X-rays have been widely exploited to unravel the structure of matter since their discovery in 1895. Nowadays, with the emergence of new X-ray sources with higher intensity and very short pulse duration, notably X-ray Free Electron Lasers, the number of experiments that may be considered in the X-ray regime has increased dramatically, making the characterization of gas phase atoms and molecules in space and time possible. This thesis explores in the theoretical analysis and calculation of X-ray scattering atoms and molecules, far beyond the independent atom model. Amethod to calculate inelastic X-ray scattering from atoms and molecules is presented. The method utilizes electronic wavefunctions calculated using ab-initio electronic structure methods. Wavefunctions expressed in Gaussian type orbitals allow for efficient calculations based on analytical Fourier transforms of the electron density and overlap integrals. The method is validated by extensive calculations of inelastic cross-sections in H, He+, He, Ne, C, Na and N2. The calculated cross-sections are compared to cross-sections from inelastic X-ray scattering experiments, electron energy-loss spectroscopy, and theoretical reference values. We then begin to account for the effect of nuclear motion, in the first instance by predicting elastic X-ray scattering from state-selected molecules. We find strong signatures corresponding to the specific vibrational and rotational state of (polyatomic) molecules. The ultimate goal of this thesis is to study atomic and molecular wavepackets using time-resolved X-ray scattering. We present a theoretical framework based on quantum electrodynamics and explore various elastic and inelastic limits of the scattering expressions. We then explore X-ray scattering from electronic wavepackets, following on from work by other groups, and finally examine the time-resolved X-ray scattering from non-adiabatic electronic-nuclear wavepackets in the H2 molecule, demonstrating the importance of accounting for the inelastic effects.

Os estudos de modelagem molecular das interações entre ligantes baseado em oxindóis (isaepy, isapn, [Cu(isapn)]², isaenim e o SU9516) e as proteínas kinases dependentes de ciclina (CDK1 e CDK2) são apresentados neste trabalho. Uma inibição na atividade da CDK1 e CDK2, que catalisam a fosforilação de grupos específicos em proteínas, tem implicações na indução da apoptose celular. O objetivo é tentar determinar qual destes ligantes potencializa a inibição da síntese de ATP (adenosina trifosfato) em ADP (adenosina difosfato) no sítio ativo da CDK1 e CDK2 para, desta forma, induzir a apoptose de células cancerígenas. Os estudos realizados neste trabalho indicam que dentre os ligantes analisados, o isaepy e o isapn obtiveram melhores resultados de estabilidade e ligações de hidrogênio entre aminoácidos dentro do sítio. Analisamos a influência do íon Cu no aumento da eficácia do isapn na atividade inibitória (complexo [Cu(isapn)]²) e comparamos os resultados obtidos dos estudos do isapn e [Cu(isapn)]², quando inseridos no sítio de ligação do ATP da CDK1, com medidas de eletroforese em gel. Verificamos que os nossos resultados foram corroborados com as medidas de eletroforese. Também discutimos os resultados de cálculos de acoplamento hiperfino para o Cu no [Cu(isapn)]² em diferentes ambientes químicos e fizemos a comparação destes resultados com medidas de EPR. Desta forma, conseguimos verificar o ambiente químico do íon Cu e um aumento da estabilidade do isapn dentro do sítio estudado com a inserção do íon Cu. Este trabalho visa contribuir para a síntese de novos ligantes que aumentem a eficácia da inibição da síntese de ATP em ADP nas CDKs e também para a minimização dos custos através da diminuição da realização de experimentos que se baseiam em métodos de tentativa e erro. / Molecular modeling studies of the interaction of oxindol based ligands (isaepy, isapn [Cu(isapn)]²,isaenim and SU9516) with Cyclin Dependent Kinases proteins (CDK1 and CDK2) are presented here. CDK1 and CDK2 catalyze the phosphorylation of specific groups in proteins and inhibition of its activities implies in induction of cancer cells apoptosis. The goal is to determine which ligands increase the inhibition of ATP (adenosine triphosphate) into ADP (adenosine diphosphate) synthesis which occurs inside the CDK1 and CDK2 active site. We analyze the influence of the Cu ion on increasing the inhibitory activity in isapn ([Cu(isapn)]² metal complex). Comparisons between the results obtained from studies of the isapn and [Cu(isapn)]² inserted into the ATP binding site of CDK1 with measurements of gel electrophoresis were performed. The hyperfine coupling at Cu ion in [Cu(isapn)]² in different chemical environments are here obtained and the results are compared with EPR measurements. This work aims to contribute to the development of new ligands which increase the inhibition of the synthesis of ATP into ADP in the CDKs moreover we aim to assist in the reduction of the costs of measurements that are based on trial and error aproaches.

Dans cette thèse, nous explorons des matériaux basés sur le bismuth qui peuvent présenter des propriétés topologiques. Bi est un composant d’Isolants Topologiques identifiés qui consistent en un volume isolant tout en présentant aussi des états électroniques conducteurs en surface topologiquement protégés. En particulier, ces états de surface sont polarisés en spin et sont protégés par la symétrie du renversement du temps. L’attrait des Isolants Topologiques découle non seulement de leur intérêt évident du point de vue de la physique fondamentale, mais aussi du fait qu’ils puissent trouver une application en spintronics et dans les ordinateurs quantiques.Dans ces systèmes, le couplage spin-orbit joue un rôle central. Le couplage spin-orbit peut aussi mener à la levée de dégénérescences de Rashba ou de Dresselhaus, phénomènes découlant de la brisure en symétrie respectivement engendrée par la surface/interface d’un système ou de l’inhérente structure cristalline atomique.L’interprétation de mesures de structures de bandes dépendantes du spin, comme observées par spectroscopie par photoemission résolue en angle (et en spin), est appuyée et complémentée par des calculs ab-initio Korringa-Kohn-Rostoker de la structure électronique qui incluent tous les aspects des systèmes examinés : en particulier le couplage spin-orbit, fondamentalement compris grâce à une approche entièrement relativiste.Nous avons d’abord déposé des couches minces de Bi sur un substrat d’InAs(111). Un cristal de Bi de très bonne qualité est obtenu, confirmé par la reproduction par étude théorique des bandes électroniques mesurées. En parallèle de la croissance de la couche de Bi, nous observons que l’In et le Bi forment des cristaux d’InBi, exposant des états de surface topologiques. Nos analyses théoriques confirment que ces états de surface sont polarisés en spin.Dans la seconde partie de la thèse, Bi est utilisé comme un dopant dans InAs, donnant un alliage d’InAsBi. L’intense couplage spin-orbit apporté par le Bi génère simultanément des effets Rashba et Dresselhaus mesurables, levant par conséquence la dégénérescence des états de surface de manière complètement atypique, donnant des états non-hélicoïdaux polarisés en spin. / In this thesis, we explore bismuth based materials that may exhibit topological properties. Bi is a parent compound of known Topological Insulators which consist of an insulating bulk while also presenting topologically protected conducting electronic surface states. In particular, these surface states are spin polarised and are protected by time-reversal symmetry. The dual appeal of topological insulators stems not only from their obvious interest from a fundamental physics point of view, but also from the fact that they may find use in spintronics and quantum computing.In those systems the spin-orbit coupling plays a central role. Spin-orbit coupling can also lead to the Rashba or Dresselhaus splitting, phenomena arising from the symmetry breaking respectively engendered by the surface/interface of a system or from the inherent atomic crystal structure.The interpretation of measured spin dependent band structure, as observed in (Spin-) and Angle-Resolved Photoemission Spectroscopy, was supported and completed by ab-initio Korringa-Kohn-Rostoker electronic structure calculations which account for all aspects of the investigated systems: in particular spin-orbit coupling, fundamentally included thanks to a fully relativistic approach.We first deposited Bi thin films onto a InAs(111) substrate. A crystal of Bi of very high quality was grown, confirmed by reproduction of the measured electronic bands by theoretical investigation. In parallel to Bi film growth, we observed that In and Bi form InBi crystals, exhibiting topological surface states. Our theoretical analyses confirm that these surface states are spin polarised.In the second part of the thesis, Bi was used as a dopant within InAs, forming an InAsBi alloy system. The strong spin-orbit coupling brought on by Bi generated simultaneously measurable Rashba and Dresselhaus effects, consequently splitting surface states in a completely atypical manner, giving non-helical spin polarised states.

A fotodinâmica de sistemas moleculares representa um dos principais tópicos atuais da físico-química molecular. O conhecimento das propriedades dos estados eletrônicos excitados tem permitido desenvolver áreas de vital importância como das energias renováveis, da fotomedicina, dos sensores fluorescentes, entre outras. O objetivo desta tese está orientado a estudar teoricamente a influência do meio (ou efeito de solvente) na fotofísica e nas propriedades dos estados eletrônicos excitados de sistemas moleculares. Nesta tese, primeiramente foi feito um estudo em fase gasosa da superfície de energia potencial do sistema molecular HSO2 e do efeito da energia rotacional na reação OH+SO. Na superfície de energia potencial foram caracterizadas um grande número de estruturas estacionárias e foi encontrado um estado de transição que liga a região mais energética da superfície com a menos energética. Em relação ao papel da energia rotacional na reação mencionada, foi realizado um estudo de trajetórias quase-clássicas, onde foi observado um decréscimo da reatividade com o aumento da energia rotacional total depositada nos reagentes. Posteriormente, foi estudado o efeito do solvente nas propriedades dos estados eletrônicos excitados e nos mecanismos de decaimento de três sistemas moleculares, acetona, 1-nitronaftaleno e daidzein. Na acetona, foi estudada a influência da polarização eletrônica do estado excitado n* provocada pelo solvente no deslocamento espectral da banda de fluorescência. A banda de emissão obtida em água mostra um deslocamento espectral muito pequeno em relação à fase gasosa, em concordância com as evidencias experimentais. Também foi observada pouca dependência do deslocamento espectral com o grau de polarização eletrônica desse estado excitado. O sistema molecular 1-nitronaftaleno foi estudado a fim de esclarecer a ultrarápida desativação eletrônica não fluorescente observada experimentalmente após a transição de absorção, assim como, caracterizar os espectros de absorção transitória também observados nos experimentos. Foi encontrado um intersystem crossing muito eficiente entre o primeiro estado excitado singleto e o segundo estado tripleto, que explica o decaimento não fluorescente deste sistema molecular. O modelo de decaimento proposto permite descrever corretamente os espectros de absorção transitória nos solventes metanol e etanol, através de transições de absorção dos estados eletrônicos tripletos. Finalmente, o sistema molecular daidzein foi estudado a fim de entender porque em solvente polar prótico, como a água, o sistema é fluorescente, mostrando um valor de Stokes shift consideravelmente grande e na presença de solvente polar aprótico, como a acetonitrila, não é observada fluorescência. Nesse sentido, foi estudada a evolução dos estados eletrônicos excitados, na presença dos solventes água e acetonitrila, após as transição de absorção. A topologia dos estados eletrônicos excitados é diferente para cada um dos solventes, em acetonitrila o sistema tem acesso a um intersystem crossing muito eficiente que permite o decaimento não fluorescente. Em água o panorama é diferente, neste caso, não é possível a ocorrência do intersystem crossing e o sistema decai por fluorescência para o estado fundamental. No estado eletrônico fluorescente é observada uma polarização eletrônica significativa que provoca o grande valor de Stokes shift observado experimentalmente. / The photodynamics of molecular systems represents one of the most important topics of the molecular physical chemistry today. The knowledge of the excited electronic states properties has allowed the development of several important areas, such as the renewable energies, the photomedicine, fluorescent sensors, etc. The aim of this thesis is oriented to the theoretical study of the solvent effect on the photophysics and on the excited electronic states properties of molecular systems. In this thesis, it was initially studied the potential energy surface of the HSO2 molecular system in gas phase and the rotational energy effect on the reactivity of the OH+SO reaction. In the potential energy surface a large number of stationary structures were characterized and it was found a transition state which connects the highest energetic region to the lowest one. Regarding the role of rotational energy on the mentioned reaction, a quasi-classical trajectories study was performed, indicating a decrease in the reactivity when the total rotational energy deposited in the reactants is increased. Subsequently, it was studied the solvent effect on the excited electronic states and on the deactivation mechanisms of three molecular systems, acetone, 1-nitronaphthalene and daidzein. In the acetone molecular system, it was studied the influence of the electronic polarization, caused by the solvent, in the fluorescence spectral shift of the n* excited state. The emission band obtained in water shows a small spectral shift compared to the gas phase, in agreement with the experimental evidences. It was also observed a little dependence of the spectral shift with the degree of the excited state polarization. The 1-nitronaphthalene molecular system was studied to clarify the ultrafast non-fluorescent deactivation mechanism experimentally observed after the absorption transitions, as well as to characterize the transient absorption spectra also observed in the experiments. A very efficient intersystem crossing was found between the first singlet excited state and the second triplet state, which explains the nonfluorescent decay of this molecular system. The proposed deactivation model allows properly describing the transient absorption spectra in methanol and ethanol solvents by absorption transitions from the triplet electronic states. Finally, the daidzein molecular system was studied to understand why in polar protic solvent, such as water, the system is fluorescent, showing a very large Stokes shift value and in polar aprotic solvent, such as acetonitrila, the fluorescence is not observed. In that sense, it was studied the evolution of the excited electronic states in water and in acetonitrile after the absorption transition. The topology of the excited electronic states is different for each solvent, in acetonitrile the system is accessible to a very efficient intersystem crossing that enables the non-fluorescent decay. In water the picture is different, the intersystem crossing is not possible to occur and the system decays by fluorescence to the ground electronic state. In the fluorescent state is observed a considerable electronic polarization that causes the so large Stokes shift value experimentally observed.

<p>The present thesis concerns method development and applications in the field of first principles electronic structure calculations.</p><p>Augmented planewaves combine the simple planewaves with exact solutions of the Schrödinger equation for a spherical potential. This combination yields a very good set of basis functions for describing the electronic structure everywhere in a crystal potential. In the present work, developments of the original augmented planewave (APW) method are presented. It is shown that the exact APW eigenvalues can be found using information from the eigenvalues of the APW secular matrix. This provides a more efficient scheme to solve the APW eigenvalue problem, than the traditional evaluation of the secular determinant. Further, a new way of linearizing the APW method is presented and compared to the traditional linearized APW method (LAPW). Using a combination of the original APW basis functions and the so called local orbitals (lo), the APW+lo linearization is found to reproduce the results of the LAPW method, but already at a smaller basis set size. Another advantage of the new linearization is a faster convergence of forces, with respect to the basis set size, as compared to the LAPW method.</p><p>The applications include studies of the non-collinear magnetic configuration in the fcc-based high-temperature phase of iron, γ-Fe. The system is found to be extremely sensitive to volume changes, as well as to a tetragonal distortion of the cubic unit cell. A continuum of degenerate spin spiral configurations, including the global energy minimum, are found for the undistorted crystal. The in-plane anisotropy of the ideal interface between a ferromagnetic layer of bcc Fe and the semiconducting ZnSe crystal is also investigated. In contrast to the four-fold symmetric arrangement of the atoms at the interface, the in-plane magnetic anisotropy displays a large uniaxiality. The calculated easy axes are in agreement with experiments for both Se and Zn terminated interfaces. In addition, calculations of the hyperfine parameters were performed for Li intercalated battery materials.</p>

<p>Transport properties within the Boltzmann transport equation for metallic multi-layer structures as well as bulk materials, were the prime topic of this work. <i>Ab initio</i> total energy calculations for Hydrogen loaded metallic multi-layers were performed in order to shed some light onto problem of H depleted layers at the interfaces that have been experimentally observed. It was explained in connection with structural relaxation of the interface layers. </p><p>Further on conductivity behavior of Fe/V vs. Mo/V during Hydrogen load was discussed. The difference in, on first sight, rather similar multi-layer structures was explained by the magnitude of Hydrogen induced Vanadium expansion. Problem of variation of conductivity with changed c/a ratio of metals and semiconductors in general was addressed as well. The variations due to change of the Fermi surface of the corresponding materials were observed as well as some intriguing general patterns. The phenomenon could be regarded as piezoresistivity on electronic structure level. For the 3d transition metals variation of conductivity/resistivity through the period was studied.</p><p>A possible explanation for anomalous behavior of Manganese resistivity due to its much greater lattice constant in comparison to its neighbors in the period is presented. Field of disordered alloys and low dimensional magnetism was touched by discussing Mo/Ru formation energy as well as magnetic nano-wires grown on surfaces.</p><p>All total energy calculations as well as band structure calculations were performed by using Density Functional Theory based numerical computations. A short but comprehensive review of most common linear-response electron transport techniques is given.</p>

<p>This thesis is divided in three parts. In the first part, a study of materials aimed for spintronics applications is presented. More specifically, calculations of the critical temperature in diluted magnetic semiconductors (DMS) and half-metallic ferromagnets are presented using a combination of electronic structure and statistical methods. It is shown that disorder and randomness of the magnetic atoms in DMS materials play a very important role in the determination of the critical temperature.</p><p>The second part treats materials in reduced dimensions. Studies of multilayer and trilayer systems are presented. A theoretical model that incorporates interdiffusion in a multilayer is developed that gives better agreement with experimental observations. Using Monte Carlo simulations, the observed magnetic properties in the trilayer system Ni/Cu/Co at finite temperatures are qualitatively reproduced.</p><p>In the third part, electronic structure calculations of complex Mn-based compounds displaying noncollinear magnetism are presented. The calculations reproduce with high accuracy the observed magnetic properties in these compounds. Furthermore, a model based on the electronic structure of the necessary conditions for noncollinear magnetism is presented.</p>

<p>The subject of the present thesis is theoretical first principles electronic structure calculations on designer hard materials such as the transition metal carbides and oxides. The theoretical investigations have been made in close collaboration with experimental research and have addressed both bulk electronic properties and surface electronic properties of the materials.</p><p>Among the bulk studies are investigations on the effects of substoichiometry on the relative phase stabilities and the electronic structure of several phases of MoC and the nature of the resulting vacancy peaks. The changes in phase stabilities and homo-geneity ranges in the group IV to VI transition metal carbides have been studied and explained, from calculations of the T=0 energies of formation and cohesive energies. The anomalous volume behavior and phase stabilities in substoichiometric TiC was studied including effects of local relaxations around the vacancy sites. The vacancy ordering problem in this compound was also studied by a combination of electronic structure calculations and statistical physics.</p><p>The studies of the surface electronic properties include research on the surface energies and work functions of the transition metal carbides and an investigation on the segregation of transition metal impurities on the TiC (100) surface.</p><p>Theoretical studies with the aim to facilitate the realization of novel designer hard materials were made, among these a survey of means of stabilizing potentially super-hard cubic RuO₂, studying the effects of alloying, substoichiometry and lattice strains. A mechanism for enhancing hardness in the industrially important hard transition metal carbides and nitrides, from the discovery of multi-phase/polytypic alloys, has also been predicted from theoretical calculations.</p>

<p>In many materials, changes in chemical composition, pressure or temperature can induce metal to insulator transitions. It is recently observed in yttrium hydride, for example, changes from a shiny mirror (YH₂) to a transparent window (YH₃), which has important technological application in optical devices. We have tuned the above transition by choosing <i>pressure</i> instead of composition. Our predicted finding is confirmed by recent experiments and opens a new way to design optical switches.</p><p>The unique role that gold plays in society is to a large extent related to the fact that it is the most <i>noble</i> of all metals.We have studied the noble nature of gold by choosing <i>pressure</i> as tool. Our prediction shows that gold transforms from a face centered cubic to an hexagonal closed packed phase above 200 GPa whereas platinum, another noble metal, does not show any phase transition up to 500 GPa. This prediction has also been confirmed by experiments suggesting that platinum is more noble than gold.</p><p>The growing concern about climate change and fossil fuel availability, the direct conversion of solar irradiation into electricity appears to be an ideal alternative to conventional energy sources. Power generation by solar cells is a direct method of solar energy conversion. We report a new cubic phase of TiO₂ which can be stabilized at ambient conditions. This phase has an absorption three or four orders of magnitude larger than the conventional state-of-the-art solar cell based on anatase TiO₂. Therefore, we are introducing a well established material with a new structure for future generation solar cells. The same effect is also observed in cubic SnO₂.</p><p>Electronic and optical properties of other materials such as Be_xZn_1-xTe, RuO₂ and IrO₂ are also studied in present thesis. In particular, for Be_xZn_1-xTe, we have used composition as a tool to tune the optical properties.</p>

<p>Theoretical studies based on first-principles theory are presented for a number of different magnetic systems. The first part of the thesis concerns spin dynamics and the second part concerns properties of magnetic multilayers. The theoretical treatment is based on electronic structure calculations performed by means of density functional theory.</p><p>A method is developed for simulating atomistic spin dynamics at finite temperatures, which is based on solving the equations of motion for the atomic spins by means of Langevin dynamics. The method relies on a mapping of the interatomic exchange interactions from density functional theory to a Heisenberg Hamiltonian. Simulations are performed for various magnetic systems and processes beyond the reach of conventional micromagnetism. As an example, magnetization dynamics in the limit of large magnetic and anisotropy fields is explored. Moreover, the method is applied to studying the dynamics of systems with complex atomic order such as the diluted magnetic semiconductor MnGaAs and the spin glass alloy CuMn. The method is also applied to a Fe thin film and a Fe/Cr/Fe trilayer system, where the limits of ultrafast switching are explored. Current induced magnetization dynamics is investigated by calculating the current induced spin-transfer torque by means of density functional theory combined with the relaxation time approximation and semi-classical Boltzmann theory. The current induced torque is calculated for the helical spin-density waves in Er and fcc Fe, where the current is found to promote a rigid rotation of the magnetic order.</p><p>Properties of magnetic multilayers composed of magnetic and nonmagnetic layers are investigated by means of the Korringa-Kohn-Rostocker interface Green's function method. Multilayer properties such as magnetic moments, interlayer exchange coupling and ordering temperatures are calculated and compared with experiments, with focus on understanding the influence of interface quality. Moreover, the influence on the interlayer exchange coupling of alloying the nonmagnetic spacer layers with small amounts of a magnetic impurity is investigated.</p>