPES data, we propose a new method with a convolutional neural network (CNN) that achieves comparable or better results than traditional derivative based methods. Besides ARPES study, this thesis also includes the study of surface reconstruction for the layered material Bi2O2Se with the analysis of Scanning Tunnelling Microscopy (STM) images. To explain the origin of the pattern, we propose a tile model that produces the identical statistics with the experiment.

A series of 2,5-diarylidene-cyclopentanones (ndbcp), their protonated cations (ndbcp-H+), and a substituted compound, 2,5-bis-[3-(4-dimethylamino-phenyl)-allylidene-cyclopentanone (2dbma) have been synthesized. Their electronic absorption and fluorescence spectra have been measured. The absorption spectra have been assigned with the aid of INDO/S calculations. Molecular structures used for the INDO/S calculations were computed with the PM3 Hamiltonian. Polarized excitation spectra have been measured for 2dbcp and 3dbcp at 77 K in ethanol/methanol glass and used as an aid for the assignments of electronic transitions. Absorption and fluorescence spectra have been measured in solvents of varying polarity for all compounds synthesized. The influence of hydrogen bonding on the excitation spectra of compounds has been investigated. Solvent induced shifts in the absorption and fluorescence spectra of 3dbcp and 2dbma in combination with the PM3 calculated ground state dipole moment have been used to determine the excited state dipole moment of these compounds. Fluorescence quantum yields have been obtained to analyze the changes in the nonradiative rate of decay from S1. The protonated cations have been prepared in acids of different strength. The influence of acid strength on the excitation and emission spectra has been analyzed by gradually diluting acid solution. Evidence for excited state proton transfer in weak acids has been obtained for 2dbcp and 3dbcp. Brief photochemical studies of 1dbcp and 1dbcp-H+ have been carried out and analyzed by HPLC.

The interest in two-dimensional materials and materials physics has grown dramatically over the past decade. The family of two-dimensional materials, which includes graphene, transition metal dichalcogenides, phosphorene, hexagonal boron nitride, etc., can be fabricated into atomically thin films since the intralayer bonding arises from their strong covalent character, while the interlayer interaction is mediated by weak van der Waals forces. Among them, molybdenum disulfide (MoS₂) has attracted much interest for its potential applications in opto-electronic and valleytronics devices. Previously, much of the experimental studies have concentrated on optical and transport measurements while neglecting direct experimental determination of the electronic structure of MoS₂, which is crucial to the full understanding of its distinctive properties. In particular, like other atomically thin materials, the interactions with substrate impact the surface structure and morphology of MoS₂, and as a result, its structural and physical properties can be affected. In this dissertation, the electronic structure and surface structure of MoS₂ are directly investigated using angle-resolved photoemission spectroscopy and cathode lens microscopy. Local-probe angle-resolved photoemission spectroscopy measurements of monolayer, bilayer, trilayer, and bulk MoS₂ directly demonstrate the indirect-to-direct bandgap transition due to quantum confinement as the MoS₂ thickness is decreased from multilayer to monolayer. The evolution of the interlayer coupling in this transition is also investigated using density functional theory calculations. Also, the thickness-dependent surface roughness is characterized using selected-area low energy electron diffraction (LEED) and the surface structural relaxation is investigated using LEED I-V measurements combined with dynamical LEED calculations. Finally, bandgap engineering is demonstrated via tuning of the interlayer interactions in van der Waals interfaces by twisting the relative orientation in bilayer-MoS₂ and graphene-MoS₂-heterostructure systems.

Estudos teóricos e experimentais acerca de danos em biomoléculas induzidos pela captura eletrônica em meio biológico têm sido largamente discutidos ao longo da última década. No presente trabalho, abordou-se o problema da captura eletrônica pelo nucleotídeo monofosfato 3\'-dGMP com técnicas de estrutura eletrônica, explorando estados ligados do ânion. Buscou-se investigar o ânion em fase gasosa e em solução aquosa, além de estimar barreiras de energia pontecial e energia livre associadas à sua dissociação (quebra da ligação ribose-fosfato). Utilizando os modelos de solvatação implícita (PCM) e explícita (simulação computacional com o método de Monte Carlo), concluiu-se que, em meio aquoso, o estado fundamental do ânion 3 -dGMP apresenta caráter de valência sobre a base nitrogenada (orbital com ocupação simples), em oposição ao resultado em fase gasosa, que prevê um estado ligado por dipolo. A barreira de dissociação, relativa ao estiramento da ligação entre os grupos ribose e fosfato, foi estimada em 16-30 kcal/mol, dependendo da técnica de solvatação utilizada. / Theoretical and experimental studies on the damage to biomolecules induced by electron attachment in the biological environment have been widely discussed over the past decade. In the present work, we addressed electron capture by the monophosphate nucleotide 3 -dGMP with electronic structure techniques, exploring bound anion states. We have investigated these anion states in gas phase and in aqueous solution, and estimated the potential and free energy barriers related to the dissociation reaction (breakage of the ribose-phosphate bond). Employing implicit (PCM) and explicit (computer simulation with the Monte Carlo method) solvation models, we have concluded that, in aqueous environment, the ground state of the 3-dGMP specie has valence character with the singly occupied molecular orbital localized on the base. In contrast, the gas phase results point out a dipole-bound ground state. The free energy barrier for the dissociation mechanism, according to the present results, would be around 16-30 kcal/mol in aqueous solution, depending on the salvation model.

Neste trabalho estudamos propriedades estruturais, magnéticas e eletrônicas de complexos de cobre em duas classes de ligantes semelhantes com potenciais aplicações nas áreas de nanotecnologia e farmacologia. A primeira classe de ligantes é do tipo bases de Schiff, conhecidas por sua vasta gama de aplicações em química e biologia, aqui estudadas como miméticos de sítios de proteínas e também como potenciais metalo-fármacos. Procuramos investigar as características estruturais e eletrônicas buscando correlacionar as informações obtidas experimentalmente com as obtidas através de cálculos de estrutura eletrônica. Em especial, no estudo da competição pelo íon Cu entre as bases de Schiff e a proteína albumina, mostramos a influência de diversos fatores como, por exemplo, a geometria dos ligantes e a sua estrutura eletrônica. A segunda classe estudada é constituída de bases modificadas de DNA com a habilidade de complexar metais (espécie [M-DNA]) e formar estruturas com acoplamento ferromagnético. Observamos para as espécies [M-DNA] que o acoplamento ferromagnético é estabilizado através de dois efeitos: a) diferentes estados de carga que podem gerar distorções na coordenação quadrado planar; b) a adição do backbone do DNA. Utilizamos neste estudo o método Projector Augmented Wave (PAW) e também bases locais dentro da Teoria do Funcional da Densidade, atrav´es dos c´odigos computacionais CP-PAW e Gaussian03. / We studied structural, electronic and magnetic properties of copper complexes with two similar classes of ligands with potential applications in nanotechnology or pharmacology. The first class of compounds consists of Schiff bases and corresponding copper complexes. We investigated structural and electronic properties of these complexes searching for correlations among the information obtained experimentally and by electronic structure calculations. In special, in the study of the competition for the Cu ion between Schiff bases and the albumin protein, we show the influence of different factors such as the geometry of the ligands and their electronic structure. The second class of ligands focused in our studies are modified DNA bases coordinated to copper, where EPR studies have shown ferromagnetic interactions among the metal centers. We studied in this case the influence of the charge state and of the backbone in the magnetization of the Cu chain. In all cases presented here, we used ab-initio electronic structure calculations in the framework of the Density Functional Theory (DFT). This has been done using the CP-PAW code and the Gaussian03 code.