Chemistry Commons^™

Exploration Of The Chemical And Biological Processes Through Molecular Dynamics Simulation And Blocklocalized Wavefunction Method, Yuchun Lin

Dissertations

Computer simulation plays a crucial role in interpreting, unifying and guiding experimental observations. In this dissertation, molecular dynamics (MD) simulations and the block-localized wavefunction (BLW) method have been used to explore the chemical and biological processes.

Detailed MD simulations were performed to study the transportation of NH₄⁺, NH₃ and H₂O through the Escherichia coli ammonium transporter (AmtB) membrane protein. A periplasmic recruitment vestibule was identified and the entrance of an NH₄⁺ into this vestibule requires only 3.1 kcal/mol. In the end of this vestibule, the phenyl ring of Phe107 dynamically opens and …

Broadband Dielectric Spectroscopy Studies Of Nafion, David Walter Rhoades

Dissertations

In light of available literature regarding Nafion® materials, it is apparent that an information gap exists between the current state of understanding of Nafion relaxations and the dielectric behavior of these materials. Although the currently available dielectric relaxation data is accurate it is very limited in its scope—specifically in-depth broadband analyses are not available. As a result, very little information is available regarding the dependence of the relaxation processes on frequency and temperature. This presents an important opportunity for the exploration of the dielectric broadband relaxation behavior of Nafion® materials. The primary intent of this research is to quantify the …

Synthesis And Characterization Of Polymeric Materials Derived From Multifunctional Alkyl A-Hydroxymethylacrylates, Jean-Francois Morizur

Dissertations

The research presented in this dissertation covers the investigation of new materials derived from alkyl a-hydroxymethylacrylates (RHMA). The first project exposed in Chapter II involves the synthesis, characterization of RHMA-based reactive surfactants and their successful incorporation in acrylic latexes. The amphiphilic monomers testify of a good copolymerization behavior with other acrylic monomers such as methyl methacrylate and butyl acrylate although their extensive bulkiness. They led to the formation of well-defined polymeric particles via a seeded emulsion polymerization process and permitted decreasing significantly the water sensitivity of the resulting films as compared to film incorporating conventional emulsifier such as sodium dodecyl …

Photopolymerization And Characterization Of Crosslinked Thiol-Ene Networks And Poss/Thiol-Ene Nanocomposites, Tolecia Sharonda Shaunee Clark

Dissertations

Interests in the area of thiol-ene photopolymerization are rapidly expanding due to the numerous advantages over the polymers produced by traditional solvent based polymerizations. Although current research of photoinitiated thiol-ene polymerization is diverse, numerous opportunities are available for investigating structure/property and structure/reactivity relationships and novel material applications. This research in this dissertation includes a fundamental study of the effect of monomelic thiol functionality on thiol-ene polymerization kinetics and formation of the thiol-ene network structure, and an investigation of the development of novel silicate based thiol-ene nanocomposites. The first fundamental study investigates the effect of thiol functionality on the kinetics and …

The Design, Synthesis, And Controlled Polymerization Of Cationic And Zwitterionic Norbornene Derivatives, David Allen Rankin

Dissertations

Ring-opening metathesis polymerization (ROMP) has been exploited for the controlled polymerization of cationic and zwitterionic norbornene-based monomers and employed in the preparation of homo- and block-copolymer systems in homogeneous organic media without the use of post-polymerization modification or protecting group chemistries. Relying on previous knowledge of certain halogenated alcoholic organic solvents capable of solubilizing hydrophilic monomers, the first study, describes the synthesis and controlled polymerization of a series of new permanently cationic ammonium exo-7- oxanorbornene derivatives M31 via ROMP, with the first generation Grubbs catalyst 17, in a novel solvent mixture comprised of 1:1 vol/vol 2,2,2-trifluoroethanol (TFE)/methylene chloride (CH2CI2). This …

Raft Synthesis Of Water-Soluble, Stimuli-Responsive Ab Diblock Copolymers, Ran Wang

Dissertations

A series of water-soluble, stimuli-responsive AB diblock copolymers were synthesized via the reversible addition-fragmentation chain transfer (RAFT) polymerization technique employing 2-(2- carboxyethylsulfanylthiocarbonylsulfanyl)propionic acid (CTA26) as the RAFT mediating agent.

First, a series of diacid functional trithiocarbonate chain transfer agents (CTA's) were synthesized and examined for their effectiveness as mediating agents in controlling the polymerization of «-butyl acrylate (nBA). Overall, CTA26 demonstrated good control in the homopolymerization of nBA with respect to the molecular weight and the molecular weight distribution, as well as its ability to form block copolymers with high reinitiating efficiency, and thus was chosen as the CTA for …

Synthesis, Study Of Self-Assembly, And Trivalent Lanthanide Metal Ion Recognition Characteristics Of Amphiphilic Acylpyrazolones And Amphiphilic Acylisoxazolones, Venkat Reddy Guduru

Dissertations

This research project focused on the separation of trivalent lanthanide metal ions by HPLC using amphiphilic acylpyrazolones and amphiphilic acylisoxazolones. The central hypothesis of our research project is that the nanoscale self-assembly nature of amphiphilic ligands (chelating lingads) can influence their metal ion recognition and separation. To test the central hypothesis, we have synthesized a family of novel amphiphilic ligands and employed them as model systems for the separation of trivalent lanthanide metal ions. Several novel intermediates such as 4-acylated. N -acylated, O -acylated pyrazolones and isoxazolones, have been efficiently synthesized and fully characterized.*

The trivalent lanthanide metal ion recognition …

Synthesis And Characterization Of Stilbenoids And Their Aza-Analogs As Photoluminescent Materials For The Detection Of Nerve Agent Mimics, Chun Wang

Dissertations

A novel series of stilbenoids and their aza analogs were synthesized, characterized and used as photoluminescent components in the detection of nerve agents. Their structure-property relationship was elucidated through UV-visible and fluorescence spectroscopy. The research in this thesis is driven by the hypothesis that the two-block sensor system consisting of a receptor incorporated ruthenium complex and a fluorescent signal molecule of stilbenoids, is capable of detecting chemical warfare agents. The sensor anchored onto nanoparticles and subsequently the nanoparticles were arranged through mediated self-assembly. While photo-induced electron transfer is a well-known mechanism for sensor design, the described system showed that photo-induced …

The Effect Of Chloramphenicol On Bb88 Murine Erythroleukemia Cells, Peter K. W. Harris

Dissertations

DNA microarrays can be used to measure genome-wide transcript levels. These measurements may be useful in understanding cellular changes induced by a chemical agent. In this study, Affymetrix microarray technology has been used to study the effects of chloramphenicol, an antibiotic that inhibits bacterial and mitochondrial protein synthesis, on the transcription profile in mammalian cells. Transcript levels in BB88 murine erythroleukemia cells treated with 50 micromolar ( mu M) chloramphenicol, a concentration shown to inhibit BB88 proliferation, are measured. Using total RNA from treated cells, biotin-labeled cRNA was prepared and hybridized to Affymetrix U74Av2 microarrays. From these hybridizations, expression levels …

The Global Hepatic Transcriptional Response Of Male Fisher Rats To Dietary Aroclor 1254 Exposure, Trisha M. Basford

Dissertations

Dietary intake is a primary route for biomagnification of environmentally persistent polychlorinated biphenyls (PCBs) within humans and animals. Aroclor 1254, a mixture of PCBs, is associated with a variety of toxic responses including alterations in blood and lipid biochemistry and tumor promotion. Measurement of the transcriptional responses to low-level dietary exposure to A1254 has not been reported to date, and is important given the persistence of PCBs, and range of effects associated with exposure. The aims of this study were to characterize changes in rat hepatic global gene expression due to sub-acute and sub-chronic dietary exposure to A1254, and to …

Ligand-Based Drug Design : I. Conformational Studies Of Gbr 12909 Analogs As Cocaine Antagonists; Ii. 3d-Qsar Studies Of Salvinorin A Analogs As Kappa Opioid Agonists, Deepangi Pandit

Dissertations

Ligand-based drug design (LBDD) techniques are applied when the structure of the receptor is unknown but when a series of compounds or ligands have been identified that show the biological activity of the interest. Generally, availability of a series of compounds with high activity, with no activity, and also with a range of intermediate activities for the desired biological target is required. It is common that structures of membrane-bound proteins (for example, monoamine transporter proteins and opioid receptor proteins) are unknown as these proteins are notoriously difficult to crystallize.

In Part I of this study, analogs of the flexible dopamine …

Bioengineering Of Protein Nanotubes And Protein Nanomaterial Composites, Thilak Kumara Mudalige

Dissertations

Flagella of Mesophilic bacteria such as E. coli are extremely ordered structures consisting of self-assemblies of flagellin 11-mers resulting in protein nanotubes of 2--3 nm inner diameter, 23 nm outer diameter, several microns in length and 5.4 nm separation between 11-mer segments. They are as a result attractive scaffolds and templates for the generation of uniform nanotubes and ordered array of nanoparticles. In this study fusion protein of bacterial flagellin (Fli C) and core thioredoxin (Trx), pFliTrx was used as peptide display on bacterial flagella. This was accomplished in the current research by introducing various peptide loops such as cysteine, …

Global And Quantitative Gene Expression Analysis Of The Effects Of Drinking Water Exposure To Lead Acetate In Fisher 344 Male Rats Liver, Worlanyo Eric Gato

Dissertations

The primary objective of this research is to analyze global gene expression patterns occurring in Fisher 344 rat livers exposed to varying levels of lead and times. The hypotheses were that: (1) effects associated with Pb exposure are both dose and time dependent and (2) several genes will be over-expressed or repressed including transcripts associated with calcium signaling. Initially, the effects of Pb exposures upon morphometnc indices, liver and kidney tissue histology, Pb distribution, Pb interaction with other trace metals including Zn, Cu, Co, Fe, Ni and Ca were assessed. Results showed a significant accumulation of lead in blood, liver, …

Regulation Of A Dna-Compacting Plastid Nucleoid Protein, Steven William Adamson

Dissertations

DCP68, a DNA-compacting nucleoid protein, was further characterized in order to understand how plastid nucleoid proteins affect the structure and function of chloroplast DNA. Previously, DCP68 was identified as ferredoxin: sulfite reductase, an enzyme that participates in reductive sulfur assimilation and inhibits chloroplast DNA replication and transcription in vitro [1, 2]. In this study, the portion of SiR that was found to be present in soluble and plastid nucleoid-enriched fractions indicated that most SiR was stromal in Arabidopsis and soybean plants. Although SiR was detected in Arabidopsis chloroplast nucleoid-enriched fractions, the study of nucleoid dynamics proved to be difficult due …

Synthesis And Fundamental Characterization Of Nanoparticles And Their Clusters, Ke Du

Dissertations

Nanoparticles of gold derivatized with monolayers of thiocarboxylic acid ligands, core/shell nanoparticle composites of gold and silica, gold-glutathioneclusters, and titania nanoparticles were synthesized and their surface properties (extent of ligand coverage, net negative charge, and zeta potential) characterized by capillary electrophoresis as a function of pH, ionic strength, and dielectric constant for the first time. The hydrodynamic radii of thenanoparticles were determined by dynamic laser light scattering and used to calculate the net surface charge, extent of ligand coverage, and zeta potentials ofthe nanoparticles from electrophoresic mobilities. The ligand derivatized nanoparticles had similar hydrodynamic radius of about 20 nm which …

Gas Chromatography On Self Assembled Single Walled Carbon Nanotubes, Mahesh Kumar Karwa

Dissertations

Carbon nanotubes (CNTs) are nano-sized carbon-based sorbents, which have high surface area, large aspect ratio, can be self-assembled and are known to be stable at high temperatures. It is therefore conceivable that separation techniques, such as, gas chromatography (GC) can benefit from their unique properties and nano-scale interactions. Self-assembly, in-contrast to packing these materials in a tube, prevents them from agglomeration and thus facilitates in retaining their nano-characteristics. In this research, novel substrates, such as, steel tubings, on a scaled-up level have been explored for the self-assembly process of CNTs, for applications such as gas chromatography, where the CNTs served …

Investigations Of Poly[(Styrene-Co-P-Methylstyrene)-Risobutylene- R-(Styrene-Co-P-Methylstyrene)] And Poly[(Acrylic Acid)-5-Styrene-Jb-Is0butylene-5-Styrene-Jb-(Acrylic Acid)], James Grabill Kopchick

Dissertations

The pMe study was conducted to understand the morphological and physical property changes that occur as the ratio of pMe to styrene is increased, effectively increasing the aliphatic units. By the introduction of pMe, the interface region becomes more blended/compatible as the pMe migrates to the interface. These pMe groups are theorized in effect to create multiple ‘anchors’ to distribute the loads experienced at the interface more effectively creating a synergistic effect on the final properties of the copolymers. The primary goals of the pentablock study were the characterization of unique membranes as related to …

Synthetic Studies Of 1,10-Phenanthroline Derivatives As Novel Catalysis Ligands And Their Application In Transition Metals Catalyzed Reactions, Son Duc Tran

Dissertations

The preparation of 1,10-phenanthroline derivatives entailed ring opening reactions of 1,10-phenanthroline epoxide as a key transformation, affording novelbidentate nitrogen ligands with new stereogenic centers in the 5- and 6-position. This research was concerned with (i) the epoxidation of 1,10-phen, (ii) epoxide ring opening reactions, (iii) the formation of trans -5,6-disubstituted-1,10-phenanthroline metal complexes, and (iv) application of 1,10-phenanthroline derivatives in metal-catalyze reactions such as palladium-catalyzed allylic substitution and aminohalogenation reactions; Zinc-catalyzed direct aldolreaction, and acetophenone reduction; Nickel-catalyzed Michael addition reaction.

Ligand-Based Design Of Dopamine Reuptake Inhibitors : Fuzzy Relational Clustering And 2-D And 3-D Qsar Modleing, Milind Misra

Dissertations

As the three-dimensional structure of the dopamine transporter (DAT) remains undiscovered, any attempt to model the binding of drug-like ligands to this protein must necessarily include strategies that use ligand information. For flexible ligands that bind to the DAT, the identification of the binding conformation becomes an important but challenging task. In the first part of this work, the selection of a few representative structures as putative binding conformations from a large collection of conformations of a flexible GBR 12909 analogue was demonstrated by cluster analysis. Novel structurebased features that can be easily generalized to other molecules were developed and …

Study Of Organic Reactions In Pyridinium-Based Ionic Liquids, Ying Xiao

Dissertations

Recently, ionic liquids have attracted a lot of attention as novel materials for organic transformations. This is due to their unique properties, which make them suitable substitutes for organic solvents. Most of the available literature is focused on the application of imidazolium-based ionic liquids for organic reactions, while very limited information is available on the application of pyridinium-based ionic liquids.

In this study, two different ionic liquids, 1 -ethyl-pyridinium tetrafluoroborate ([EtPy]⁺[BF₄]^-) and 1 -ethyl-pyridinium trifluoroacetate ([EtPy]⁺[CF₃COO]^-) have been investigated. Compared to previous reports, the synthetic technique for preparation …

A Study Of How Precursor Key Concepts For Organic Chemistry Success Are Understood By General Chemistry Students, Patrick Gerard Meyer

Dissertations

This study examines college student understanding of key concepts that will support future organic chemistry success as determined by university instructors. During four one-hour individual interviews the sixteen subjects attempted to solve general chemistry problems. A think-aloud protocol was used along with a whiteboard where the students could draw and illustrate their ideas. The protocols for the interviews were adapted from the Covalent Structure and Bonding two-tiered multiple choice diagnostic instrument (Peterson, Treagust, & Garnett, 1989) and augmented by the Geometry and Polarity of Moleculessingle-tiered multiple choice instrument (Furió & Calatayud, 1996). The interviews were videotaped, transcribed, and coded …

Functionalization, Growth And Applications Of Single Wall Carbon Nanotubes, Yubing Wang

Dissertations

Because of their remarkable structural, mechanical and electrical properties, carbon nanotubes, and especially single wall carbon nanotubes (SWNTs), represent one of the most widely investigated materials today in the emerging field of nanotechnology. The development of oriented growth of SWNTs critical for applications, novel approaches for the creation of functional SWNTs, and applications of both as-prepared and chemically functionalized SWNTs for electrochemically-induced hydrogen storage, in-situ formation of new polymer and ceramic nanocomposites with SWNTs, and the fabrication and study for the first time, to the best of our knowledge, of a SWNT-based biofuel cell and self-powered biosensor, are the thrusts …

Acylpyrazolones: Synthesis, Self-Assembly And Lanthanide Metal Ion Separation, Jun Yang

Dissertations

The central hypothesis that nanoscale self-assemblies can provide excellent metal ion recognition has been substantiated by employing acylpyrazolones and trivalent lanthanide metal ions as model systems. Several novel acylpyrazolones and their amphiphilic analogs have been designed, synthesized, and characterized. Their lanthanide metal ion recognition efficacies have been demonstrated through baseline separations of a mixture of light, middle, and heavy lanthanide metal ions by employing them in the aqueous mobile phase of high performance liquid chromatography (HPLC) with octadecylsilanized silica (ODS) as the stationary phase. The complex separation mechanism is influenced by the structures of acylpyrazolone and amphiphilic moieties, and spontaneous …

Synthesis And Spectroscopic Characterization Of Manganese Doped Zinc Sulfide Quantum Dot Nanocrystals, Pedro A. Gonzalez Beerman

Dissertations

Zinc sulphide quantum dots were synthesized in aqueous media using sodium polyphosphate as the stabilizer. The nanoparticles were 2.5 ± 0.5 nm and 5.0 ± 0.5 nm diameter depending on the synthetic procedure employed and the amount of Mn doped varied from 0.003 to 0.32% (w/w). The nanoparticles were characterized by UV-Vis absorption, luminescence, EPR, near edge x-ray absorption fine structure (NEXAFS), and x-ray photoelectron spectroscopy (XPS), and x-ray diffraction (XRD), and transmission electron microscopy (TEM). These quantum dots show a strong emission at 590 nm due to the ⁴T₁ -⁶A₁ transition characteristic of Mn …

Modeling Of Flexible Drug-Like Molecules : Qsar Of Gbr 12909 Analog Dat/Sert Selectivity, Kathleen Mary Gilbert

Dissertations

The dopamine reuptake inhibitor GBR 12909 and related dialkyl piperazine and piperidine analogs have been studied as agonist substitution therapies acting on the dopamine transporter (DAT) to treat cocaine addiction. Undesirable binding to the serotonin transporter (SERT) can vary greatly depending on the specific substituents on the molecule. This study uses Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Indices (CoMSIA) techniques to determine a stable and predictive model for DAT/SERT selectivity for a set of flexible GBR 12909 analogs.

Families of analogs were constructed from six pairs of naphthyl-substituted piperazine and piperidine templates identified by hierarchical clustering as …

Analysis Of Benzo(A)Pyrene-Induced Gene Expression Changes In Fisher 344 Rat Liver By Affymetrix Microarray And Quantitative Real-Time Pcr, Alhaji Umar N’Jai

Dissertations

No abstract provided.

Thermochemistry And Kinetics In Pyrolysis And Oxidation Reaction Of Oxygenate Chlorocarbons, Neopentane, And Ortho-Xylene, Hongyan Sun

Dissertations

Thermochemical properties of chlorinated alcohols, chlorinated hydroperoxides and corresponding alkoxy, hydroxy alkyl radicals, peroxy and hydroperoxy alkyl radicals are determined by ab initlo and density functional calculations for modeling and optimization of complex chemical processes for combustion or incineration of chlorinated hydrocarbons. The entropy and heat capacities from vibrational, translational, and external rotational contributions are calculated by statistical mechanics, and the hindered rotational contributions to S^°₂₉₈ and C_p(T)'s are calculated by using direct integration over energy levels of the internal rotational potentials. The values of ΔH_f^°₂₉₈ are determined using isodesmic reactions …

Pharmacophore Derivation Using Discotech And Comparison Of Semi-Emperical, Ab Initio And Density Functional Comfa Studies For Sigma 1 And Sigma 2 Receptor-Ligands, Dawoon Jung

Dissertations

This study describes the development of pharmacophore and CoMFA models for sigma receptor ligands. CoMFA studies were performed for 48 bioactive sigma 1 receptorligands using [H³ ](+) pentazocine as the radioligand, for 30 PCP derivatives for sigma 1 receptor-ligands using [³H](+)SK-F 10047 as the radioligand and for 24 bioactive sigma 2 receptor-ligands using the radioligand [H³](+)DTG in the presence of pentazocine. Distance Comparisons (DISCOtech) was used as the starting point for CoMFA studies. The conformers, derived by DISCOtech were optimized using AMi, or HF/3-21G* in Gaussian 98. The optimized geometries were aligned with the pharmacophore, …

A Microfabricated Microconcentrator For Sensors And Chromatography, Minhee Kim

Dissertations

The detection and quantitative measurement of trace components is a challenging task. The key component in such an instrument is the concentration step where the analytes are accumulated before the analysis. In this research, simple and inexpensive processes for the microfabrication of microconcentrator that can be used with sensors and as an injector in GC were developed. Analytes are selectively concentrated in the microconcentrator. Rapid electrical heating of the microconcentrator releases the adsorbed species as a 66 concentration pulse", which serves as an injection for the detection system. The relatively small size of the microconcentrator allows it to be heated …

Catalytic Reduction Of Nitric Oxide By Solid Carbonaceous Material Under Lean Condition, Shan Xiao

Dissertations

The reactions of O₂, NO_x and soot from Diesel exhaust over Cu containing catalysts can significantly reduce soot and NO_x emissions while producing N₂ and CO₂. The author has evaluated the performance of Cu ion exchanged ZSM-5 and Cu adsorbed on Granulated Activated Carbon (Cu-GAC) using GAC as a surrogate for soot in a packed bed reactor. CO, formed primarily by the oxidation of GAC with O₂, appears to be a stable intermediate in the reduction of NO. With experimental parameters chosen to simulate Diesel exhaust conditions, Cu-GAC is much more …