Metals in Chemistry and Biology: Computational Chemistry Studies

Metals in Chemistry and Biology: Computational Chemistry Studies

Date: May 2007
Creator: Dinescu, Adriana
Description: Numerous enzymatic reactions are controlled by the chemistry of metallic ions. This dissertation investigates the electronic properties of three transition metal (copper, chromium, and nickel) complexes and describes modeling studies performed on glutathione synthetase. (1) Copper nitrene complexes were computationally characterized, as these complexes have yet to be experimentally isolated. (2) Multireference calculations were carried out on a symmetric C2v chromium dimer derived from the crystal structure of the [(tBu3SiO)Cr(µ-OSitBu3)]2 complex. (3) The T-shaped geometry of a three-coordinate β-diketiminate nickel(I) complex with a CO ligand was compared and contrasted with isoelectronic and isosteric copper(II) complexes. (4) Glutathione synthetase (GS), an enzyme that belongs to the ATP-grasp superfamily, catalyzes the (Mg, ATP)-dependent biosynthesis of glutathione (GSH) from γ-glutamylcysteine and glycine. The free and reactant forms of human GS (wild-type and glycine mutants) were modeled computationally by employing molecular dynamics simulations, as these currently have not been structurally characterized.
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Mechanical behavior and performance of injection molded semi-crystalline polymers.

Mechanical behavior and performance of injection molded semi-crystalline polymers.

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Date: August 2003
Creator: Simoes, Ricardo J. F.
Description: I have used computer simulations to investigate the behavior of polymeric materials at the molecular level. The simulations were performed using the molecular dynamics method with Lennard-Jones potentials defining the interactions between particles in the system. Significant effort was put into the creation of realistic materials on the computer. For this purpose, an algorithm was developed based on the step-wise polymerization process. The resulting computer-generated materials (CGMs) exhibit several features of real materials, such as molecular weight distribution and presence of chain entanglements. The effect of the addition of a liquid crystalline (LC) phase to the flexible matrix was also studied. The concentration and distribution of the second phase (2P) were found to influence the mechanical and tribological properties of the CGMs. The size of the 2P agglomerates was found to have negligible influence on the properties within the studied range. Moreover, although the 2P reinforcement increases the modulus, it favors crack formation and propagation. Regions of high LC concentration exhibit high probability of becoming part of the crack propagation path. Simulations of the tensile deformation under a uniaxial force have shown that the molecular deformation mechanisms developing in the material depend on several variables, such as the magnitude of ...
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Knowledge Discovery of Nanotube Mechanical Properties With an Informatics-Molecular Dynamics Approach

Knowledge Discovery of Nanotube Mechanical Properties With an Informatics-Molecular Dynamics Approach

Date: May 2012
Creator: Borders, Tammie L.
Description: Carbon nanotubes (CNT) have unparalleled mechanical properties, spanning several orders of magnitude over both length and time scales. Computational and experimental results vary greatly, partly due to the multitude of variables. Coupling physics-based molecular dynamics (MD) with informatics methodologies is proposed to navigate the large problem space. The adaptive intermolecular reactive empirical bond order (AIREBO) is used to model short range, long range and torsional interactions. A powerful approach that has not been used to study CNT mechanical properties is the derivation of descriptors and quantitative structure property relationships (QSPRs). For the study of defected single-walled CNTs (SWCNT), two descriptors were identified as critical: the density of non-sp2 hybridized carbons and the density of methyl groups functionalizing the surface. It is believed that both of these descriptors can be experimentally measured, paving the way for closed-loop computational-experimental development. Informatics can facilitate discovery of hidden knowledge. Further evaluation of the critical descriptors selected for Poisson’s ratio lead to the discovery that Poisson’s ratio has strain-varying nonlinear elastic behavior. CNT effectiveness in composites is based both on intrinsic mechanical properties and interfacial load transfer. In double-walled CNTs, inter-wall bonds are surface defects that decrease the intrinsic properties but also improve load transfer. ...
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Modeling wild type and mutant glutathione synthetase.

Modeling wild type and mutant glutathione synthetase.

Access: Use of this item is restricted to the UNT Community.
Date: August 2004
Creator: Dinescu, Adriana
Description: Glutathione syntethase (GS) is an enzyme that belongs to the ATP-grasp superfamily and catalyzes the second step in the biosynthesis of glutathione. GS has been purified and sequenced from a variety of biological sources; still, its exact mechanism is not fully understood. Four highly conserved residues were identified in the binding site of human GS. Additionally, the G-loop residues that close the active site during catalysis were found to be conserved. Since these residues are important for catalysis, their function was studied computationally by site-directed mutagenesis. Starting from the reported crystal structure of human GS, different conformations for the wild type and mutants were obtained using molecular dynamics technique. The key interactions between residues and ligands were detected and found to be essential for enzyme activity.
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FT-NMR and Raman Spectroscopic Studies of Molecular Dynamics in Liquids

FT-NMR and Raman Spectroscopic Studies of Molecular Dynamics in Liquids

Date: December 1993
Creator: Wang, Kuen-Shian
Description: NMR relaxation and Raman lineshape analysis are well known methods for the study of molecular reorientational dynamics in liquids. The combination of these two methods provides another approach to tackle the characterization of molecular dynamics in liquids. Investigations presented here include (1) NMR relaxation study of polycyclic compounds in solution, (2) the study of nitromethane reorientational dynamics using the NMR and Raman methods, and (3) Raman lineshape analysis of reorientation hexafluorobenzene/benzene mixtures.
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Growth Mechanisms, and Mechanical and Thermal Properties of Junctions in 3D Carbon Nanotube-graphene Nano-architectures

Growth Mechanisms, and Mechanical and Thermal Properties of Junctions in 3D Carbon Nanotube-graphene Nano-architectures

Date: December 2014
Creator: Niu, Jianbing
Description: Junctions are the key component for 3D carbon nanotube (CNT)-graphene seamless hybrid nanostructures. Growth mechanism of junctions of vertical CNTs growing from graphene in the presence of iron catalysts was simulated via quantum mechanical molecular dynamics (QM/MD) methods. CNTs growth from graphene with iron catalysts is based on a ‘‘base-growth’’ mechanism, and the junctions were the mixture of C-C and Fe-C covalent bonds. Pure C-C bonded junctions could be obtained by moving the catalyst during CNT growth or etching and annealing after growth. The growth process of 3D CNT-graphene junctions on copper templates with nanoholes was simulated with molecular dynamic (MD) simulation. There are two mechanisms of junction formation: (i) CNT growth over the holes that are smaller than 3 nm, and (ii) CNT growth inside the holes that are larger than 3 nm. The growth process of multi-layer filleted CNT-graphene junctions on the Al2O3 template was also simulated with MD simulation. A simple analytical model is developed to explain that the fillet takes the particular angle (135°). MD calculations show that 135° filleted junction has the largest fracture strength and thermal conductivity at room temperature compared to junctions with 90°,120°, 150°, and 180° fillets. The tensile strengths of the ...
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Atomistic Computer Simulations of Diffusion Mechanisms in Lithium Lanthanum Titanate Solid State Electrolytes for Lithium Ion Batteries

Atomistic Computer Simulations of Diffusion Mechanisms in Lithium Lanthanum Titanate Solid State Electrolytes for Lithium Ion Batteries

Date: August 2014
Creator: Chen, Chao-Hsu
Description: Solid state lithium ion electrolytes are important to the development of next generation safer and high power density lithium ion batteries. Perovskite-structured LLT is a promising solid electrolyte with high lithium ion conductivity. LLT also serves as a good model system to understand lithium ion diffusion behaviors in solids. In this thesis, molecular dynamics and related atomistic computer simulations were used to study the diffusion behavior and diffusion mechanism in bulk crystal and grain boundary in lithium lanthanum titanate (LLT) solid state electrolytes. The effects of defect concentration on the structure and lithium ion diffusion behaviors in LLT were systematically studied and the lithium ion self-diffusion and diffusion energy barrier were investigated by both dynamic simulations and static calculations using the nudged elastic band (NEB) method. The simulation results show that there exist an optimal vacancy concentration at around x=0.067 at which lithium ions have the highest diffusion coefficient and the lowest diffusion energy barrier. The lowest energy barrier from dynamics simulations was found to be around 0.22 eV, which compared favorably with 0.19 eV from static NEB calculations. It was also found that lithium ions diffuse through bottleneck structures made of oxygen ions, which expand in dimension by 8-10% ...
Contributing Partner: UNT Libraries