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.

<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>

The present thesis concerns method development and applications in the field of first principles electronic structure calculations. 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. 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.

Orientador: Augusto Batagin Neto / Resumo: Polímeros orgânicos conjugados são considerados materiais de grande relevância para aplicações tecnológicas variadas, principalmente devido às suas propriedades optoeletrônicas únicas e métodos utilizados em sua síntese. Nesse contexto, os derivados de polipirrol (PPy) têm sido amplamente empregados. A grande variabilidade de síntese desse material permite a produção de uma série de derivados com propriedades distintas, permitindo sua aplicação em diversas áreas. Neste trabalho, cálculos de estrutura eletrônica foram realizados para avaliar a influência de grupos laterais nas propriedades estruturais, ópticas, eletrônicas e de reatividade de derivados de PPy, em especial para aplicações como sensores químicos. Os cálculos foram feitos para sistemas oligoméricos aplicando a teoria do funcional da densidade. Estudos de preliminares foram conduzidos utilizando dois funcionais distintos para otimização de geometria e avaliação de propriedades optoeletrônicas. Estudos comparativos da alternância de comprimento de ligação, distribuição espacial e energética dos orbitais de fronteira, gaps eletrônicos, energias de ligação de éxcitons, espectros de absorção óptica, densidade eletrônica de estados e reatividade local foram conduzidos para cada derivado e a influência dos grupos laterais foi discutida em termos de suas propriedades de inserção/retirada de elétrons. Um conjunto de regras simples (equações lineares) foi proposto para a predição de propriedades optoeletrônicas de derivado... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Conjugated organic polymers have been considered interesting materials for varied technological applications, mainly due to their unique optoelectronic properties and variety of methods employed in their synthesis. In this context, polypyrrole (PPy) derivatives have been widely employed. The great versatility of synthesis of this material allows the production of a number of derivatives with distinct properties, allowing their application in several areas. In this report, aiming to guide the design of compounds with specific features, electronic structure calculations were conducted to evaluate the influence of side groups in the structural, optical and electronic properties of PPy derivatives, specially for application in chemical sensors. The calculations were carried out for oligomeric systems in the framework of the density functional theory. Preliminary benchmark studies were conducted by employing two distinct functionals for geometry optimization and evaluation of optoelectronic properties. Comparative studies of the bond length alternation, spatial and energetic distribution of the frontier orbitals, electronic gaps, exciton binding energies, optical absorption spectra, electronic density of states and local reactivity were conducted for each derivative and the influence of the side groups was discussed in terms of their electron donation/withdrawing properties. A set of simple rules (linear equations) was proposed for the prediction of optoelectronic properties of PP... (Complete abstract click electronic access below) / Mestre

Neste trabalho realizamos um estudo do comportamento do momento magnético e do deslocamento isomérico de uma impureza intersticial de Fe em hospedeiros metálicos de valências 4 (Ti, Zr), 3 (Sc, Y). Investigamos também impurezas intersticiais e substitucionais de Mo e Fe em hospedeiros divalentes. Para realizar este estudo fizemos cálculos de estrutura eletrônica utilizando o RS-LMTO-ASA (\"Real Space - Linear Muffin-Tin Orbital - Atomic Spherical Approximation\"), um método de primeiros princípios dentro da aproximação do funcional densidade local, implementado no espaço real. Calculamos o momento magnético no sítio da impureza nos sistemas acima e constatamos que a impureza intersticial de Fe é não magnética nos hospedeiros de valências 4 e 3, e que tanto as impurezas intersticiais como as substitucionais podem apresentar momento magnético nos hospedeiros divalentes. Mostramos que para os sistemas divalentes o momento magnético depende fortemente da relaxação. Os nossos resultados são explicados através de um modelo simples, baseado no modelo de Wolff. Investigamos também o comportamento do deslocamento isomérico no sítio da impureza de Fe nesses vários sistemas. Constatamos que os nossos resultados concordam razoavelmente bem com os dados experimentais e explicam o comportamento das tendências observadas. / In the present work, we have studied the magnetic moments and the behavior of the isomer shift at the interstitial Fe impurity site in Ti, Sc, Zr and Y hosts. We have also investigated interstitial and substitutional Fe and Mo impurities in Ca, Sr and Yb hosts. To perform the calculations, we have used the RS-LMTO-ASA scheme, a first principles method, within the local spin density approximation, implemented in real space. We calculated the magnetic moments at the impurity site in the above systems and all the substitucional impurities are found to be magnetic. The results show that interstitial Fe is non-magnetic in the tri- and tetravalent hosts, but interstitial Fe and Mo impurities could develop local magnetic moment in divalent hosts. \'We show that the magnetic moment at the impurity site in these divalent hosts is strongly dependent on lattice relaxation. The results can be explained using simple arguments based on Wolff model. We have investigated in a systematic way the behavior of the isomer shift of Fe impurities in these systems. We observed that our results are in generally good agreement with experiment and lead to better understanding of the observed trends in terms of the volume occupied by the Fe in each host.

<p>Thin metal films have found their use in many magnetic devices. They form pseudo two-dimensional systems, where the mechanisms for the magnetic interactions between the layers are not completely understood. Layered crystal structures have an advantage over such artificial systems, since the layers can be strictly mono-atomic without any unwanted admixture. In this study, some model systems of layered magnetic crystal structures and their solid solutions have been investigated by x-ray and neutron diffraction, Mössbauer and electron spectroscopy, heat-capacity and magnetic measurements, and first-principle electronic structure calculations, with the goal of deepening our understanding through controlled chemical synthesis.</p><p>The compounds TlCo₂S₂, TlCo₂Se₂ and their solid solution TlCo₂Se_2-xS_x, all containing well separated cobalt atom sheets, order with the moments ferromagnetically aligned within the sheets. In TlCo₂S₂, the net result is ferromagnetism, while TlCo₂Se₂ exhibits antiferromagnetism. The inter-layer distance is crucial for the long-range coupling, and it was varied systematically through Se-S substitution. The incommensurate helical magnetic structure found for TlCo₂Se₂ (x = 0) prevails in the composition range 0 ≤ x ≤ 1.5 but the pitch of the helix changes. The accompanying reduction in inter-layer distance on sulphur substitution varies almost linearly with the coupling angle of the helix. An additional competing commensurate helix (90°) appears in the medium composition range (found for x = 0.5 and 1.0).</p><p>The systems TlCo_2-xMe_xSe₂ show helical magnetic ordering for Me = Fe or Cu, while a collinear antiferromagnetic structure occurs for Me = Ni. Magnetic order is created by iron substitution for copper in the Pauli paramagnetic TlCu₂Se₂, but now with the moments perpendicular to the metal sheets.</p><p>TlCrTe₂ forms a quite different crystal structure, with intra-layer ferromagnetic alignment and net collinear antiferromagnetism. In contrast to the other phases, the values of the moments conform well to a localised model for Cr³⁺.</p>

In this thesis point defects in semiconductors are studied by electronic structure calculations. Results are presented for the stability and equilibrium concentrations of native defects in GaP, InP, InAs, and InSb, for the entire range of doping conditions and stoichiometry. The native defects are also studied on the (110) surfaces of InP, InAs, and InSb. Comparing the relative stability at the surface and in the bulk, it is concluded that the defects have a tendency to migrate to the surface. It is found that the cation vacancy is not stable, but decomposes into an anion antisite-anion vacancy complex. The surface charge accumulation in InAs is explained by complementary intrinsic doping by native defects and extrinsic doping by residual hydrogen. A technical investigation of the supercell treatment of defects is performed, testing existing correction schemes and suggesting a more reliable alternative. It is shown that the defect level of [2VCu-IIICu] in the solarcell-material CuIn1-xGaxSe2 leads to a smaller band gap of the ordered defect γ-phase, which possibly explains why the maximal efficiency for CuIn1-xGaxSe2 has been found for x=0.3 and not for x=0.6, as expected from the band gap of the α-phase. It is found that Zn diffuses via the kick-out mechanism in InP and GaP with activation energies of 1.60 eV and 2.49 eV, respectively. Explanations are found for the tendency of Zn to accumulate at pn-junctions in InP and to why a relatively low fraction of Zn is found on substitutional sites in InP. Finally, it is shown that the equilibrium solubility of dopants in semiconductors can be increased significantly by strategic alloying. This is shown to be due to the local stress in the material, and the solubility in an alloy can in fact be much higher than in either of the constituting elements. The equilibrium solubility of Zn in Ga0.9In0.1P is for example five orders of magnitude larger than in GaP or InP.

Thin metal films have found their use in many magnetic devices. They form pseudo two-dimensional systems, where the mechanisms for the magnetic interactions between the layers are not completely understood. Layered crystal structures have an advantage over such artificial systems, since the layers can be strictly mono-atomic without any unwanted admixture. In this study, some model systems of layered magnetic crystal structures and their solid solutions have been investigated by x-ray and neutron diffraction, Mössbauer and electron spectroscopy, heat-capacity and magnetic measurements, and first-principle electronic structure calculations, with the goal of deepening our understanding through controlled chemical synthesis. The compounds TlCo2S2, TlCo2Se2 and their solid solution TlCo2Se2-xSx, all containing well separated cobalt atom sheets, order with the moments ferromagnetically aligned within the sheets. In TlCo2S2, the net result is ferromagnetism, while TlCo2Se2 exhibits antiferromagnetism. The inter-layer distance is crucial for the long-range coupling, and it was varied systematically through Se-S substitution. The incommensurate helical magnetic structure found for TlCo2Se2 (x = 0) prevails in the composition range 0 ≤ x ≤ 1.5 but the pitch of the helix changes. The accompanying reduction in inter-layer distance on sulphur substitution varies almost linearly with the coupling angle of the helix. An additional competing commensurate helix (90°) appears in the medium composition range (found for x = 0.5 and 1.0). The systems TlCo2-xMexSe2 show helical magnetic ordering for Me = Fe or Cu, while a collinear antiferromagnetic structure occurs for Me = Ni. Magnetic order is created by iron substitution for copper in the Pauli paramagnetic TlCu2Se2, but now with the moments perpendicular to the metal sheets. TlCrTe2 forms a quite different crystal structure, with intra-layer ferromagnetic alignment and net collinear antiferromagnetism. In contrast to the other phases, the values of the moments conform well to a localised model for Cr3+.

Computational approaches play an important role in today's materials science owing to the remarkable advances in modern supercomputing architecture and algorithms. Ab initio simulations solely based on a quantum description of matter are now very able to tackle materials problems in which the system contains up to a few thousands atoms. This dissertation aims to address the modern electronic structure calculation methods applied to a range of various materials such as liquid and amorphous phase materials, nanostructures, and small organic molecules. Our simulations were performed within the density functional theory framework, emphasizing the use of real-space ab initio pseudopotentials. On the first part of our study, we performed liquid and amorphous phase simulations by employing a molecular dynamics technique accelerated by a Chebyshev-subspace filtering algorithm. We applied this technique to find l- and a- SiO₂ structural properties that were in a good agreement with experiments. On the second part, we studied nanostructured semiconducting oxide materials, i.e., SnO₂ and TiO₂, focusing on the electronic structures and optical properties. Lastly, we developed an efficient simulation method for non-contact atomic force microscopy. This fast and simple method was found to be a very powerful tool for predicting AFM images for many surface and molecular systems. / text

Electronic structure calculations constitute a valuable tool to predict the properties of materials. In this study we propose an efficient scheme to study correlated electron systems with essentially only one free parameter, the screening length of the Coulomb potential. A general reformulation of the exchange energy of the correlated electron shell is combined with this method in order to analyze the calculations. The results are interpreted in terms of different polarization channels, due to different multipoles. The method is applied to various actinide compounds, in order to increase the understanding of the complicate behaviour of 5f electrons in these systems. We studied the non-magnetic phase of δ-Pu, where the spin polarization is taken over by a spin-orbit-like term that does not break the time reversal symmetry. We also find that a non-trivial high multipole of the magnetization density, the triakontadipole, constitutes the ordering parameter in the mysterious hidden order phase of the heavy-fermion superconductor URu2Si2. This type of multipolar ordering is also found to play an essential role in the hexagonal-based superconductors UPd2Al3,  UNi2Al3 and UPt3 and in the dioxide insulators UO2, NpO2 and PuO2. The triakontadipole moments are also present in all magnetic actinides we considered, except for Cm. These results led us to formulate a new set of rules for the ground state of a system, that are valid in presence of strong spin-orbit coupling interaction instead of those of Hund; the Katt's rules. Finally, we applied our method to a new class of high-Tc superconductors, the Fe-pnictides, where the Fe 3d electrons are moderately correlated. In these materials we obtain the stabilization of a low spin moment solution, in agreement with experiment, over a large moment solution, due to the gain in exchange energy in the formation of large multipoles of the spin magnetization density. / Felaktigt tryckt som Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 705