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

Silicon (Si)-based materials have recently emerged as a promising candidate for anodes in lithium-ion batteries because they exhibit much higher energy-storage capacities than the conventional graphite anode. However, the practical use of Si is hampered by its poor cycleability; during lithiation, Si forms alloys with Li and undergoes significant structural and volume changes, which can cause severe cracking/pulverization and consequent capacity fading arising from the loss of electrical contacts. To overcome these drawbacks, many innovative approaches have been explored with encouraging results; however, many fundamental aspects of the lithiation behavior remain ambiguous. Hence, the focus of this work is to develop a better understanding of the lithiation process at the atomistic scale using quantum mechanical calculations. In addition, based on the improved understanding, we attempt to address the fundamental mechanisms behind the successful approaches to enhance the anode performance. To lay a foundation for the investigation of alloy-type anodes, in Chapter 3, we first examine how lithiation occurs in Si and the formation of crystalline and amorphous LixSi alloys (0 ≤ x ≤ 4); followed by assessing the lithiation-induced changes in the energetics, atomic structure, electronic and mechanical properties, and Li diffusivity. The same approach is then extended to analyze the lithiation behavior of germanium (Ge) and tin (Sn) for developing a generalized understanding on the Group IV alloy-type anodes. Along this comparative study, we notice a few distinguishing features pertain only to Si (or Ge), such as the facile Li diffusion in Ge and facet-dependent lithiation in Si, which are discussed in Chapter 4. Beyond the fundamental research, we also look into factors that may contribute to the improved anode performance, including (i) finetuning of the oxidation effects in Si-rich oxides, [alpha] -SiO [subscript 1/3] (Chapter 5), (ii) maximizing the surface effects through nano-engineered structures (Chapters 6 & 7), and finally (iii) the role of interface in Si-graphene (carbon) composites (Chapter 8).

In addition to their potential use at low to moderate temperatures in mobile fuel cell technologies, metal hydrides may also find application as high temperature tritium getterers in the U.S. DOE Next Generation Nuclear Plant (NGNP). We use Density Functional Theory to identify metal hydrides capable of sequestering tritium at temperatures in excess of 1000 K. First we establish the minimum level of theory required to accurately capture the thermodynamics of highly stable metal hydrides and determine that isotope effects can be neglected for material screening. Binary hydride thermodynamics are largely well established, and ternary and higher hydrides typically either do not form or decompose at lower temperatures. In this thesis we investigate anomalous systems with enhanced stability in order to identify candidates for the NGNP application beyond the binary hydrides. Methods implemented in this work are particularly useful for deriving finite temperature phase stability behavior in condensed systems. We use grand potential minimization methods to predict the interstitial Th−Zr−H phase diagram and apply high throughput, semi-automated screening methodologies to identify candidate complex transition metal hydrides (CTMHs) from a diverse library of all known, simulation ready ternary and quaternary CTMHs (102 materials) and 149 hypothetical ternary CTMHs based on existing prototype structures. Our calculations significantly expand both the thermodynamic data available for known CTMHs and the potential composition space over which previously unobserved CTMHs may be thermodynamically stable. Initial calculations indicate that the overall economic viability of the tritium sequestration system for the NGNP will largely depend on the amount of protium rather than tritium in the metal hydride gettering bed feed stream.

Functional materials with controllable phase transitions have been widely used in devices for information storage (e.g. hard-disk, CD-ROM, memory) and energy storage (e.g. battery, shape memory alloy). One of the important issues to design such materials is to realize the desirable phase transition processes, in which atomistic simulation can be used for the prediction of materials properties. The accuracy of the prediction is largely dependent on searching the true value of the transition rate, which is determined by the minimum energy barrier between stable states, i.e. the saddle point on a potential energy surface (PES). Although a number of methods that search for saddle points on a PES have been developed, they intend to locate only one saddle point with the maximum energy along the transition path at a time. In addition, they do not consider the input uncertainty associated with the calculation of potential energy. To overcome the limitations, in this dissertation, new saddle point search methods are developed to provide a global view of energy landscape with improved efficiency and robustness. First, a concurrent search algorithm for multiple phase transition pathways is developed. The algorithm is able to search multiple local minima and saddle points simultaneously without prior knowledge of initial and final stable configurations. A new representation of transition paths based on parametric Bézier curves is introduced. A curve subdivision scheme is developed to dynamically locate all the intermediate local minima and saddle points along the transition path. Second, a curve swarm search algorithm is developed to exhaustively locate the local minima and saddle points within a region concurrently. The algorithm is based on the flocking of multiple groups of curves. A collective potential model is built to simulate the communication activities among curves. Third, a hybrid saddle-point search method using stochastic kriging models is developed to improve the efficiency of the search algorithm as well as to incorporate model-form uncertainty and numerical errors associated with density functional theory calculation. These algorithms are demonstrated by predicting the hydrogen diffusion process in FeTiH and body-centered iron Fe8H systems.