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(4+2)-Cycloaddition Reactions of Ketenes; Pyranones

Description: This study deals with the (4+2)-cycloaddition reactions of 4-π electron compounds with ketenes. Chloroketenes were generated in situ from the corresponding chlorinated acid chlorides in the presence of the ketenophiles. Chloro-, dichloro- and diphenylketenes reacted with 1-methoxy-3-trimethylsiloxy-l,3-butadiene, and 2,4-bis(trimethylsiloxy)-1,3-pentadiene to yield the corresponding dihydropyrans. The dihydropyrans yielded substituted 4-pyranones on hydrolysis.
Date: August 1983
Creator: Agho, Michael O. (Michael Osarenogowu)

Adhesion/Diffusion Barrier Layers for Copper Integration: Carbon-Silicon Polymer Films and Tantalum Substrates

Description: The Semiconductor Industry Association (SIA) has identified the integration of copper (Cu) with low-dielectric-constant (low-k) materials as a critical goal for future interconnect architectures. A fundamental understanding of the chemical interaction of Cu with various substrates, including diffusion barriers and adhesion promoters, is essential to achieve this goal. The objective of this research is to develop novel organic polymers as Cu/low-k interfacial layers and to investigate popular barrier candidates, such as clean and modified tantalum (Ta) substrates. Carbon-silicon (C-Si) polymeric films have been formed by electron beam bombardment or ultraviolet (UV) radiation of molecularly adsorbed vinyl silane precursors on metal substrates under ultra-high vacuum (UHV) conditions. Temperature programmed desorption (TPD) studies show that polymerization is via the vinyl groups, while Auger electron spectroscopy (AES) results show that the polymerized films have compositions similar to the precursors. Films derived from vinyltrimethyl silane (VTMS) are adherent and stable on Ta substrates until 1100 K. Diffusion of deposited Cu overlayers is not observed below 800 K, with dewetting occurred only above 400 K. Hexafluorobenzene moieties can also be incorporated into the growing film with good thermal stability. Studies on the Ta substrates demonstrate that even sub-monolayer coverages of oxygen or carbide on polycrystalline Ta significantly degrade the strength of Cu/Ta chemical interactions, and affect the kinetics of Cu diffusion into bulk Ta. On clean Ta, monolayer coverages of Cu will de-wet only above 600 K. A partial monolayer of adsorbed oxygen (3L O2 at 300 K) results in a lowering of the de-wetting temperature to 500 K, while saturation oxygen coverage (10 L O2, 300 K) results in de-wetting at 300 K. Carbide formation also lowers the de-wetting temperature to 300 K. Diffusion of Cu into the Ta substrate at 1100 K occurs only after a 5-minute induction period. This induction period increases ...
Date: December 1999
Creator: Chen, Li

Analysis of Acid Gas Emissions in the Combustion of the Binder Enhanced d-RDF by Ion Chromatography

Description: Waste-to-energy has become an attractive alternative to landfills. One concern in this development is the release of pollutants in the combustion process. The binder enhanced d-RDF pellets satisfy the requirements of environmental acceptance, chemical/biological stability, and being storeable. The acid gas emissions of combusting d-RDF pellets with sulfur-rich coal were analyzed by ion chromatography and decreased when d-RDF pellets were utilized. The results imply the possibility of using d-RDF pellets to substitute for sulfur-rich coal as fuel, and also substantiate the effectiveness of a binder, calcium hydroxide, in decreasing emissions of SOx. In order to perform the analysis of the combustion sample, sampling and sample pretreatment methods prior to the IC analysis and the first derivative detection mode in IC are investigated as well. At least two trapping reagents are necessary for collecting acid gases: one for hydrogen halides, and the other for NOx and SOx. Factors affecting the absorption of acid gases are studied, and the strength of an oxidizing agent is the main factor affecting the collection of NOx and SOx. The absorption preference series of acid gases are determined and the absorption models of acid gases in trapping reagents are derived from the analytical results. To prevent the back-flushing of trapping reagents between impingers when leak-checking, a design for the sampling train is suggested, which can be adopted in sample collections. Several reducing agents are studied for pretreating the sample collected in alkali-permanganate media. Besides the recommendation of the hydrogen peroxide solution in EPA method, methanol and formic acid are worth considering as alternate reducing agents in the pretreatment of alkaline-permanganate media prior to IC analysis. The first derivative conductivity detection mode is developed and used in IC system. It is efficient for the detection and quantification of overlapping peaks as well as being applicable for non-overlapping ...
Date: August 1988
Creator: Jen, Jen-Fon

Biological Inhibitors

Description: Four isosteric series of plant growth-regulating compounds were prepared. Using an Avena sativa coleptile assay system, derivatives in series I and IV inhibited segment elongation to a greater degree than did comparable derivatives in series II and III.
Date: December 1971
Creator: Sargent, Dale Roger

Bonding Studies in Group IV Substituted n,n-dimethylanilines

Description: The purpose of the present work is to study the effects of the trimethylsilyl and trimethylgermyl substituents on the N,N-dimethylamino ring system. Both ground and excited state interactions were studied and their magnitudes determined. The experimental data were then used in conjunction with molecular orbital calculations to differentiate among, and determine the importance of, d-p bonding, hyperconjugation or polarization of the trimethylsilyl group on the ground and excited state bonding.
Date: December 1971
Creator: Drews, Michael James

Calcium Aluminates Synthesis, Characterization, and Hydration Behavior

Description: The hydration behavior of the calcium aluminates as a function of the glass content, the curing temperature, and the water-solid ratio was investigated. In order to keep them from influencing the results, the free-lime content and the surface area of all samples were kept constant, whenever possible. Samples were hydrated with a water-solid ratio of 10/1 for periods of 1 to 90 days. Three curing temperatures were studied; 2°C, 25°C, and 50°C. Samples were hydrated in tightly sealed polyethylene containers to prevent reactions with atmospheric carbon dioxide. The hydration was followed by X-ray diffraction and thermal analysis. Only two samples, Hexacalcium Tetra-alumino Magnesium Silicate and Tricalcium Magnesium Dialuminate, were successfully prepared in an amorphous form. These compounds were used to investigate the effect of glass content on the hydration behavior. Results indicate that when the glass content is increased a corresponding increase is found in the percent combined water. Samples hydrated at 25°C were influenced by changes in the glass content to a greater degree than were those hydrated at either 2°C or 50°C. The effect of the water-solid ratio on the hydration behavior of the calcium aluminates was studied using the compounds; Hexacalcium Tetra-Alumino Magnesium Silicate/ and Dodecacalcium Hepta-Aluminate. In general, samples that were hydrated with large water-solid ratios reacted more completely than did those hydrated with small water-solid ratios. The presence of sufficient water to theoretically hydrate the samples to completion did not guarantee that the sample would do so. The curing temperature influenced the hydration behavior to a greater degree than did the glass content or the water-solid ratio. Increasing the curing temperature not only increased the rate of hydration, but, in some cases, also changed the hydration products.
Date: December 1984
Creator: Griffin, Joseph George

Catalytic Calcination of Calcium Carbonate

Description: The calcination of calcium carbonate in a cement or a lime kiln uses approximately two to four times the theoretical quantity of energy predicted from thermodynamic calculation depending upon the type of the kiln used (1.4 x 10^6 Btu/ton theoretical to 6 x 10^6 Btu/ton actual). The objective of this research was to attempt to reduce the energy required for the calcination by 1. decreasing the calcination temperature of calcium carbonate, and/or 2. increasing the rate of calcination at a specific temperature. Assuming a catalytic enhancement of 20 percent in the industrial applications, an energy savings of 300 million dollars annually in the United States could be reached in the cement and lime industries. Three classes of compounds to date have shown a positive catalytic effect on the calcination of calcium carbonate. These include alkali halides, phospho- and silico-molybdate complexes, and the fused carbonates system.
Date: August 1985
Creator: Safa, Ali Ibrahim, 1953-

Characterization of Low Barrier Hydrogen Bonds in Enzyme Catalysis: an Ab Initio and DFT Investigation

Description: Hartree-Fock, Moller-Plesset, and density functional theory calculations have been carried out using 6-31+G(d), 6-31+G(d,p) and 6-31++G(d,p) basis sets to study the properties of low-barrier or short-strong hydrogen bonds (SSHB) and their potential role in enzyme-catalyzed reactions that involve proton abstraction from a weak carbon-acid by a weak base. Formic acid/formate anion, enol/enolate and other complexes have been chosen to simulate a SSHB system. These complexes have been calculated to form very short, very short hydrogen bonds with a very low barrier for proton transfer from the donor to the acceptor. Two important environmental factors including small amount of solvent molecules that could possibly exist at the active site of an enzyme and the polarity around the active site were simulated to study their energetic and geometrical influences to a SSHB. It was found that microsolvation that improves the matching of pK as of the hydrogen bond donor and acceptor involved in the SSHB will always increase the interaction of the hydrogen bond; microsolvation that disrupts the matching of pKas, on the other hand, will lead to a weaker SSHB. Polarity surrounding the SSHB, simulated by SCRF-SCIPCM model, can significantly reduce the strength and stability of a SSHB. The residual strength of a SSHB is about 10--11 kcal/mol that is still significantly stable compared with a traditional weak hydrogen bond that is only about 3--5 kcal/mol in any cases. These results indicate that SSHB can exist under polar environment. Possible reaction intermediates and transition states for the reaction catalyzed by ketosteroid isomerase were simulated to study the stabilizing effect of a SSHB on intermediates and transition states. It was found that at least one SSHB is formed in each of the simulated intermediate-catalyst complexes, strongly supporting the LBHB mechanism proposed by Cleland and Kreevoy. Computational results on the activation energy for ...
Date: August 1999
Creator: Pan, Yongping

Chemical Equilibria in Binary Solvents

Description: Dissertation research involves development of Mobile Order Theory thermodynamic models to mathematically describe and predict the solubility, spectral properties, protonation equilibrium constants and two-phase partitioning behavior of solutes dissolved in binary solvent mixtures of analytical importance. Information gained provide a better understanding of solute-solvent and solvent-solvent interactions at the molecular level, which will facilitate the development of better chemical separation methods based upon both gas-liquid and high-performance liquid chromatography, and better analysis methods based upon complexiometric and spectroscopic methods. Dissertation research emphasizes chemical equilibria in systems containing alcohol cosolvents with the understanding that knowledge gained will be transferable to more environmentally friendly aqueous-organic solvent mixtures.
Date: August 1997
Creator: McHale, Mary E. R.

Chromatographic and Spectroscopic Studies on Aquatic Fulvic Acid

Description: High Performance Liquid Chromatography (HPLC) was used to investigate the utility of this technique for the analytical and preparative separation of components of aquatic fulvic acids (FA). Three modes of HPLC namely adsorption, anion exchange and reversed phase were evaluated. Aquatic fulvic acids were either extracted from surface water and sediment samples collected from the Southwest of the U.S., or were provided in a high purity form from the USGS. On the adsorption mode, a major fraction of aquatic fulvic acid was isolated on a semipreparative scale and subjected to Carbon-13 NMR and FAB Mass Spectroscopy. Results indicated that (1) The analyzed fraction of fulvic acid contains more aliphatic than aromatic moieties; (2) Methoxy, carboxylic acids, and esters are well-defined moieties of the macromolecule; (3) Phenolic components of the macromolecules were not detected in the Carbon-13 NMR spectrum possibly because of the presence of stable free radicals. Results of the anion exchange mode have shown that at least three types of acidic functionalities in aquatic fulvic acid can be separated. Results also indicated that aquatic fulvic acid can be progressively fractionated by using subsequent modes of HPLC. Results of reversed phase mode have shown that (1) The fractionation of aquatic fulvic acid by RP-HPLC is essentially controlled by the polarity and/or pH of the carrier solvent system; (2) Under different RP-HPLC conditions aquatic fulvic acid from several locations are fractionated into the same major components; (3) Fulvic acid extracted from water and sediment from the same site are more similar than those extracted from different sites; (4) Cationic and anionic ion pair reagents indicated the presence of amphoteric compounds within the polymeric structure of fulvic acid. Each mode of HPLC provided a characteristic profile of fulvic acid. The results of this research provided basic information on the behavior of aquatic ...
Date: August 1986
Creator: Chang, David Juan-Yuan

Combined Electrochemistry and Spectroscopy of Complexes and Supramolecules containing Bipyridyl and Other Azabiphenyl Building Blocks

Description: A group of azabiphenyl complexes and supramolecules, and their reduced and oxidized forms when possible, were characterized by cyclic voltammetry and electronic absorption spectroscopy. The oxidized and reduced species, if sufficiently stable, were further generated electrochemically inside a specially designed quartz cell with optically transparent electrode, so that the spectra of the electrochemically generated species could be taken in situ. Assignments were proposed for both parent and product electronic spectra. Species investigated included a range of Ru(II) and Pt(II) complexes, as well as catenanes and their comparents. Using the localized electronic model, the electrochemical reduction can be in most cases assigned as azabiphenyl-based, and the oxidation as transition metal-based. This is consistent with the fact that the azabiphenyl compounds have a low lying π* orbital. The electronic absorption spectra of the compounds under study are mainly composed of π —> π* bands with, in some cases, charge transfer bands also.
Date: August 1995
Creator: Yang, Lei

Computational Investigation of DNA Repair Enzymes: Determination and Characterization of Cancer Biomarkers and Structural Features

Description: Genomic integrity is important for living cells' correct functioning and propagation. Deoxyribonucleic acid as a molecule is a subject to chemical reactions with agents that can come from environment as well as from internal metabolism processes. These reactions can induce damage to DNA and thus compromise the genetic information, and result in disease and death of an organism. To mitigate the damage to DNA, cells have evolved to have multiple DNA repair pathways. Presented here is a computational study of DNA repair genes. The structure of the Homo sapiens direct DNA repair gene ALKBH1 is predicted utilizing homology modeling methods and using AlkB and DBL proteins as templates. Analysis of the obtained structure and molecular dynamics simulations give insights into potentially functionally important residues of the protein. In particular, zinc finger domains are predicted, and lysines that could perform catalytic activities are investigated. Subsequent mutagenesis experiments revealed the effect of the residues predicted to form zinc fingers on activity of ALKBH1. Structure and dynamics of AlkD, a Bascillus cereus base excision DNA repair protein is also studied. This protein has been shown to bind DNA with large alkyl adducts and perform excision catalysis without base flipping which is characteristic to other enzymes in the same family. MD simulations of AlkD revealed that B helix, which interacts with DNA, has higher fluctuations when AlkD is not bound to DNA, and thus could have a role in binding and recognition of DNA. For the purpose of finding biomarkers and to further our understanding of a mode of action of DNA repair genes, statistical methods were applied to identify mutations that are linked to cancer phenotypes. Analysis was based on case-control studies of patients with cancers of prostate, breast, pancreas, lung as well as chronic lymphocytic leukemia from NCBI dbGAP database. Those mutations ...
Date: May 2018
Creator: Silvestrov, Pavel

Computational Simulations of Cancer and Disease-Related Enzymatic Systems Using Molecular Dynamics and Combined Quantum Methods

Description: This work discusses applications of computational simulations to enzymatic systems with a particular focus on the effects of various small perturbations on cancer and disease-related systems. First, we cover the development of carbohydrate-based PET imaging ligands for Galectin-3, which is a protein overexpressed in pancreatic cancer tumors. We uncover several structural features for the ligands that can be used to improve their binding and efficacy. Second, we discuss the AlkB family of enzymes. AlkB is the E. coli DNA repair protein for alkylation damage, and has human homologues with slightly different functions and substrates. Each has a conserved active site with a catalytic iron and a coordinating His...His...Asp triad. We have applied molecular dynamics (MD) to investigate the effect of a novel single nucleotide polymorphism for AlkBH7, which is correlated with prostate cancer and has an unknown function. We show that the mutation leads to active site distortion, which has been confirmed by experiments. Thirdly, we investigate the unfolding of hen egg white lysozyme in 90% ethanol solution and low pH, to show the initial steps of unfolding from a native-like state to the disease-associated beta-sheet structure. We compare to mass spectrometry experiments and also show differing pathways based on protonation state. Finally, we discuss three different DNA polymerase systems. DNA polymerases are the primary proteins that replicate DNA during cell division, and have various extra or specific functions. We look at a proofreading-deficient DNA polymerase III mutant, the effects of solvent on DNA polymerase IV's ability to bypass bulky DNA adducts, and a variety of mutations on DNA polymerase kappa.
Date: May 2018
Creator: Walker, Alice Rachel

Computational Studies of C–H/C–C Manipulation Utilizing Transition Metal Complexes

Description: Density Functional Theory (DFT) is an effective tool for studying diverse metal systems. Presented herein are studies of a variety of metal systems, which can be applied to accomplish transformations that are currently difficult/impossible to achieve. The specific topics studied utilizing DFT include: 1) C–H bond activation via an Earth-abundant transition metal complex, 2) C–H bond deprotonation via an alkali metal superbase, 3) and amination/aziridination reactions utilizing a CuI reagent. Using DFT, the transformation to methanol (CH3OH) from methane (CH4) was examined. The transition metal systems studied for this transformation included a model FeII complex. This first-row transition metal is an economical, Earth-abundant metal. The ligand set for this transformation includes a carbonyl ligand in one set of complexes as well as a phosphite ligand in another. The 3d Fe metal shows the ability to convert alkyls/aryls to their oxidized counterpart in an energetically favorable manner. Also, “superbasic” alkali metal amides were investigated to perform C—H bond cleavage. Toluene was the substrate of interest with Cs chosen to be the metal of interest because of the highly electropositive nature of this alkali metal. These highly electrophilic Cs metal systems allow for very favorable C—H bond scission with a toluene substrate. Finally, the amination and aziridination of C–H and C=C bonds, respectively, by a CuI reagent was studied. The mechanism was investigated using DFT calculations. Presently, these mechanisms involving the use of coinage metals are debated. Our DFT simulations shed some insight into how these transformations occur and ultimately how they can be manipulated.
Date: May 2015
Creator: Pardue, Daniel B.

Computational Studies of Selected Ruthenium Catalysis Reactions.

Description: Computational techniques were employed to investigate pathways that would improve the properties and characteristics of transition metal (i.e., ruthenium) catalysts, and to explore their mechanisms. The studied catalytic pathways are particularly relevant to catalytic hydroarylation of olefins. These processes involved the +2 to +3 oxidation of ruthenium and its effect on ruthenium-carbon bond strengths, carbon-hydrogen bond activation by 1,2-addition/reductive elimination pathways appropriate to catalytic hydrogen/deuterium exchange, and the possible intermediacy of highly coordinatively unsaturated (e.g., 14-electron) ruthenium complexes in catalysis. The calculations indicate a significant decrease in the Ru-CH3 homolytic bond dissociation enthalpy for the oxidation of TpRu(CO)(NCMe)(Me) to its RuIII cation through both reactant destabilization and product stabilization. This oxidation can thus lead to the olefin polymerization observed by Gunnoe and coworkers, since weak RuIII-C bonds would afford quick access to alkyl radical species. Calculations support the experimental proposal of a mechanism for catalytic hydrogen/deuterium exchange by a RuII-OH catalyst. Furthermore, calculational investigations reveal a probable pathway for the activation of C-H bonds that involves phosphine loss, 1,2-addition to the Ru-OH bond and then reversal of these steps with deuterium to incorporate it into the substrate. The presented results offer the indication for the net addition of aromatic C-H bonds across a RuII-OH bond in a process that although thermodynamically unfavorable is kinetically accessible. Calculations support experimental proposals as to the possibility of binding of weakly coordinating ligands such as dinitrogen, methylene chloride and fluorobenzene to the "14-electron" complex [(PCP)Ru(CO)]+ in preference to the formation of agostic Ru-H-C interactions. Reactions of [(PCP)Ru(CO)(1-ClCH2Cl)][BAr'4] with N2CHPh or phenylacetylene yielded conversions that are exothermic to both terminal carbenes and vinylidenes, respectively, and then bridging isomers of these by C-C bond formation resulting from insertion into the Ru-Cipso bond of the phenyl ring of PCP. The QM/MM and DFT calculations on full complexes ...
Date: December 2007
Creator: Barakat, Khaldoon A.

Computational Study of Small Molecule Activation via Low-Coordinate Late First-Row Transition Metal Complexes

Description: Methane and dinitrogen are abundant precursors to numerous valuable chemicals such as methanol and ammonia, respectively. However, given the robustness of these substrates, catalytically circumventing the high temperatures and pressures required for such transformations has been a challenging task for chemists. In this work, computational studies of various transition metal catalysts for methane C-H activation and N2 activation have been carried out. For methane C-H activation, catalysts of the form LnM=E are studied, where Ln is the supporting ligand (dihydrophosphinoethane or β-diketiminate), E the activating ligand (O, NCH3, NCF3) at which C-H activation takes place, and M the late transition metal (Fe,Co,Ni,Cu). A hydrogen atom abstraction (HAA) / radical rebound (RR) mechanism is assumed for methane functionalization (CH4 à CH3EH). Since the best energetics are found for (β-diket)Ni=O and (β-diket)Cu=O catalysts, with or without CF3 substituents around the supporting ligand periphery, complete methane-to-methanol cycles were studied for such systems, for which N2O was used as oxygen atom transfer (OAT) reagent. Both monometallic and bimetallic OAT pathways are addressed. Monometallic Fe-N2 complexes of various supporting ligands (LnFe-N2) are studied at the beginning of the N2 activation chapter, where the effect of ligand on N2 activation in end-on vs. side-on N2 isomers is discussed. For (β-diket)Fe-N2 complexes, the additional influence of diketiminate donor atom (N(H) vs. S) is briefly addressed. The remainder of the chapter expands upon the treatment of β-diketiminate complexes. First, the activation and relative stabilities of side-bound and end-bound N2 isomers in monometallic ((β-diket)M-N2) and bimetallic ((β-diket)M-N2-M(β-diket)) first row transition metal complexes are addressed. Second, the thermodynamics of H/H+/H- addition to (β-diket)Fe-bound N2, followed by subsequent H additions up to release of ammonia, is discussed, for which two mechanisms (distal and alternating) are considered. Finally, the chapter concludes with partial distal and alternating mechanisms for H addition to N2 ...
Date: May 2010
Creator: Pierpont, Aaron

Computer Simulations of Dilute Polymer Solutions: Chain Overlaps and Entanglements

Description: Chain conformations and the presence of chain overlaps and entanglements in dilute polymer solutions have been analyzed. The fundamental problem of existence of chain overlaps in dilute solutions is related to the drag reduction phenomenon (DR). Even though DR occurs in solutions with the concentration of only few parts per million (ppm), some theories suggest that entanglements may play an important role in DR mechanism. Brownian dynamics technique have been used to perform simulations of dilute polymer solutions at rest and under shear flow. A measure of interchain contacts and two different measures of entanglements have been devised to evaluate the structure of polymer chains in solution. Simulation results have shown that overlaps and entanglements do exist in static dilute solutions as well as in solutions under shear flow. The effect of solution concentration, shear rate and molecular mass have been examined. In agreement with the solvation theory of DR mechanism, simulation results have demonstrated the importance of polymer + polymer interactions in dilute solutions.
Date: August 1996
Creator: Drewniak, Marta