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.

Pollution from automobile exhaust is one of the most major environmental problems because of increasing usage of engine technologies. Diesel and lean burn gasoline engines operate under oxygen rich (lean) conditions and they emit harmfull gases to the atmosphere (CO,CO2, NO, NO2). The control of NOx emission from exhaust has become a challenging issue in engine industry because of the worldwide environmental regulations. Therefore lean-burn NOx emission control technologies have been developed to reduce emission of harmfull gases from exhausts, and the NOx storage/reduction (NSR) catalysts is one of the most promising candidates to reduce the pollution caused by lean-burn engines. In NSR systems, NO from the emission is first oxidized to NO2 over noble metal sites (Pt, Rh, Pd) during lean-burn engine operation. After that NO2 is stored as nitrites and nitrates in alkali earth oxides (BaO,MgO, CaO) particles or monolayer which is well dispersed on a substrate (Gamma-Al2O3, TiO2, SiO2). Finally, stored NOx compound are broken into N2 and O2 on noble metal sites. The Pt/BaO/Gamma-Al2O3 system is one of the most popular subjects in literature both experimentally and theoretically since this system is known to be catalytically more active and ecient in interactions between NOx and Pt-BaO components are still not clearly explained. For this reason, in this thesis, the interaction between catalytic redox components, Pt and Rh, and the support material Gamma-Al2O3 and the eects of Pt and Rh in atomic and diatomic clusters forms on the adsorption of the NO2 molecule on the Gamma-Al2O3(100) surface have been investigated by using density functional theory (DFT).

No description available.

<p>This thesis is part of an effort to enable large-scale Hartree-Fock/Kohn-Sham (HF/KS) calculations. The objective is to model molecules and materials containing thousands of atoms at the quantum mechanical level. HF/KS calculations are usually performed with the Self-Consistent Field (SCF) method. This method involves two computationally intensive steps. These steps are the construction of the Fock/Kohn-Sham potential matrix from a given electron density and the subsequent update of the electron density usually represented by the so-called density matrix. In this thesis the focus lies on the representation of potentials and electron density and on the density matrix construction step in the SCF method. Traditionally a diagonalization has been used for the construction of the density matrix. This diagonalization method is, however, not appropriate for large systems since the time complexity for this operation is σ(n³). Three types of alternative methods are described in this thesis; energy minimization, Chebyshev expansion, and density matrix purification. The efficiency of these methods relies on fast matrix-matrix multiplication. Since the occurring matrices become sparse when the separation between atoms exceeds some value, the matrix-matrix multiplication can be performed with complexity σ(n).</p><p>A hierarchic sparse matrix data structure is proposed for the storage and manipulation of matrices. This data structure allows for easy development and implementation of algebraic matrix operations, particularly needed for the density matrix construction, but also for other parts of the SCF calculation. The thesis addresses also truncation of small elements to enforce sparsity, permutation and blocking of matrices, and furthermore calculation of the HOMO-LUMO gap and a few surrounding eigenpairs when density matrix purification is used instead of the traditional diagonalization method.</p>