Cerium(IV) oxide (CeO2), ceria, is an active metal oxide used in solid oxide fuel cells and for the purification of exhaust gases in vehicle emissions control. Behind these technically important applications of ceria lies one overriding feature, namely ceria's exceptional reduction-oxidation properties. These are enabled by the duality of the cerium ion which easily toggles between Ce4+ and Ce3+. Here the cerium 4f electrons and oxygen vacancies (missing oxygen ions in the structure) are key players. In this thesis, the nature of ceria's f electrons and oxygen vacancies are in focus, and examined with theoretical calculations. It is shown that for single oxygen vacancies at ceria surfaces, the intimate coupling between geometrical structure and electron localisation gives a multitude of almost degenerate local energy mimima. With many vacancies, the situation becomes even more complex, and not even state-of-the-art quantum-mechanical calculations manage to predict the experimentally observed phenomenon of vacancy clustering. Instead, an alternative set of computer experiments managed to produce stable vacancy chains and trimers consistent with experimental findings from the literature and revealed a new general principle for surface vacancy clustering. The rich surface chemistry of ceria involves not only oxygen vacancies but also other active oxygen species such as superoxide ions (O2−). Experiments have shown that nanocrystalline ceria demonstrates an unusually large oxygen storage capacity (OSC) and an appreciable low-temperature redox activity, which have been ascribed to superoxide species. A mechanism explaining these phenomena is presented. The ceria surface is also known to interact with SOx molecules, which is relevant both in the context of sulfur poisoning of ceria-based catalysts and sulfur recovery from them. In this thesis, the sulfur species and key mechanisms involved are identified.

The phase behaviors and microstructures of various realistic and model mixtures of macro and micro molecules, such as polyolefin solutions and nanoparticle block copolymer composites, have been accurately predicted by the application of Statistical Associating Fluid Theory (SAFT) based approaches through various extensions that improve both the physical description of molecular interactions and efficiency of computations. The extensions are presented in a generic sense that is applicable to other studies. These rigorously derived theories have been demonstrated to capture material structure-property relationships and can be applied broadly to other fields including biology, medicine and energy industry. On the phenomenogical scale, the novel SAFT-Dimer equation of state has been extended to study the liquid-liquid phase boundary (cloud point) in polyolefin solutions. A simplified model of the polyolefin molecules has been followed and the effect of various parameters, such as temperature, molecular weight, solvent quality and comonomer content, on the phase behavior has been successfully captured by the theoretical model through comparison with experimental measurements. The presented approach requires less parameters than previous methods and is of critical value to the industrial productions of polymers, especially polyolefins with long branches. On the molecular scale, the interfacial SAFT (iSAFT) Density Functional Theory (DFT) has been extended to include a dispersion free energy functional that explicitly accounts for molecular correlations. The Order-Disorder Transition (ODT) between lamellar and disordered phase has then been investigated for pure block copolymer and copolymer nanocomposite systems. The extension has been shown to dramatically improve the ODT predictions of iSAFT as well as the self assembled microstructures in nanocomposites over previous DFT calculations, in comparison to coarse grained molecular simulations. The behavior of the equilibrium spacing of ordered structures is also examined against the variation of copolymer size and interactions. An efficient numerical scheme, Fast Fourier Transform (FFT), has been implemented and shown to drastically increase the computation efficiency. The theory has then been extended to study block copolymer morphologies with density variations in multiple dimensions. Comprehensive phase diagrams including lamellar, cylindrical and disordered phases have been obtained for copolymer nanocomposites for the first time using a single framework molecular theory. In addition, the nanoparticle induced morphological transition between cylindrical and lamellar phase has been studied using a pseudo arc-length continuation method. Transition evolution is tracked and metastable morphologies are examined and compared with existing experimental reports and theoretical calculations. With these extensions, iSAFT offers a powerful prediction tool that closely relates molecular structure to thermophysical properties and provides an efficient alternative to screen parameter space for specified material properties.

The chloro and pyridinate derivatives of rhenium(I) tricarbonyl complexes containing the diimine ligands 2,2’-bipyrazine (bpz) and 5,5’-dimethyl-2,2’-bipyrazine (Me2bpz) are discussed. When compared to similar rhenium(I) tricarbonyl complexes of 2,2’-bipyridine (bpy) and 2,2’-bipyrimidine (bpm), the Me2bpz complexes are comparable to bpm derivatives and their properties are intermediate between those of bpy and bpz complexes. Also discussed is the synthesis and properties of two new analogues of ruthenium(II) tris-bipyridine, a monomer and dimer. The complexes contain the ligand 6,6’-(1,2-ethanediyl)bis-2,2’-bipyridine (O-bpy) which contains two bipyridine units bridged in the 6,6’ positions by an ethylene group. Crystal structures of the two complexes formulated as [Ru(bpy)(O-bpy)](PF6)2 and [(Ru(bpy)2)2(O-bpy)](PF6)4 reveal structures of lower symmetry than D3 which affects the electronic properties of the complexes as revealed by Density Functional Theory (DFT) and Time Dependent Density Functional Theory (TDDFT) calculations. Iron(II) tris-bipyrazine undergoes dissociation in solution with loss of the three bipyrazine ligands. The rate of the reaction in acetonitrile depends on the concentration of anions present in the solution. The rate is fastest in the presence of Cl- and slowest in the presence of Br-. In a second discussion DFT calculations are used to explore four iron(II) diimine complexes. DFT calculations show the higher energy HOMO (highest occupied molecular orbital) orbitals of the four complexes are metal centered and the lower energy LUMO (lowest unoccupied molecular orbitals) are ligand centered. / Dissertation(Ph.D.)--Wichita State University, College of Liberal Arts and Sciences, Dept. of Chemistry

In the first part of this dissertation, we study mainly novel boron structures and their electronic and mechanical properties, using ab initio calculations. The electronic structure and construction of the boron buckyball B80, and boron nanotubes as the α-sheet wrapped around a cylinder are studied. The α-sheet is considered so far to be the most stable structure energetically out of the two dimensional boron assemblies. We will argue however that there are other sheets close in energy, using cluster expansion method. The boron buckyball is shown to have different possible isomers. Characterization of these isomers according to their geometry and electronic structure is studied in detail. Since the B80 structure is made of interwoven double-ring clusters, we also investigate double-rings with various diameters. We investigate the properties of nanotubes obtained from α-sheet. Computations confirm their high stability and identify mechanical stiffness parameters. Careful relaxation reveals the curvature-induced buckling of certain atoms off the original plane. This distortion opens up the gap in narrow tubes, rendering them semi-conducting. Wider tubes with the diameter d  1.7 nm retain original metallic character of the α-sheet. We conclude this part by investigation into hydrogen storage capacity of boron-rich compounds, namely the metallacarboranes. In the second part of dissertation, we switch our focus to electronic and transport properties of carbon nano-structures. We study the application of carbon nanotubes as electro-chemical gas sensors. The effect of physisorption of NO2 gas molecules on electron transport properties of semi-conducting carbon nanotubes is studied using ab initio calculations and Green’s function formalism. It is shown that upon exposure of nanotube to different concentrations of gas, the common feature is the shift in conductance towards lower energies. This suggests that physisorption of NO2 will result in a decrease (increase) in conductance of p-type (n-type) nanotubes with Fermi energies close to the edge of valence and conduction band. Finally we study the effect of torsion on electronic properties of carbon nano-ribbons, using helical symmetry of the structures.

In this study, we used the Density functional theory (DFT) and Molecular dynamics (MD) to obtain the suitable hydrogen storage of platinum nanoclusters on the (5,5) and (9,0) carbon nanotubes (CNTs) and Li atoms on the (5,5) carbon nanotube. platinum nanoclusters on the CNT is chemisorption because hydrogen molecules dissociated. Li atoms on the CNT is physisorption due to hydrogen molecule do not dissociated. We hope that two different hydrogen storage models can achieve the goal which was set by Department of Energy US. There are three parts in this study. There were three parts in this study: The first part: It is very important for obtaining the suitable potential parameters in the Molecular dynamics simulation to reflect the interaction between materials. However, we can not find the suitable parameters from the references to simulate our system. Hence, we use the Force-matching method and Density functional theory to obtain the potential parameter in our system. The Molecular dynamics simulation is utilized to simulate the hydrogen adsorption qith the modified potential parameters. The second part: The dynamics behavior of different platinum nanopartilces on the (5, 5) and (9, 0) CNTs at different temperature are investigated by the Molecular dynamics simulation when new parameters are obtained. The migration trajectory, square displacement and mean square displacement of the mass center of platinum nanoclusters are used to analyze to find what sizes of platinum nanoparticle and temperature are the best for hydorgen storage. The third part: Density functional theory simulation is utilized to simulate hydrogen molecules adsorbed on the (5, 5) pristine CNT and CNT with lithium atoms. The pressure and temperature effects are used to analyze the hydrogen storage system. Moreover, the different arrangements of CNTs array are also studied, such as, Van der Waals distance (VDW) and shape of array (triangular and square arrangement). Finally, the adsorbed and released phenomenon are also analyzed by the gravimetric capacity (wt%) of hydrogen molecule for hydrogen.

The hydrogenation of aromatic sulfonyl chloride to produce aromatic thiol is an important industrial reaction. The aromatic thiol is a critical intermediate in the production of many pharmaceuticals as well as several agrochemicals. Density Functional Theory (DFT), a quantum mechanical method, was used to investigate the new aromatic thiol production technology at the molecular level in aspects including reaction species adsorption and transition state determination. Plant design methods and economic analysis were performed to determine the economic feasibility of the new technology in the current specialty chemicals market. The quantum mechanical calculations showed that the molecules adsorbed to three simulated (100) Pd catalyst surfaces will preferentially move to configurations that are favorable for reaction progression. The calculations also show that the proposed reaction sequence by DuPont is the most feasible option despite the investigation into an alternative sequence that arose from molecular observations during calculations. Predicted activation energies (Ea) were in the range of 6.88 ? 38.1 kcal/mol which is comparable to the 14.58 kcal/mol determined experimentally by DuPont, and the differences between experimental and simulated values are easily explained. Plant design calculations show that a semi-batch reactor plant can easily produce 2MM lb of thiol/year, giving the owner of the plant an immediate 18% market share in the worldwide market of benzenethiol. Economic analysis shows that a grassroots plant construction is not currently an economically feasible option for corporate investment unless a source of cheap, skilled labor can be found in addition to a means of a 25% discount on certain raw material feed stocks. However, if both of these requirements can be fulfilled then new plant construction will have a payback time of 3.71 years based on the price of benzenethiol in the summer of 2007, $2.27/lb thiol.

Recently a new outlook on dealing with dipolar ultracold fermions based on density functional methods has received attention. A Thomas-Fermi treatment coupled with a variational approach has been developed for a collection of fermions trapped in a harmonic potential interacting via dipole-dipole forces. In this thesis, firstly our alternative formalism for Thomas-Fermi method by performing some calculations based on the Kohn-Sham formalism which is one of the main idea of density functional theory is investigated. Furthermore, density distributions are obtained dependent to the parameters / rescaled interaction strength, dipole-dipole energy and the trap parameter which determine the trap geometry based on this theory. The thesis starts with a brief outline of the density functional theory and theory of our system, continues with calculations based on this theory, which are free of any variational assumptions for the density profile. Moreover, results of density graphics for harmonic trap will be followed by discussion of comparison and contrast with Thomas-Fermi method based on the paper of Goral et al.. These discussions are mainly about the shape of the density distribution, variation of the cloud parameters and energy behaviours according to the rescaled interaction strength. The thesis concludes with an analysis of contribution of density functional theory to this fermionic system.

We have used the first-principle molecular-dynamics method to study the dependence of the sticking property of a C gas-phase atom on C (100) on its initial position. For all the three cases, Cn never penetrates through the dimer layer even when Cn impinges on an opening in the surface. We find Cn becomes bonded with two substrate C atoms and one hydrogen atom with the hydrogen atom moving on the vacuum side.

Computational methods are very useful tools in the study of enzymatic reactions, as they can provide a detailed understanding of reaction mechanisms and the sources of various selectivities. In this thesis, density functional theory has been employed to examine four different enzymes of potential importance for biocatalytic applications. The enzymes considered are limonene epoxide hydrolase, soluble epoxide hydrolase, arylmalonate decarboxylase and phenolic acid decarboxylase. Besides the reaction mechanisms, the enantioselectivities in three of these enzymes have also been investigated in detail. In all studies, quite large quantum chemical cluster models of the active sites have been used. In particular, the models have to account for the chiral environment of the active site in order to reproduce and rationalize the experimentally observed selectivities. For both epoxide hydrolases, the calculated enantioselectivities are in good agreement with experiments. In addition, explanations for the change in stereochemical outcome for the mutants of limonene epoxide hydrolase, and for the observed enantioconvergency in the soluble epoxide hydrolase are presented. The reaction mechanisms of the two decarboxylases are found to involve the formation of an enediolate- or a quinone methide intermediate, supporting thus the main features of the proposed mechanisms in both cases. For arylmalonate decarboxylase, an explanation for the observed enantioselectivity is also presented. In addition to the obtained chemical insights, the results presented in this thesis demonstrate that the quantum chemical cluster approach is indeed a valuable tool in the field of asymmetric biocatalysis. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript. Paper 4: Manuscript.</p><p> </p>

Hydroxyapatite (HA, Ca₁₀(PO₄)₆(OH)₂) is one of the most abundant materials in mammal bone. It crystallizes in an aqueous environment within spaces between tropocollagen protein chains. However, despite its abundance and possible usefulness in the medical field this complex physical system remains poorly understood to date. We present a theoretical study of the energetics of hydroxyapatite, its electronic, mechanical and thermodynamic properties. Our mechanical and thermodynamic properties from first principles are in excellent agreement with the rare available experimental data. The monoclinic and hexagonal phases are lowest in energy. A comparison of the phonon dispersions of these two phases reveals that a phase transition occurs due to a difference in vibrational free energy. The transition is of order-disorder type. Our calculated phase transition temperature is 680 K, in decent agreement with the experimentally determined 470 K. An alternative theoretical model yields 882 K. The phase transition is mediated by OH libration modes. We also report for the first time on a peculiarity in the phonon spectrum of hexagonal and monoclinic HA. When studying the Lyddane-Sachs-Teller shifts in the spectrum close to the [Gamma]-point we identify two vibration modes showing a systematically increasing Lyddane-Sachs-Teller shift in frequency with decreasing dielectric constant. In experiment, the dielectric constant varies between 5 and 20 depending on the Ca/P ratio in the sample. The frequency shifts in the affected modes are as large as 20 cm⁻¹ as one spans the range of the dielectric constant. Thus, a simple spectroscopic analysis of a sample of bone may determine the quality of the sample in a physiological sense. We also identify the chemically stable low energy surface configurations as function of the OH, PO₄ and Ca concentration. In the experimentally relevant OH-rich regime we find only two surfaces competing for lowest energy. The surface most stable over almost the entire OH-rich regime is OH-terminated, and is currently being investigated in the presence of water and atomic substitutions on the HA surface. / text