Browsing by Subject "Density Functional Theory"
Now showing 1 - 8 of 8
Results Per Page
Sort Options
Item Computational Studies of the Electronic Structures and Mechanisms of Late Transition Metal Systems(2013-08-27) Pitts, AmandaLate transition metal species are heavily studied because of their diverse applications in industrial, synthetic, and biological processes. Transition metals can alter the thermodynamic aspects of a reaction by creating an alternative, lower-energy pathway, which is not accessible without a metal. Numerous investigations have been performed to better understand the elementary steps within these reactions. The significant increase in available computing power coupled with the further development of transition-metal friendly quantum chemical methods has assisted in making computational chemistry an important method in predicting transition-metal mechanisms. This dissertation is divided into four parts, one for each of the transition-metal systems that were studied. The first system focuses on the formation of a carbon-bromine bond from the reaction of Ni(Ar)(Br)(pic) (Ar = 2-phenylpyridine, pic = 2-picoloine) with Br2. Unlike the typical behavior of heavier group 10 metals that have a wider range of stable oxidation states, Ni was found to undergo a change multiplicity during this reaction. The mechanism proceeds through a triplet state pathway that is stabilized by a Br2-/NiIII interaction instead of the NiIV singlet state pathway. The second two systems are concerned with inter- and intramolecular carbon-hydrogen bond activation, respectively. In the second system the lifetimes of carbon-hydrogen activation of four cycloalkanes with the Cp?Rh(CO) fragments (Cp?= ?5-C5H5 or ?5-C5Me5) were calculated. The lifetimes were found to be dependent of the size of the cycloalkane reacting and the number of possible reaction paths associated with the specific cycloalkane. A intramolecular carbon-hydrogen bond activation mechanism was calculated for the RuII(SC6H3Me2-2,6-?1S)2(PMe3)3 species for the third system. The dominant pathway was predicted to be the equatorial mechanism which proceeds through a ?-bond metathesis reaction. The final transition-metal system involves the transfer of CuI from the Atox1 metal binding site to a metal binding domain on the ATP7A or ATP7B proteins. This system was found to proceed through a dissociative pathway wich each two-coordinate and three-coordinate species stabilized by adopting the optimized the S lone pair/Cu 3d ?-overlap.Item Density functional study of graphene on insulating substrates(2009-08) Jadaun, Priyamvada; Banerjee, Sanjay; Sahu, Bhagawan R.; Fiete, GregoryThis is a study of the structural and electronic behavior and properties of graphene on α-quartz and α-sapphire using Density Functional Theory. We construct initial structures using the above 2 substrates, place a layer of graphene on them and subsequently allow the atoms to relax. After relaxation we study any structural changes, band structures, density of states, charge density to determine the electronic properties of the entire structure. Eventually this study will help in the search for good substrates for graphene based transistors.Item Density functional theory study on the interstitial chemical shifts of main-group-element centered hexazirconium halide clusters; synthetic control of speciation in [(Zr6ZCl12)] (Z = B, C)-based mixed ligand complexes(Texas A&M University, 2005-08-29) Shen, JingyiThe correlation between NMR chemical shifts of interstitial atoms and electronic structures of boron- and carbon-centered hexazirconium halide clusters was investigated by density functional theory (DFT) calculation. The influences of bridging halide and terminal ligand variations on electronic structure were examined respectively. Inverse proportionality was found between the chemical shifts and the calculated energy gaps between two Kohn-Sham orbitals of t1u symmetry, which arose from the bonding and antibonding interaction between the zirconium cage bonding orbitals and the interstitial 2p orbitals. Chemical shielding properties of the interstitial atoms were calculated with Gauge Including Atomic Orbital (GIAO) method. Stepwise ligand substitution of terminal chlorides on [(Zr6CCl12)Cl6]4-cluster by tri(n-butyl)-phosphine oxide (Bu3PO) was conducted with the aid of TlPF6. Composition of the reaction mixtures was analyzed by use of both 13C and 31P NMR. A preliminary scheme for synthesis and separation of [(Zr6CCl12)Cl6-x(Bu3PO)x]x-4 (x = 3 ?? 5) mixture based on solubility difference was reevaluated. Three 1,10-phenanthroline based bidentate ligands, namely, 2,9-Bis(diphenyl-phosphinyl)-1,10-phenanthroline, 2,9-Bis(diethoxyphosphoryl)-1,10-phenanthroline, and 2,9-Bis(di-n-butoxyphosphoryl)-1,10-phenantholine, were synthesized for bridge-chelating the hexazirconium clusters. Coordination chemistry of these ligands with the [Zr6BCl12] and [Zr6CCl12] clusters was subject to preliminary investigation.Item Elucidating Nucleation and Growth Behavior of Single-Walled Carbon Nanotubes obtained via Catalyzed Synthesis(2014-11-07) Burgos Beltran, Juan CarlosThe catalytic growth of single-walled carbon nanotubes (SWCNTs) is studied using reactive molecular dynamics (RMD) simulations and density functional theory (DFT) calculations. Computational calculations are performed in order to achieve a better understanding of the catalytic reaction mechanism at the initial stages of synthesis, where most of the structural characteristics are defined. Different process variables such as catalyst chemical composition and size, temperature, pressure, and the nature of catalyst support, can be optimized with the purpose of tuning the structure and physical properties of SWCNTs. Controlling the structure of SWCNTs during synthesis and avoiding additional purification and/or separation processes are critical for the direct use of SWCNTs in electronic devices. RMD simulations demonstrate that small catalyst particles favor the growth of lengthy nanotubes over catalyst encapsulation as a result of an increase of the curvature energies of the carbon capsule. Furthermore, simulations performed over deposited catalyst particles demonstrate that the catalyst-support adhesion must be controlled in order to grow nanotubes with high structural quality and avoid catalyst poisoning. Results herein reported suggest that growth conditions must be optimum to minimize the nucleation of topological defects in nanotubes. RMD trajectories prove the vital role played by the catalyst surface in healing defects via adsorption and diffusion. These results significantly impact the field of chirality control since the presence of defects introduce misorientation of hexagons, shifts the overall chiral angle, and therefore, modifies the physical properties of the nanotube. DFT calculations are employed to evaluate the interaction between SWCNTs and the ST-cut quartz substrate. The outstanding performance of CNT-based FET relies on the alignment of the horizontally grown nanotubes on silica substrates, as well as on the selective growth of semiconducting nanotubes. It is demonstrated that finite-length zigzag nanotubes are adsorbed stronger than armchair tubes on the quartz support. This suggests that the nanotube electronic band structure is a key factor on the preferential adsorption of zigzag tubes. DFT calculations suggest that patterns of unsaturated silicon atoms of silica surfaces define the crystallographic directions of preferential alignment. These patterns might be chemically altered in order to favor other directions of alignment.Item Integrating Experiment and Theory in Electrochemical Surface Science: Studies on the Molecular Adsorption on Noble-Metal Electrode Surfaces by Density Functional Theory, Electron Spectroscopy, and Electrochemistry(2013-08-05) Javier, Alnald CainticComputational techniques based on density functional theory (DFT) and experimental methods based on electrochemistry (EC), electrochemical scanning tunneling microscopy (EC-STM), and high-resolution electron energy loss spectroscopy (HREELS) were employed to study the adsorption of (i) sulfuric acid on Pd(111), (ii) benzene on Pd(111), (iii) hydroquinone/benzoquinone on Pd(111), (iv) hydroquinone sulfonate/benzoquinone sulfonate on Pd(111), (v) 2,3-dimethylhydroquinone/2,3-dimethylbenzoquinone on Pd(111) and polycrystalline Pd, (vi) hydrogen on 1-6 monolayers (ML) of Pd deposited on a Pt(111) substrate, and (vii) a thiolated iron hydrogenase model complex on polycrystalline Au. In situ EC-STM and DFT investigations of sulfuric acid on a Pd(111) surface indicated that two layers of water molecules and hydronium ions are assembled, non-co-planar with one another, between the rows of surface-coordinated sulfate anions; the layer that is slightly elevated is composed of hydronium counter cations. The STM images of benzene chemisorbed on a Pd(111) electrode surface were simulated and the results suggested that, when the potential of the Pd electrode is held at 0.3 V, benzene is chemisorbed on a 3-fold site; while at 0.55 V, the molecule is adsorbed on a position between a 3-fold and a 2-fold site. Computational and experimental results implied that at low concentrations, hydroquinone sulfonate undergoes oxidative chemisorption forming benzoquinone sulfonate (BQS) on the Pd(111) surface, BQS adopts a flat orientation in which the quinone ring is centered over a 2-fold site, and the C?H and C?S bonds are no longer co-planar with the quinone ring and are slightly tilted, directed away from the surface. At very dilute concentrations, when hydroquinone (H_(2)Q) undergoes oxidative chemisorption producing benzoquinone oriented flat, albeit with a slight tilt, on the Pd(111) surface, the flat-adsorbed quinone ring is centered on a bridge site where the C_(2) axis is rotated 30degree from the [110] direction of the metal substrate, the p-oxygen atoms are located above two-fold sites, and the ring is slightly puckered with the C?H bonds tilted away from the surface at approximately 20degree. When 2,3-dimethylH_(2)Q is chemisorbed on the Pd surface, at low concentrations, 2,3-dimethylH_(2)Q is oxidatively chemisorbed producing 2,3-dimethyl-1,4-benzoquinone oriented flat on the surface, the flat-adsorbed rings are centered above 2-fold sites wherein the C=O bonds are pointing 30degree from the [110] direction of the substrate, the para-oxygen atoms are located above bridge sites, the peripheral bonds are tilted away from the surface at ca. 20degree, and at higher concentrations, oxidative chemisorption occurs through activation of the ring?s C?H bonds yielding edge-oriented 2,3-dimethylH_(2)Q. Electrochemistry and DFT results also implied that at 1-2 ML of Pd on Pt(111), hydrogen is only adsorbed on a hollow site while at 3 ML of Pd or more, atomic hydrogen may be chemisorbed on the 3-fold site or absorbed in the octahedral hole underneath the hollow site. Using Au electrodes, an unbound iron hydrogenase analogue complex studied was found to slightly catalyze the H_(2) evolution process. However, when the complex was immobilized unto the Au surface, the electrocatalytic activity was greatly improved.Item Theoretical Studies of Structures and Mechanisms in Organometallic and Bioinorganic Chemistry: Heck Reaction with Palladium Phosphines, Active Sites of Superoxide Reductase and Cytochrome P450 Monooxygenase, and Tetrairon Hexathiolate Hydrogenase Model(2010-07-14) Surawatanawong, PanidaThe 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.Item Theory and simulation of colloids near interfaces: quantitative mapping of interaction potentials(2009-05-15) Lu, MingqingThe behavior of dense colloidal fluids near surfaces can now be probed in great detail with experimental techniques like video and confocal microscopy. In fact we are approaching a point where quantitative comparisons of experiments with particle-level theory, such as classical density functional theory (DFT), are appropriate. In a forward sense, we may use a known surface potential to predict a particle density distribution function from DFT; in an inverse sense, we may use an experimentally measured particle density distribution function to predict the underlying surface potential from DFT. In this dissertation, we tested the ability of the closure-based DFT to perform forward and inverse calculations on potential models commonly employed for colloidal particles and surface under different surface topographies. To reduce sources of uncertainty in this initial study, Monte Carlo simulation results played the role of experimental data. The accuracy of the predictions depended on the bulk particle density, potential well depth and the choice of DFT closure relationships. For a reasonable range of choices of the density, temperature, potential parameters, and surface features, the inversion procedure yielded particle-surface potentials to an accuracy on the order of 0.1 kBT. Our results demonstrated that DFT is a valuable numerical tool for microcopy experiments to image three-dimensional surface energetic landscape accurately and rapidly. B