X-ray absorption spectroscopy and computational chemistry have been used to probe the structure of biomolecules involved in cellular copper homeostasis. X-ray absorption spectroscopy shows that copper chaperones involved in cytochrome c oxidase assembly bind Cu(I) with trigonal coordination environments in poly-copper thiolate clusters, but the number of coppers in these clusters remains unclear. X-ray absorption spectroscopy of the metal-sensing transcription factor-1 from Drosophila melanogaster and metallothionein from Saccharomyces cerevisiae with stoichiometries of four or less shows a tetracopper cluster in an all-or-none manner in these molecules. These results suggest that cooperative binding of copper to form tetracopper clusters may be a common mechanism employed by copper control molecules. The active site structure of the novel copper-sensitive repressor CsoR in Mycobacterium tuberculosis binds copper in a trigonal coordination geometry with two sulfur and one nitrogen donors according to X-ray absorption spectroscopy results. Molecular dynamics simulations of both apo- and Cu-bound CsoR reveal local conformational changes in CsoR upon copper binding, which suggests multiple possible mechanisms of Cu-dependent transcriptional regulation by CsoR. Finally, X-ray absorption spectroscopy and X-ray fluorescence imaging have been used to understand the molecular basis of a promisng new treatment for Wilsons disease (a genetic disorder of Cu homeostasis) using tetrathiomolybdate. Overall, the results presented provide an essential structural basis for understanding copper homeostasis in living cells.

<p>The electronic structures of the nucleobases, 5-fluorouracil compounds, DNA, metallic DNA, and samples of boron nitride are investigated. Soft X-ray absorption (XAS) and emission (XES) spectroscopy using synchrotron radiation are used to probe the unoccupied and occupied partial densities of electronic states, respectively. Hartree-Fock and density functional theory calculations have been included to compare with experimental results.</p> <p>A systematic approach to understanding the complicated electronic structure of DNA and metallic DNA systems is to initially examine smaller components. Detailed experiment and theory for both absorption and emission spectroscopy was. performed for the nucleobases and 5-fluorouracil compounds. Main transitions in the XAS and XES spectra are identified. X-ray spectroscopy has proven to be extremely sensitive to changes in the environment of various DNA samples. The local chemical environment plays an important role in determining the electronic structure of DNA. In agreement with previous results indicating metallic DNA is more efficient at the transfer of electrons than DNA, XES measurements reveal that there are a higher number of charge carriers in the metallic system. Both liquid and powder samples of (Ni)·M-DNA are found to have a high spin Ni(II) configuration. The drying process significantly alters the electronic structure of the metallic DNA sample. A comparison of high quality single crystals and thin films of boron nitride found that differences between the electronic structures of the nanocrystalline films and the single crystal samples exist, and the surface roughness of the substrate plays an important role in determining the structure of the resulting deposited film.</p>

<p>The electronic structures of the nucleobases, 5-fluorouracil compounds, DNA, metallic DNA, and samples of boron nitride are investigated. Soft X-ray absorption (XAS) and emission (XES) spectroscopy using synchrotron radiation are used to probe the unoccupied and occupied partial densities of electronic states, respectively. Hartree-Fock and density functional theory calculations have been included to compare with experimental results.</p> <p>A systematic approach to understanding the complicated electronic structure of DNA and metallic DNA systems is to initially examine smaller components. Detailed experiment and theory for both absorption and emission spectroscopy was. performed for the nucleobases and 5-fluorouracil compounds. Main transitions in the XAS and XES spectra are identified. X-ray spectroscopy has proven to be extremely sensitive to changes in the environment of various DNA samples. The local chemical environment plays an important role in determining the electronic structure of DNA. In agreement with previous results indicating metallic DNA is more efficient at the transfer of electrons than DNA, XES measurements reveal that there are a higher number of charge carriers in the metallic system. Both liquid and powder samples of (Ni)·M-DNA are found to have a high spin Ni(II) configuration. The drying process significantly alters the electronic structure of the metallic DNA sample. A comparison of high quality single crystals and thin films of boron nitride found that differences between the electronic structures of the nanocrystalline films and the single crystal samples exist, and the surface roughness of the substrate plays an important role in determining the structure of the resulting deposited film.</p>

As the demand for clean and renewable energy sources continues to grow, much attention has been given to solid oxide fuel cells (SOFCs) due to their efficiency and low operating temperature. However, the components of SOFCs must still be improved before commercialization can be reached. Of particular interest is the solid electrolyte, which conducts oxygen ions from the cathode to the anode. Samarium-doped ceria (SDC) is the electrolyte of choice in most SOFCs today, due mostly to its high ionic conductivity at low temperatures. However, the underlying principles that contribute to high ionic conductivity in doped ceria remain unknown, and so it is difficult to improve upon the design of SOFCs. This thesis focuses on identifying the atomistic interactions in SDC which contribute to its favourable performance in the fuel cell. Unfortunately, information as basic as the structure of SDC has not yet been found due to the difficulty in experimentally characterizing and computationally modelling the system. For instance, to evaluate 10.3% SDC, which is close to the 11.1% concentration used in fuel cells, one must investigate 194 trillion configurations, due to the numerous ways of arranging the Sm ions and oxygen vacancies in the simulation cell. As an exhaustive search method is clearly unfeasible, we develop a genetic algorithm (GA) to search the vast potential energy surface for the low-energy configurations, which will be most prevalent in the real material. With the GA, we investigate the structure of SDC for the first time at the DFT+U level of theory. Importantly, we find key differences in our results from prior calculations of this system which used less accurate methods, which demonstrate the importance of accurately modelling the system. Overall, our simulation results of the structure of SDCagree with experimental measurements. We identify the structural significance of defects in the doped ceria lattice which contribute to oxygen ion conductivity. Thus, the structure of SDC found in this work provides a basis for developing better solid electrolytes, which is of significant scientific and technological interest. Following the structure search, we perform an investigation of the electronic properties of SDC, to understand more about the material. Notably, we compare our calculated density of states plot to XPS measurements of pure and reduced SDC. This allows us to parameterize the Hubbard (U) term for Sm, which had not yet been done. Importantly, the DFT+U treatment of the Sm ions also allowed us to observe in our simulations the magnetization of SDC, which was found by experiment. Finally, we also study the SDC surface, with an emphasis on its structural similarities to the bulk. Knowledge of the surface structure is important to be able to understand how fuel oxidation occurs in the fuel cell, as many reaction mechanisms occur on the surface of this porous material. The groundwork for such mechanistic studies is provided in this thesis.

In this thesis the conductivity of strained materials has been investigated using density functional theory and a semiclassical transport theory based on the Boltzmann equation. In transition metals trends are reproduced without adjustable parameters. The introduction of one temperature dependent cross section allowed the reproduction of resistivity trends between 10 and 1000K. The effect of strain on transition metals in bcc and fcc structure was studied deforming the unit cell along the tetragonal deformation path. The anisotropy of the conductivity varied on wide range of the c/a-ratio. The orbitals at the Fermi level determined the principal behavior. Pairs of elements with permutated number of electrons and holes in the 4d band showed similar behavior. The concept of the tetragonal deformation was also applied on semiconductors. The deformation of Vanadium in X/V superlattices (X=Cr,~Fe,~Mo) due to Hydrogen loading depends on the properties of X. It was found that counteracting effects due to the presence of Hydrogen influence the conductivity. It is shown that a small magnetic moment of the V host reduces the hydrogen solubility. Depending on the magnitude of the tetragonal distortion of V, the hydrogen dissolution becomes favored for larger moments. Finally, extra charge filling of the bandstructure of Cr and Mo decreases the Fermi velocity and increases the density of states at the Fermi energy.

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 pressure instead of composition. Our predicted finding is confirmed by recent experiments and opens a new way to design optical switches. The unique role that gold plays in society is to a large extent related to the fact that it is the most noble of all metals.We have studied the noble nature of gold by choosing pressure 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. 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. Electronic and optical properties of other materials such as BexZn1-xTe, RuO2 and IrO2 are also studied in present thesis. In particular, for BexZn1-xTe, we have used composition as a tool to tune the optical properties.

The general application of soft X-ray spectroscopy in the study of the electronic structure of materials is discussed, with particular emphasis on broad band materials. Several materials are studied using both soft X-ray spectroscopy and density functional theory to provide experimental and theoretical electronic structures, respectively. In particular, bonding, cation hybridization, and band gaps for several binary oxides (the alkali oxides: BeO, MgO, CaO, SrO, BaO; the post-transition metal oxides: ZnO, CdO, HgO; and the period 5 oxides In2O3, SnO, SnO2, Sb2O3, Sb2O5, and TeO2) are studied. The technique of using the peaks in the second derivatives of an X-ray emission and an X-ray absorption spectrum to estimate the band gap of a material is critically analyzed, and a more accurate ``semi-empirical'' method that involves both measured spectra and theoretical calculations is proposed. The techniques used in the study of binary oxides are then applied to a more interesting (and industrially relevant) group of ternary oxides based on TiO2 (PbTiO3, Sn2TiO4, Bi2Ti4O11, Bi4Ti3O12, and ZnTiO3), and a general rule for the band gaps of these materials is suggested based on empirical data. This research may help direct efforts in synthesizing a hydrogen-producing photocatalyst with a band gap that can efficiently harness the bulk of the solar spectrum. Finally, several layered pnictide superconductors and related compounds (CaFe2As2, Co-, Ni- and Cu-doped BaFe2As2, LiFeAs, LiMnAs, CaCu1.7As2, SrCu2As2, SrCu2(As0.84Sb0.16)2, SrCu2Sb2, and BaCu2Sb2) are studied. The X-ray spectra provide rather strong evidence that these materials lack strong on-site Hubbard-like correlations, and that their electronic structures are almost entirely like those of a broad band metal. In particular, it is shown that the notion that the transition metals are all divalent is completely wrong for copper in a layered pnictide, and that at best in these systems the copper is monovalent.

Monoatomic chain formation for Ag, Au, Pd and Pt has been investigated using a model for the tip structure. First-principles calculations, mostly spin polarized, were performed within the framework of the Density Functional theory. Results are presented and discussed on the basis of the electronic structure. Tendencies for chain formation were noted for Ag, Au and Pt.

X-ray absorption spectroscopy and computational chemistry have been used to probe the structure of biomolecules involved in cellular copper homeostasis. X-ray absorption spectroscopy shows that copper chaperones involved in cytochrome c oxidase assembly bind Cu(I) with trigonal coordination environments in poly-copper thiolate clusters, but the number of coppers in these clusters remains unclear. X-ray absorption spectroscopy of the metal-sensing transcription factor-1 from Drosophila melanogaster and metallothionein from Saccharomyces cerevisiae with stoichiometries of four or less shows a tetracopper cluster in an all-or-none manner in these molecules. These results suggest that cooperative binding of copper to form tetracopper clusters may be a common mechanism employed by copper control molecules. The active site structure of the novel copper-sensitive repressor CsoR in Mycobacterium tuberculosis binds copper in a trigonal coordination geometry with two sulfur and one nitrogen donors according to X-ray absorption spectroscopy results. Molecular dynamics simulations of both apo- and Cu-bound CsoR reveal local conformational changes in CsoR upon copper binding, which suggests multiple possible mechanisms of Cu-dependent transcriptional regulation by CsoR. Finally, X-ray absorption spectroscopy and X-ray fluorescence imaging have been used to understand the molecular basis of a promisng new treatment for Wilsons disease (a genetic disorder of Cu homeostasis) using tetrathiomolybdate. Overall, the results presented provide an essential structural basis for understanding copper homeostasis in living cells.

Single walled carbon nanotubes have been attracting interest for their electronic, magnetic, chemical and mechanical properties. Moreover, since they are ideal nano-containers, the adsorption and absorption properties provide them to be used as Li/Li+ ion batteries. The capacity, rate capability and cycle life of the batteries are the important points which must be improved to have better results. In this thesis Li/Li+ ion doped carbon nano structures are investigated theoretically in order to contribute to the lithium battery technology. The present studied carbon nano structures are the fullerenes, single-walled carbon nanotubes, pristine and defected (Stone-Wales and mono-vacancy defected) carbon nanocapsules. The Li/Li+ interactions with these nano structures have been investigated using semi-empirical molecular orbital method at PM3 level, density functional theory method with B3LYP exchange-correlation functional using 3-21G or 6-31G basis sets. Furthermore, the systems have been investigated by molecular dynamics simulations in which Tersoff potential and an empirical many-body potential have been used to define the various interactions. In this thesis the optimized geometries, thermodynamical quantities, interfrontier molecular orbital eigenvalues and dipole moments of the studied systems have been reported.