Nowdays, coupled cluster method belongs to one of the most used quantum chemical methods. However, the single-reference coupled cluster methods are not able to describe systems where the static correlation have an important role. Multireference coupled cluster methods developed in our group can describe both static and dy- namic correlation and can be used for problematic systems. Together with explicitly correlated wavefunction, which can properly describe the electronic cusp and speed up the convergence to the complete ba- sis set limit, they are able to calculate computationally demanding diradicals. Multireference CC calculations of tetramethylenethane have been perforemd and the performance of explicitly correlated version is discussed. Calculations of the isomerization of bicyclobu- tane using the multireference approach are presented as well. 1

This PhD thesis deals with research activity in organic electronics, an extremely exciting field offundamental science, which is complemented by relevant applications in every-day life: optoelectronics,solar energy conversion (photovoltaics), sensing and information technology, just to mentiona few. In this area, charge transfer/energy transfer processes, as well as light matter interaction,play a major role. Within this topic, this work focus on the theoretical study of the electronic structureand related charge transfer/spectroscopic properties of various molecular systems: Coronenecrystals, F4TCNQ/perylene co-crystals, polythiophenes, PCPDT/PCPDT-BT homo- and copolymerbased on thiophene, chemisorbed ferrocene on Si(111) substrate. Particular attention wasdevoted to the calculation of infrared (IR) and electronic spectra associated with the so-called “polaronsignature” in doped organic semiconductors. To assess the reliability and physical meaning of electronic quantities involved in the calculations(like the HOMO/LUMO gap, theoretical spectroscopic intensity and vibrational modes, pursuingthe comparison between neutral and charged systems) a number of different levels of the theoryhave been systematically varied from HF (Hartree-Fock) to “pure” DFT (Density Functional Theory),as well as hybrid B3LYP (Becke 3-Parameter (Exchange), Lee, Yang and Parr 1,2) and longrange corrected Coulomb-Attenuating Method (CAM-B3LYP) functionals. In the attempt to untanglethe physics underlying the polaron formation in charged molecular systems (as evidenced by theoccurrence of giant intensity bands found in IR spectra), the mapping of the vibrational mode betweenneutral and charged systems has been calculated. A major achievement in this work is thatthe vibrational (giant) mode associated with the “polaron” emerges as a new mode (peculiar of thecharged state) not related to any mode existing in the neutral system.

CoordenaÃÃo de AperfeiÃoamento de NÃvel Superior / SÃo apresentados aqui cÃlculos de primeiros princÃpios realizados para a obtenÃÃo de propriedades Ãpticas e eletrÃnicas da molÃcula e do cristal de L-alanina. No caso da molÃcula, foi efetuada a otimizaÃÃo da geometria para trÃs conformaÃÃes e usando trÃs mÃtodos diferentes: aproximaÃÃo de Hartree-Fock na base 6-31++G(d,p), aproximaÃÃo de Hartree-Fock na base 6-311++G(3d,3p) e teoria do funcional da densidade (funcional de troca e correlaÃÃo B3LYP) na base 6-31++G(d,p). A partir da otimizaÃÃo das geometrias para diferentes conformaÃÃes, foram obtidas a energia total, momentos de dipolo e quadrupolo, polarizabilidades, propriedades termodinÃmicas, modos normais de vibraÃÃo, espectros Raman, infravermelho e VCD, nÃveis de energia eletrÃnicos e orbitais HOMO e LUMO, com comparaÃÃes com resultados experimentais ao longo do trabalho. Para o cristal de L-alanina, a geometria dos Ãtomos na cÃlula unitÃria foi otimizada usando as aproximaÃÃes LDA e GGA, determinando-se a estrutura de bandas, massas efetivas, funÃÃo dielÃtrica, absorÃÃo, refletividade e Ãndice de refraÃÃo. Estes dados sÃo usados na investigaÃÃo do espectro de luminescÃncia do cristal de L-alanina puro e dopado com manganÃs. Os cÃlculos ab initio permitem associar os picos de fotoluminescÃncia no visÃvel a processos de natureza excitÃnica relacionados a nÃveis de polaron e impurezas aprisionadoras de portadores. Calculando as transiÃÃes vertical e adiabÃtica entre os estados excitados e o estado fundamental de uma molÃcula de L-alanina simples na forma zwitteriÃnica, o pico estreito da fotoluminescÃncia no ultravioleta à atribuÃdo a transiÃÃes intramoleculares nas molÃculas de L-alanina fracamente interagentes dentro do cristal, o que deixa uma assinatura molecular especÃfica do aminoÃcido. Jà o estudo da fotoluminescÃncia integrada do cristal dopado com Mn2+ revela um forte quenching da luminescÃncia provocado pela presenÃa do Ãon metÃlico nos interstÃcios da cÃlula unitÃria. Resultados de cÃlculos ab initio preliminares indicam que tal quenching esta relacionado ao modo como a distribuiÃÃo de energias excitÃnicas muda quando o Ãon e inserido num interstÃcio da cÃlula unitÃria. / Ab initio calculations for the molecule and crystal of L-alanine are presented. Geometry optimizations were performed for three L-alanine molecular conformers using three different methods: Hartree-Fock approximation with a 6-31++G(d,p) basis, Hartree-Fock approximation with a 6-311++G(3d,3p) basis and Density Functional Theory (B3LYP exchange-correlation functional) with a 6-31++G(d,p) basis. From the geometry optimizations, total energies, dipole and quadrupole moments, polarizabilities, thermodynamical properties, normal modes, Raman, infrared and VCD spectra, energy levels and frontier molecular orbitals were obtained and comparisons with experimental results were carried out. For the L-alanine crystal, geometry optimization was performed within the framework of DFT (LDA and GGA), and band structures, effctive masses, dielectric function, absorption, reflectivity and refraction index were calculated. Those results were employed to investigate the photoluminescence spectra of undoped and Mn-doped L-alanine crystals. The ab initio results allow assignment of the photoluminescence peaks in the visible region to lattice-related processes of exciton nature associated with polaron levels and defect trapping centers for carriers. By evaluating the vertical and adiabatic transitions between the ground state and excited states of a single L-alanine molecule in the zwitterion form, the very thin photoluminescence peak in the ultraviolet region is assigned to intramolecular transitions in the weakly interacting L-alanine molecules forming the crystals, being a signature of the type of the crystalline amino acid. In the case of Mn-doped alanine crystal, the integrated photoluminescence intensity is shown to be dramatically quenched by the intersticial manganese, with a decrease greater than 65% for higher doping. Preliminar ab initio calculations indicate that this quenching is related to the change of exciton energy levels due to the charge redistribution in the unit cell when manganese ions are present.

Submitted by Rosivalda Pereira (mrs.pereira@ufma.br) on 2017-08-23T17:31:16Z No. of bitstreams: 1 AndreCortez.pdf: 8621619 bytes, checksum: a2c58769de7cc646bd6e13cee7259a78 (MD5) / Made available in DSpace on 2017-08-23T17:31:16Z (GMT). No. of bitstreams: 1 AndreCortez.pdf: 8621619 bytes, checksum: a2c58769de7cc646bd6e13cee7259a78 (MD5) Previous issue date: 2012-01-28 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / In this work we address a theoretical calculation of the electronic spectra in Si-Ge atomic chain that is arranged in a Fibonacci quasi-periodic sequence, by using semi-empirical quantum method based on Hückel extended model. We apply the Fibonacci substitutional sequences in the atomic building blocks A(Si) and B(Ge) through the in ation rule or recursion relation. In our ab initio calculations we use only a single point which is the sufi cient condition to consider all the orbitals and charge distribution across the entire system. Although the calculations presented here are more complete than the models adopted in the literature which take into account the electronic interaction, up to the second and third neighbors, an interesting property remains in their electronic spectra: the fractality (which is the main signature of this kind of system). We discuss this fractality of the spectra and we compare them with the randomic arrangement of Si-Ge atomic chain, and with previous results based on the tight-binding approximation of Schorödinger equation considering until the nearest neighbor. / Neste trabalho abordamos um cálculo teórico dos espectros eletrônicos em cadeia atômica de Si-Ge que é organizado em uma sequência Fibonacci quasi-periódica, usando o método semi-empírico com base no modelo quântico Hückel estendido. Nós aplicamos as sequências substitucional de Fibonacci nos blocos de construção atômica A(Si) e B(Ge) através da relação de recursão. Em nossos cálculos ab initio, usamos apenas um único ponto, que é a condição sufi ciente para considerar todos os orbitais e a distribuição de cargas em todo o sistema. Embora os cálculos apresentados aqui sejam mais completos do que os modelos adotados na literatura que levam em conta a interação eletrônica, até segundos e terceiros vizinhos, uma propriedade interessante permanece em seus espectros eletrônicos: a fractalidade (que é a assinatura principal deste tipo de sistema). Discutimos essa fractalidade dos espectros e as comparamos com os espectros de cadeia atômica randômica de Si-Ge, e, também, com os resultados prévios baseados na aproximação tight-binding da equação Schorödinger considerando até o vizinho mais próximo.

Approximately 50 percent of all known peptide hormones are post-translationally modified at their C-terminus. These peptide hormones are responsible for cellular functions critical to survival. Peptidylglycine alpha-amidating monooxygenase (PAM) is a bi-functional enzyme which catalyzes the conversion of peptide pro-hormones to peptide hormones. PAM is the only known mammalian enzyme that catalyzes the necessary alpha-amidation to activate these peptide hormones. PAM has previously been found to perform N-dealkylation, as well as O-dealkylation. We report here that a novel chemistry for PAM, S-dealkylation, has now been shown. PAM was able to catalyzes the hydroxylation and subsequent dealkylation for a series of substituted 2- (phenylthio)acetic acid analogs, leaving a product containing a free thiol capable of coordinating to copper(I). A series of cinnamic acid derivatives have been investigated as turnover dependent inactivators of PAM. It was shown that the inactivating compounds contained electron donating substituents. All compounds bound competitively versus substrate, though no catalytic activity was noted when tested as substrates. Although no Dkinact was observed when using perdeuterated cinnamic acid, one cannot rule out hydrogen abstraction from the Cα as this step may not be rate limiting for inactivation. This suggests that the activated oxygen species generated at CuM may be sufficiently reactive to abstract a hydrogen from an alkene to generate a vinyl radical. Substrate activation is believed to be facilitated by a Cu(II)-superoxo complex formed at CuM. Hydrogen abstraction from the Cα is hypothesized to generate a radical, though this has never been demonstrated spectrometrically. We report here further evidence for the generation of an Ca radical by comparing log(Vmax/KO2) vs σ+ for a series of ring-substituted 4-phenyl-3- butenoic acids. Lastly, a computational study was carried out to probe for a possible binding pocket for the reductant, ascorbate. Though crystal structures have argued that reduction of the enzymebound coppers is collisional, kinetic data for inhibitors competitive against ascorbate indicates that a discrete binding pocket may exist. Our study suggests a specific site for binding and provides free energy calculations in agreement with experimental values for binding constants.

Doctor of Philosophy / First part of the thesis is focused on experimental preparation of new hard quaternary amorphous materials Si-B-C-N with high thermal stability. Materials were prepared in the form of thin films using reactive magnetron sputtering. The technique used proved to be suitable for reproducible synthesis of these materials. The Si-B-C-N films were generally found to be amorphous with low compressive stress and good adhesion to silicon or glass substrates. The process and film characteristics were controlled by varying the sputter target composition, the Ar fraction in the N2–Ar gas mixture, the negative rf-induced substrate bias, and the substrate temperature. Main conclusions describe the relationships between process parameters, discharge and deposition characteristics and film properties (elemental composition, chemical bonding structure, material hardness, compressive stress or electrical conductivity of materials prepared). Second part of the thesis is focused on ab-initio simulations of structures of experimentally prepared Si-B-C-N materials. In the performed liquid-quench simulations, the Kohn-Sham equations for the valence electrons are expanded in a basis of plane wave functions, while core electrons were represented using Goedecker-type pseudopotentials. We simplified the ion bombardment process by assuming that the primary impact creates a localized molten region of high temperature and sufficiently short cooling time, commonly referred to as a thermal spike. Main conclusions deal with N2 formation in studied materials, effect of implanted Ar on structure and properties of prepared materials, ability of Si to relieve that part of compressive stress which is caused by implanted Ar, and ability of B to improve thermal stability of Si-B-C-N materials. The calculated results are compared with experiment.

Les propriétés des matériaux ferroélectriques proviennent principalement de l'influencedes conditions aux limites et des déformations sur la polarisation. Cette influence est encoreplus grande à de petites échelles ou des structures particulières de la polarisation apparaissent,comme les vortex dans les cubes quantiques ou des structures en rayures dans lescouches minces. Pour le calcul, à très basses échelles, de telles structures de polarisation, lesHamiltonien effectifs, basés sur les calculs ab-initio sont les plus utilisés. Parallèlement Lesmodèles continus sont préconisés à plus grandes échelles. Néanmoins, il n'existe pas de lienentre ces deux modèles. Le but de cette thèse est alors de construire une approche permettantde relier ces deux modèles et par cela même ces différentes échelles.Notre modèle se base sur un Hamiltonien effectif écrit pour le titanate de baryum enfonction de la polarisation et des déformations. Cet Hamiltonien est reformulé de façon àdécrire un milieu continu. Les difficultés de cette reformulation proviennent des interactionsnon locales. Le résultat est alors un système d'équations aux dérivées partielles, décrivantl'équilibre et les conditions aux limites. La température est ensuite introduite de façon effectivedans les coefficients de ces équations. Notre modèle ressemble fortement aux modèlesde Landau.Une telle approche est appliquée dans les cubes quantiques et les couches minces óu l'organisationdes domaines dépend de la taille. Les résultats montrent l'implication de la méthodedes éléments finis sur la précision. La formation de vortex dans les cubes quantiquesest bien reproduite. L'agencement en domaines de polarisation alternée dans les couchesminces est elle aussi bien reproduite pour les couches minces. De plus en augmentant l'épaisseurde ces couches minces, la périodicité de cet agencement alterné est modifié, comportementdécrit par la loi de Kittel qui est ici calculée et comparée aux résultats expérimentaux.

L'étude de réactions chimiques, tout comme le calcul de propriétés thermodynamiques, sont des enjeux capitaux de la chimie moderne. L'évolution des instruments et techniques expérimentales permet des mesures de plus en plus précises de ces grandeurs, pour des systèmes de plus en plus complexes. L'intérêt croissant pour l'étude du milieu interstellaire et des atmosphères planétaires se révèle également être un défi très important dans les décennies à venir. Les difficultés rencontrées lors de l'analyse de ces expériences (ou mesures), nécessitent souvent l'intervention de simulations numériques de manière à éclairer ces observations. Une autre utilisation du calcul est de prédire des paramètres moléculaires et spectroscopiques d'espèces instables difficiles à produire au laboratoire. Les outils actuels de la chimie théorique ab initio sont des moyens précieux pour la prédiction et l'interprétation de résultats expérimentaux ou de mesures astrophysiques et atmosphériques. Ces techniques de simulation ont connu des développements importants au cours des dernières décennies. Les progrès récents en matière de calculs d'interaction de configurations de grande taille permettent d'inclure une grande partie de l'énergie de corrélation. Le temps de calcul et la taille mémoire des ordinateurs restent cependant des limites importantes qui ne permettent pas d'effectuer des interactions de configurations totales dans une base suffisamment grande pour contenir la physique des systèmes étudiés au delà de petites molécules. Cet état de fait conduit à s'intéresser à des méthodes moins coûteuses comme celles des perturbations, les interactions de configurations tronquées et le Coupled Cluster, permettant d'inclure une partie de la corrélation électronique à un coût moins élevé en temps de calcul. Ce sont ces méthodes qui ont été utilisées dans ce travail pour déterminer théoriquement les paramètres moléculaires et spectroscopiques des systèmes MgO, MgO+, FeC2, FeC2+ et FeC2- avec le maximum de précision possible.Dans un premier temps, nous avons étudié la molécule MgO. C'est un système de choix car, il permet de s'initier aux méthodes de calcul ab initio sur les systèmes moléculaires les plus simples (diatomiques), de tester et de comprendre ces méthodes (différentes approximations, validité, précision, ...) et de bien interpréter les résultats obtenus (formation de la liaison chimique et des états moléculaires, leur symétrie, leurs couplages, leur stabilité, leur spectroscopie, ...) surtout qu'il a fait l'objet de plusieurs études théoriques et expérimentales. Pour profiter de notre savoir-faire pour les molécules diatomiques nous avons étudié le système MgO+ qui a fait l'objet de notre deuxième article que sera présenté en annexe.Dans un second temps, nous avons visé les systèmes moléculaires de type FenCm afin de comprendre la croissance et la dynamique des nanotubes de carbone catalysée par le Fer. Le système diatomique FeC fait l'objet de plusieurs études théoriques et expérimentales. La plus récente est celle fourni par Demeter Tzeli et Aristides Mavridi. Cette étude théorique a caractérisé son état fondamental ainsi que les 40 états électroniques les plus bas, à toutes les distances internucléaires jusqu'à la dissociation, et d'autre part de fournir des données spectroscopiques d'une précision comparable à celle donnée par l'expérience. Pour les systèmes d'ordre supérieur, confronté par le problème que ces petits systèmes moléculaires constitués de Fer et de Carbone ont des structures électroniques très compliquées, notre étude s'est limitée à l'étude des systèmes FeC2, FeC2+ et FeC2-.

This thesis presents ab-initio quantum mechanical calculations at the density functional theory (DFT) level on defect centers hosted by crystalline systems of geologic importance (i.e. fluorite, quartz, stishovite). The research brings new, complementary data to the current understanding of defect structures in minerals and explores the advantages of a theoretical approach in the field of mineral spectroscopy. This present research presents the first ab-initio calculations of the O23- type defects in crystalline solids. New data on the electronic properties and structural characteristics of O23--Y3+ defect in fluorite-type structures (CaF2 and SrF2) were obtained at the DFT level. These results confirm the stability and the molecular character of the O23--Y3+ center, revealing a spin density that is equally distributed between the two oxygen atoms. Our results report an O-O bond distance of 2.47 Å in CaF2 and 2.57 Å in SrF2. The calculated 17O and 19F hyperfine constants for of the O23--Y3+ center are in good agreement with their corresponding experimental values reported by previous electron paramagnetic resonance (EPR) and electron nuclear double resonance (ENDOR) studies, while discrepancies are notable for the 89Y hyperfine constants and are probably attributable to an inadequate basis set for Y.<p> The present study provides a more complete picture of the coupled Al-M substitution for Si in quartz, while investigating the characteristics and electronic properties of the diamagnetic [AlO4/M+]0 (where M = H, Li, Na and K) defects. The diamagnetic [AlO4/M+(a<)]0 defects with M = H, Li and Na have been shown to be more stable than their [AlO4/M+(a>)]0 structural analogues (where a> and a< denote the location of the charge compensating ion on the long-bond and short-bond side, respectively), correctly predicting the common occurrence of paramagnetic [AlO4/M+(a>)]+ centers. The present study confirms previous suggestions that incorporation of the [AlO4/M+]0 defects results in significant structural relaxations that extend at least to the nearest Si atoms. The [AlO4/K+]0 defects have been investigated for the first time and are shown to be stable in quartz. The results of this study have implications for the uptake of Al in quartz.<p> The present research evaluates the structural models of [AlO4/Li] paramagnetic defects in α-quartz. The results confirm the previous experimental findings and propose an additional paramagnetic defect [AlO4/Li+(csmall)]+, with the unpaired electron located on a short-bonded O atom and the Li compensator just off the edge of the small channel. Accordingly we suggest that three distinct Al-Li paramagnetic defects can be can be found in quartz, two of them having the hole located on a short-bonded O and one trapping the hole on a long-bonded O atom. However the structural similarities with the [AlO4/Li+(a>)]+ defect would require detection and measurement of the 17O hyperfine structure for an unequivocal EPR identification.<p> The present work also reports on first-principles quantum-mechanical calculations on the previously proposed [O23--Al3+] defect in stishovite. Our results show that the unpaired spin is 85% localised on one of the six oxygen atoms at an AlO6 octahedron, while the calculated 27Al hyperfine constants are similar to those determined by EPR experiments. Accordingly we propose the Al center to represent an [AlO6]0 defect, and hole hoping among equivalent oxygen atoms is responsible for its detection only at cryogenic temperatures. Theoretical calculations also show that diamagnetic precursors [AlO6/H+]0, [AlO6/Li+]0 and [AlO6/Na+]0 are stable in stishovite. The calculated OH bond distance and orientation are in excellent agreement with those inferred from FTIR spectra and previous theoretical calculations. The calculated [AlO6/Li+]0 and [AlO6/Na+]0 defects suggest that monovalent cations such as Li+ and Na+ are potentially important in accommodating Al in stishovite in the lower mantle.

Energetic materials comprise a set of systems of tremendous technological importance. Besides helping shape landscapes to establish communications, they have been used to reach fuel reservoirs, deploy safety bags and prevent heart strokes. Understanding its behavior can help in attaining strategic and tactical superiority, and importantly, preserve lives of people who handle these materials. The large discrepancy in length and time scales at which characteristic processes of energetic materials are of relevance pose a major challenge for current simulation techniques. We present a systematic study of crystalline energetic materials of different sensitivity and analyze their properties at different theoretical levels. Equilibrium structures, vibrational frequencies, conformational rearrangement and mechanical properties can be calculated within the density functional theory and molecular dynamics at finite temperatures. We have found marked differences in the calculated properties in systems with ranging sensitivities. Reactions at elevated temperatures have been studied using ab initio molecular dynamics method for crystals of nitroethane. Furthermore, while presenting the state of the art of energetic materials modeling, the limitations of each methodology are also discussed. Prospective systems and an elasticity driven approach that can be applied to other type of materials is also presented.