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.

Transition metal oxides having high dielectric constants and wide band gaps find very important and interesting technological applications in surface physics. In particular, titania is the most commonly used material in heterogeneous catalysis because of its stable and flat surfaces. Having Ti cations at different charge states within the system brings about various novel electronic properties which are mainly surface related. Adsorption of catalytically important or chemically useful molecules on titania surfaces are investigated, electronic energy bands and charge densities are calculated from first principles using the density functional theory in the GGA scheme. The comparisons with the leading theories and existing experimental data are maid.

In this thesis, the electronic properties of nanosheets derived from TiO2 anatase structure which acts as a photocatalyst, are investigated using the density functional theory. We examine bulk constrained properties of the nanosheets derived from the (001) surface and obtain their optimized geometries. We investigate properties of lepidocrocite-type TiO2 nanosheets and nanotubes of different sizes formed by rolling the lepidocrocite nanosheets. We show that the stability and the band gaps of the considered nanotubes increase with increasing diameter. We also study adsorption of Aun clusters with (n=1,2,3,4) on the clean and oxygen depleted lepidocrocite surface. Through systematic investigation of various cases we conclude that Au preferres O vacancy sites rather than clean surface in accordance with previous metal adsorption studies on TiO2 surfaces. For the clean surface, we observe that Au clusters with an odd number of atoms are weakly bonded and metallizes the system while even number of Au atoms results in small band gap semiconductors with relatively higher binding energies.

In this thesis, six small molecules (S-allylcysteine, S-allyl mercaptocysteine, allicin, methyl propyl disulfide, allyl methyl sulfide and dipropylsulfide) that are found in garlic and onion, and are known to be beneficial for human health were studied using molecular mechanics, semi-empirical methods, ab-initio (Restricted Hartree Fock), and density functional theory. Using the same methods, a synthetic pyrethroid pesticide molecule, called cyfluthrin, was also studied. Structural, vibrational and electronic properties of these molecules were found. These theoretical studies could clarify the role of these molecules on human health before they are commercially developed and used. In addition, unfolding dynamics of small peptide sequences (DDATKTFT and its variants) in immunoglobulin G-binding protein G was investigated. Protein folding and unfolding is one of the most important unsolved problems in molecular biology. Because of the large number of atoms involved in protein folding, it is a massive computational problem. The hope is that, one could understand this mechanism with the help of molecular dynamics simulation on small peptides. One of our findings is that the location of the hydrogen bonds is important for the stability of the peptide.

High fossil fuel consumption in transportation and industry results in an increase of the emission of green-house gases. To preserve clean air, new strategies are required. The main intention is to decrease the amount of CO2 emission by using lean-burn engines while increasing the combustion efficiency and decreasing the fuel consumption. However, the lean-burn engines have high air-to-fuel ratio which complicates the reduction of the oxides of nitrogen, NOx . The emission of these highly noxious pollutants, NOx , breeds both environmental and health problems. Thus, new catalytic strategies have been steadily developed. One of these strategies is the NOx storage and reduction (NSR) catalysts. Since the reduction of the NOx under excess oxygen condition is very difficult, the NSR catalysts store the NOx until the end of the lean phase that is subsequently alternated with the rich-fuel phase during which the trapped NOx is released and reduced. To develop NSR technology, different storage materials, the coverage of these metals/metal-oxides, support materials, precious metals, temperature, etc. have been widely investigated. In this thesis, the (100) surface of BaO with dopants (K, Na, Ca and La), (100) and (110) surfaces of Li2O, Na2O and K2O are investigated as storage materials. In addition, alkali metal (Li, Na and K) loaded (001) surface of TiO2 (titania) anatase is investigated as a support material for the NOx storage and reduction catalysts. The main aim is to increase the sulfur resistance. The introduction of the dopants on the BaO (100) surface has increased the stability of the NO2 . The combination of local lattice strain and different oxidation state, which is obtained by the La doped BaO (100) surface, benefit both NO2 adsorption performance and sulfur tolerance. The binding energies of NO2 adsorption configurations over the alkali metal oxide (100) and (110) surfaces were higher than the binding energies of SO2 adsorption configurations. The stability of all of NO2 adsorption geometries on the alkali metal-loaded TiO2 (001) surface were higher than the stability of SO2 adsorption geometries. Increasing basicity enhanced the adsorption of NO2 molecule.