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The electronic structures and reaction mechanisms of transition-metal complexes can be calculated accurately by density functional theory (DFT) in cooperation with the continuum solvation model. The palladium catalyzed Heck reaction, iron-model complexes for cytochrome P450 and superoxide reductase (SOR), and tetrairon hexathiolate hydrogenase model were investigated. The DFT calculations on the catalytic Heck reaction (between phenyl-bromide and ethylene to form the styrene product), catalyzed by palladium diphosphine indicate a four-step mechanism: oxidative addition of C6H5Br, migratory insertion of C6H5 to C2H4, b-hydride transfer/olefin elimination of styrene product, and catalyst regeneration by removal of HBr. For the oxidative addition, the rate-determining step, the reaction through monophosphinopalladium complex is more favorable than that through either the diphosphinopalladium or ethylene-bound monophosphinopalladium. In further study, for a steric phosphine, PtBu3, the oxidative-addition barrier is lower on monopalladium monophosphine than dipalladium diphosphine whereas for a small phosphine, PMe3, the oxidative addition proceeds more easily via dipalladium diphosphine. Of the phosphine-free palladium complexes examined: free-Pd, PdBr-, and Pd(h2-C2H4), the olefin-coordinated intermediate has the lowest barrier for the oxidativeaddition. P450 and SOR have the same first-coordination-sphere, Fe[N4S], at their active sites but proceed through different reaction paths. The different ground spin states of the intermediate FeIII(OOH)(SCH3)(L) model {L = porphyrin for P450 and four imidazoles for SOR} produce geometric and electronic structures that assist i) the protonation on distal oxygen for P450, which leads to O-O bond cleavage and formation of (FeIV=O)(SCH3)(L) H2O, and ii) the protonation on proximal oxygen for SOR, which leads to (FeIII-HOOH)(SCH3)(L) formation before the Fe-O bond cleavage and H2O2 production. The hydrogen bonding from explicit waters also stabilizes FeIII-HOOH over FeIV=O H2O products in SOR. The electrochemical hydrogen production by Fe4[MeC(CH2S)3]2(CO)8 (1) with 2,6-dimethylpyridinium (LutH ) were studied by the DFT calculations of proton-transfer free energies relative to LutH and reduction potentials (vs. Fc/Fc ) of possible intermediates. In hydrogen production by 1, the second, more highly reductive, applied potential (-1.58 V) has the advantage over the first applied potential (-1.22 V) in that the more highly reduced intermediates can more easily add protons to produce H2.

The design and production of efficient metal-hydrides for hydrogen storage is a long standing subject. Over the years, many different types of intermetallic hydride systems were studied and some of them came out to be operable. However, none of them meet all the storage criteria perfectly. In this study, total energies, hydrogen storage capacity and stability of AB (A = Al, Be, Cu, Fe, Ni, Sb, V and B = Ti) type intermetallics were investigated with the goal of spotting a potential hydrogen storage material. The relation between thermodynamic properties and the atomic and the electronic structure of hydrides are also pointed out. For this task, first principles pseudopotential method within the generalized gradient approximation (GGA) to density functional theory (DFT) was used. Calculations correctly predict experimentally determined structures except for CuTiH. Moreover, the atomic and cell parameter were found within the allowable error interval for DFT. In CuTi intermetallic, a structure having considerably lower formation energy than experimentally found mono-hydride was determined. This contradiction may be due to metastability of the experimental phase and high activation energy for the hydrogen movement in the system. It was found that AlTi and SbTi are not suitable candidates for hydrogen storage since their hydrides are too unstable. For the other intermetallic systems, the stability of the hydrides decreases in the order of VTi, CuTi, NiTi, BeTi, FeTi. For VTi, FeTi and NiTi, a change in metallic coordination around hydrogen from octahedron to tetrahedron is predicted when tetra-hydride (MTiH4) is formed. Additionally, at this composition, FeTi and NiTi have hydride structures with positive but near-zero formation energy which may be produced with appropriate alteration in chemical makeup or storage parameters. VTi is a promising intermetallic by means of storage capacity in that even VTiH6 is found to have negative formation energy but the hydrides are too stable which can be a problem during hydrogen desorption.

In this work, the use of theoretical tools of molecular modeling for tailoring 1D novel nanomaterials is demonstrated. There are four selected nano-structures as examples, each tailored for a specic demand of nano-technology that is yet to be fullled. For the purpose of modeling/calculating the electronic and structural properties, various methods of dening the interatomic interaction, such as empirical potential energy functions, semi-empirical methods and density functional theory, are used. Each of these methods have a dierent level of approximations leading to limitations in their use. Furthermore, each method needs to be calibrated carefully in order to obtain physically meaningful results. Examples being novel nano-structures, there does not exist any experimental observations directly studying the material at hand. Thus, in order to obtain a parameter set that best describes the system, a series of pre-existing structures that are physically and/or chemically related are used. Among the methods employed, the density functional theory (DFT) is certainly the most popular one, due to its accuracy and more importantly the framework it provides for perturbative extensions otherwise nearly impossible to calculate in Hartree-Fock level.

Wide band gap metal oxides have recently become one of the most investigated materials in surface science. Among these metal oxides especially TiO2 attracts great interest, because of its wide range applications, low cost, biocompatibility and ease of analysis by all experimental techniques. The usage of TiO2 as a component in solar cell technology is one of the most investigated applications of TiO2 . The wide band gap of TiO2 renders it inecient for isolated use in solar cells. TiO2 surface are therefore coated with a dye in order to increase eciency. This type of solar cells are called dye sensitized solar cells . The eciency of dye sensitized solar cells is directly related with the absorbed light portion of the entire solar spectrum by the dye molecule. Inspite of the early dyes, recent dye molcules, which are called wider wavelength response dye molecules, can absorb a larger portion of entire solar spectrum. Thus, the eciency of dye sensitized solar cells is increased by a considerably amount. In this thesis the electronic structure of organic rings, which are the fundamental components of the dye molecules, adsorbed on anatase (001) surface is analyzed using density functionaltheory. The main goal is to obtain a trend in the electronic structure of the system as a function of increasing ring number. Electronic structure analysis is conducted through band structure and density of states calculations. Results are presented and discussed in the framework of dye sensitized solar cells theory.

In this work pentacene adsorption on both flat and stepped Ag(111) surfaces were investigated by using Density Functional Theory within Projected Augmented Wave method. On the flat Ag(111) surface favorable adsorption site for a single pentacene molecule was determined to be the bridge site with an angle of 60&amp / #9702 / between pentacene molecular long axis and [011] lattice direction. Potential energy surface was found to be flat, especially along lattice directions. Diffusion and rotation barriers for pentacene on this surface were found to be smaller than 40 meV indicating the possibility of a two dimensional gas phase. Calculated adsorption energies for the flat surface indicate a weak interaction between molecule and the surface indicating physisorption. On the flat surface monolayer case is found to have lower adsorption energy than the isolated case due to pentacene&amp / #8722 / pentacene interactions. On the stepped Ag(233) surface, close to the step edge, adsorption energy increased significantly due to the stronger interaction between pentacene molecule and low coordinated silver step atoms. On the terraces of this surface, far from step edges, however a flat potential energy surface was observed similar to the case of flat Ag(111) surface. On the stepped surface pentacene found its favorable configuration as parallel to the step with a tilt angle similar to the observed thin film phase of pentacene on Ag(111) surface. Pentacene molecule showed small distortions on stepped surface and are closer to the silver step atoms 1 &Aring / more than the case of flat surface, hinting a chemical interaction as well as van der Waals interactions. However on Ag(799) surface, the perpendicular orientation of the pentacene molecule to the step direction showed no strong interaction due to less matching of carbon atoms with silver step atoms.

In this thesis, We have calculated the optimized geometries, electronic structures and spin distributions of metal and non-metal elements Li, Na, N and P doped C60 fullerene dimers and trimers with different spin multiplicities using hybrid density functional theory (DFT) at the B3LYP/6-31G level of theory. Natural population analysis and Mulliken population analysis show that non-metal elements (N, P) inside the C60 fullerene dimers and trimers are well isolated and preserve their electronic structures while charge transfer processes occur between metal elements(Li, Na) and C60 structures. Energy calculations showed that both doped and undoped linear C60 structures are energetically lower than triangular C60 structures. Calculated spin density distributions make non-metal doped C60 structures advantageous over metal doped C60 cages as spin cluster qubits.

Energy need in transportation and industry is mainly met by fossil fuels. This causes consumption of resources and some environmental problems. Diesel and gasoline engines are developed to consume fuel efficiently in vehicles. Since these engines work in a low fuel to air ratio, it becomes difficult to reduce nitrogen oxide emission. For this reason NO x storage/reduction (NSR) catalysts have been developed. While engines are operating under lean conditions alkaline or alkaline-earth component of NSR catalysts capture nitrogen oxides and during fuel rich period stored nitrates are reduced to nitrogen and oxygen gases. To develop this technology, different system parameters, for example system components and reaction environments have been widely investigated experimentally. To supplement the experimental findings, binding energies and structural properties of NO x on different catalyst components have been investigated theoretically. It has been experimentally observed that adding TiO2 to other conventional support materials increases resistance against sulfur poisoning, which is one of the main problems concerning NSR catalysts. For this reason, in this thesis (001) and (101) anatase surfaces have been investigated. Moreover, the effects of barium oxide units and layers on the electronic properties of the (001) anatase surface have been studied. To observe the effects of TiO2 as a support component, interactions of NO2 and SO2 on the unsupported and anatase supported (100) BaO surfaces have been compared. A clear increase in sulfur resistance has been observed in the presence of TiO2 in the catalyst under certain conditions.

We use the first-principles molecular-dynamics¡@simulation method (MD), which is based on the density functional theory (DFT) with local-density approximation (LDA), to calculate the sticking property of a carbon atom on hydrogen covered C(100) surface. We focused on trajectories and kinetic energy transfer of the gas-phase C atom for four incident angles of =0, £k/8, £k/6 and £k/4. We find that the calculated trajectories and the kinetic energy transfer of the gas-phase atom, Cn, overall are not very sensitive to the change of the incident angle. The insensitivity of the sticking property on the incident angle may be due to a large chemisorption energy, which bends the trajectory of Cn toward the surface, so that Cn is confined to move within a small range.

In this thesis, mechanical and electronic properties of a (4,4) SiC nanotube under different tensile strain were investigated by density functional theory (DFT) calculation. The HOMO-LUMO gap of nanotube will significantly decrease linearly with the increase of axial strain. Two different slopes are found before and after an 11% strain in the profile of HOMO-LUMO gap versus strain. The partial density of states, bond order and electronic deformation density were discussed for demonstrating the strain effect on the electronic properties of SiC nanotube under axial strain. The adsorption mechanism of CO on SiC nanotubes with different axial strains as well as the charge distributions after the adsorption were also discussed.