Physical Sciences and Mathematics Commons^™

Ranking Methods For Global Optimization Of Molecular Structures, John Norman Mcmeen Jr

Electronic Theses and Dissertations

This work presents heuristics for searching large sets of molecular structures for low-energy, stable systems. The goal is to find the globally optimal structures in less time or by consuming less computational resources. The strategies intermittently evaluate and rank structures during molecular dynamics optimizations, culling possible weaker solutions from evaluations earlier, leaving better solutions to receive more simulation time. Although some imprecision was introduced from not allowing all structures to fully optimize before ranking, the strategies identify metrics that can be used to make these searches more efficient when computational resources are limited.

Oxidative Damage To Dna 2´-Deoxyribose By Carbonate Radicals: Reaction Mechanisms And Products, Terence J. Moore

Electronic Theses and Dissertations

The carbonate radical anion (CO₃^•-, CR) is an important reactive oxygen species produced in vivo by one-electron oxidation of CO₂ or bicarbonate, constituents of the major physiological buffer. It was demonstrated for the first time by using an HPLC-based analysis of low-molecular products of DNA damage that CRs react with DNA 2΄-deoxyribose by the hydrogen abstraction mechanism. CRs exhibit a ~ 800-fold preference for one-electron oxidation of guanine over hydrogen abstraction from DNA sugar, in sharp contrast with •OH. CRs also have, as compared to •OH, an increased preference for the H1΄ abstraction, which is the …

Aminooxy Reagents In Nanomedicine And Bioanalysis., Stephanie Mattingly

Electronic Theses and Dissertations

The development of nanomaterials as medical diagnostic and therapeutic agents is a rapidly expanding field. A brief search of the literature revealed that roughly half of all articles related to nanoparticle-based drug delivery were published after the onset of this thesis research, over the past 4 years. A few nano-based formulations have entered into clinical use, including liposomal drug formulations, protein-linked drugs, and nanoparticle-based MRI contrast agents. The chemistry that enables conjugation of a functional cargo, whether a drug, a targeting element, or a radionucleotide, to a nanocarrier is thus a critical component for development. Oximation is one of the …

Triggered Release Of Small Molecules From Solid Supports Using Heat Or An Applied Magnetic Field., Ralph Jacob Knipp

Electronic Theses and Dissertations

The reaction of an aminooxy moiety (RONH2) with an aldehyde or ketone carbonyl, an oximation reaction, results in the formation of robust oxime ether linkages. Oximation is a form of click chemistry and is chemoselective, occurs in a variety of solvents including water, and produces high yields with little to no purification. We were inspired to exploit the advantages of oximation reactions by attaching aminooxy-functionalized molecules to solid supports, thus allowing us to employ aminooxy chemistry in ways that cannot be achieved using solution phase. Chapter 1 provides a review of aminooxy chemistry, its advantages over similar reactions and its …

Biomarker Discovery Of Liver Diseases Using Mass Spectrometry-Based Metabolomics., Xue Shi

Electronic Theses and Dissertations

Metabolomics has emerged as one of the latest of the "-omics" disciplines that can detect metabolite biomarkers in biological samples. The diverse characteristics of metabolites make the analytical platform challenging in metabolomics. Two bioanalytical platforms were developed in this study to investigate metabolite abundance changes under different biological conditions. We first developed a bioanalytical platform that coupled linear trap quadruple - Fourier transform ion cyclotron mass spectrometer (LTQ-FTICR MS) with direct infusion chip-based nano-electrospray ionization (DI-nESI) and applied it to study polychlorinated biphenyls (PCB) effects on non-alcoholic fatty liver disease (NAFLD). We also employed this platform in conjunction with in …

Synthesis And Characterization Of [Vo(O2)H2edta] And Investigation Of The Reaction Between [Vohedta]-1 And Hydrogen Peroxide As A Model Catalyst For Haloperoxidases, Tinga C. O. Fon Mr.

Electronic Theses and Dissertations

Vanadium haloperoxidases (VHPOs) are enzymes that catalyse the oxidation of halide ions to hypohalous acids by hydrogen peroxide. There are many unanswered questions on the mechanism by which the oxidation reaction occurs. In this work, is reported the synthesis of [VO(O₂)H₂EDTA], studies of the effect of acid concentration on the decomposition of [VO(O₂)HEDTA]^-2, and mechanistic studies of the rate law. The decomposition reaction was found to be first order with respect to acid concentration and also [VO(O₂)HEDTA]^-2 concentration. The reaction of [VOHEDTA]^-1 and hydrogen peroxide progressed via a …

Electron Paramagnetic Resonance Imaging And Probes, Hanan B. Elajaili

Electronic Theses and Dissertations

EPR imaging at low frequency is an important method to measure in vivo physiology. Because native paramagnetic species exist at low concentrations in living systems, exogenous paramagnetic species are needed for in vivo EPR. Selection of the appropriate EPR probe allows the experimenter to obtain information about the environment of the imaged probe and its spatial distribution. Relaxation times for several nitroxide radicals were studied with the aim of understanding the relaxation mechanisms, which provides criteria for design of suitable in vivo imaging probes.

Amino-substituted trityl radicals have the potential to monitor pH in vivo, and the suitability for this …

Dynamics Of Polyelectrolyte Adsorption On Surfaces: Applications In The Detection Of Iron In Water, Madhira N. Gammana

Electronic Theses and Dissertations

Layer by layer (LbL) self assembly is a simple multilayer thin (nanometer scale) film fabricating technique. The mechanism of film growth remains a topic of much controversy. For example, several models have been proposed to explain the origin of linear and exponential film growth that are attributed to differences in the dynamic processes that occur at the molecular level during film formation. The problem is that there are no methods that directly measure the dynamics of polymer formation during LbL film formation. In this thesis, I describe the essential elements of an ATR-IR spectroscopic method that was developed to enable …

Mechanistic Insights And Functionalization Of Alkynes In Homogeneous Gold Catalysis., Manish Kumar

Electronic Theses and Dissertations

The focus of my dissertation work was to study the basic mechanistic insights of gold-catalyzed reactions. Although the various mechanistic pathways of gold catalysis are better understood nowadays, numerous questions still remain unanswered concerning the nature of deactivation of the catalyst's active species, high resistance towards protodeauration, and how we can solve these problems to improve the efficiency of gold catalysis. To address these challenges in gold catalysis we conducted first a detailed experimental study to understand the mechanism of deactivation of gold active species. Based on the combination of experimental data, we proposed that gold disproportionation is preferred as …

Electrochemical And Microfabrication Strategies For Remotely Operated Heavy Metal Sensor Networks For Water Analysis : The Dual Challenges Of Calibration-Less Measurement And Sample Pretreatment., Mohamed M. Marei

Electronic Theses and Dissertations

Current heavy metal monitoring in water utilizes sophisticated instrumental methods at centralized laboratories. For many applications, a preferable approach is the deployment of remote sensor networks. To this end, electrochemical methods in conjunction with microfabricated sensors potentially offer the required sensitivity and practical advantages including inexpensive sensors, reduced need for manual operation, reduced energy requirements, and also takes advantage of existing technologies such as communications networks for real-time data acquisition. The remote sensor platform developed herein consists of a photo-lithographically patterned gold electrode on SiO2 substrate within a custom stopped-flow thin-layer cell (TLC). Metal concentrations were evaluated by anodic stripping …

Molecular Encapsulation In Kinetically Trapped, Hydrogen-Bonded Pyrogallolarene Hexamers, Jennifer Christine Chapin Lake

Electronic Theses and Dissertations

Pyrogallolarene and resorcinarene hexamers are hydrogen-bonded capsules that self-assemble in the solid state and can be studied in gaseous and solution phases. Guest loading within pyrogallolarene hexamers in solution has primarily been comprised of solvent molecules with some tertiary amines. A novel solvent-free method for loading guests into the interior of the hexamer has been shown to be effective for encapsulation of a variety of molecules. Aromatic and aliphatic compounds have particularly high guest loading within the hexamers and often result in kinetically stable guest-filled capsules in solution.

Kinetic studies of the encapsulation complexes of anthracene, biphenyl, fluoranthene, fluorene, naphthalene, …

Nitroxide Radicals For Low Frequency Electron Paramagnetic Resonance Imaging (Epri), Joshua R. Biller

Electronic Theses and Dissertations

Optimization of nitroxides as probes for EPR imaging requires detailed understanding of spectral properties such as spin lattice relaxation times, spin packet linewidths, and nuclear hyperfine splitting. Initial measurements of relaxation times for six low molecular weight nitroxides at X-band stimulated further measurement at frequencies between 250 MHz and 34 GHz. The impact of tumbling was studied with perdeuterated 2,2,6,6-tetramethyl-4-piperidinyl-1-oxyl (PDT) in five solvents with viscosities resulting in tumbling correlation times, τ_R, between 4 and 50 ps. A set of three ¹⁴N/¹⁵N pairs of nitroxides in water was selected such that τ_R varied between …

Kinetics Of Formation And Oxidation Of 8-Oxo-7,8-Dihydroguanine (8oxog), Derrick Ampadu Boateng

Electronic Theses and Dissertations

8-oxo-7,8-dihydroguanine (8oxoG) is one of the most important base lesions formed during oxidative damage of DNA. The aim of the present research was to investigate the effects of DNA concentration, G content, and the nature of oxidizing species on the kinetics of 8oxoG in model DNA solutions by using HPLC. The experimentally obtained yields of 8oxoG were typically in the range of 2-2.5% of total concentration of guanine. The ratios of the rate constant of hole diffusion in DNA to the rate constant of conversion of the hole into 8oxoG (k_d/k_r) were calculated from the experimental …

Functionalization Of Silica Surface Using Chan-Lam Coupling, George Appiah Kubi

Electronic Theses and Dissertations

The reaction of base-free Chan-Lam coupling was successfully used for functionalization of surface of mesoporous silica gel. Various aromatic, aliphatic, and heterocyclic compounds were immobilized by a copper-catalyzed reaction of corresponding boronic acids with surface amino groups at mild conditions. Obtained functionalized materials were mesoporous although their surface area decreased after immobilization. The reactivity of some surface functional groups was tested in their characteristic reactions.

Synthesis Of A 4-(Trifluoromethyl)-2-Diazonium Perfluoroalkyl Benzenesuflonylimide (Pfsi) Zwitterionic Monomer For Proton Exchange Membrane Fuel Cell, Chimaroke Nworie

Electronic Theses and Dissertations

In order to achieve a more stable and highly proton conducting membrane that is also cost effective, the perfluoroalkyl benzenesulfonylimides (PFSI) polymers are proposed as electrolyte for Proton Exchange Membrane Fuel Cells. 4-(trifluoromethyl)-2-diazonium perfluoro-3, 6-dioxa-4-methyl-7-octene benzenesulfonyl imide (I) is synthesized from Nafion monomer via a 5-step schematic reaction at optimal reaction conditions. This diazonium PFSI zwitterionic monomer can be further subjected to polymerization. The loss of the diazonium N₂⁺ functional group in the monomer is believed to form the covalent bond between the PFSI polymer electrolyte and carbon electrodes support. All the intermediates and final products …

Ligand Centered Reactivity Of Metal Stabilized Thiyl Radicals In Solution, Solid And Gaseous Phase., Rajat Rajat

Electronic Theses and Dissertations

This thesis presents ligand centered reactivity studies of metal stabilized thiyl radicals in solution, solid, and gaseous phases for catalysis and sensing based applications. Chemical oxidation of tris(2-diphenylphosphinebenzenethiolato )ruthenate(II) [Ru -1]- with ferrocenium hexafluorophosphate in the presence of ethylene yields [Ru-1·C,H.]PF6, from addition of the alkene across cis sulfur sites. In the presence of base [Ru-1·C,H.]+ is selectively deprotonated at the pseudoequatorial proton on the carbon a to the sulfur trans to phosphorus, yielding the vinyl metallosulfonium derivative [Ru-1·C,H3]. "H and 31p NMR spectra of [Ru-1'C,H3 ] are temperature dependent, associated with inversion of the sulfur lone pair at the …

Synthesis Of N-Heterocycles Through Cyclization-Triggered Tandem Additions To Alkynes And The Study Of Promoters In Ionic Reactions., Junbin Han

Electronic Theses and Dissertations

Our research mainly focused on three parts related to the rapid construction of N-heterocycles and the search for ionic reaction promoters. First, N-heterocycles of different ring sizes and with different substitution patterns constitute extremely important structure classes (e.g., alkaloids) in the search for bioactivity. A contemporary challenge in organic synthesis is the mapping of new chemical spaces through tandem or cascade reactions in an atom economical fashion. Our strategy to access these biologically important heterocycles is through a cyclization-triggered tandem addition to alkynes catalyzed by readily available alkynophilic coinage metals like copper. In this manner, a variety of functional groups …

Expanding The Frontier Of Gold-Catalyzed Cyclizations And Rational Ligand Design., Deepika Malhotra

Electronic Theses and Dissertations

The focus of my dissertation work is to study the gold-catalyzed intramolecular and intermolecular cyclizations involving oxonium intermediates towards the application of synthetically interesting frameworks under ambient conditions and developing a rational approach for the effective catalyst design in gold catalysis. We explored the goldcatalyzed oxygen-transfer reactions of 2-alkynyl-1,5-diketones or 2-alkynyl-5-ketoesters to furnish five-membered rings bearing a quaternary carbon tethered to a carbonyl group. The detailed mechanistic investigation on the newly proposed intramolecular [4+2] cycloaddition mechanism was performed by means of isotopic experiments and quantum chemical calculations. The reactivity of alkynylenolate was investigated in the reactions of allenic ketones and …

Photoassisted Access To New Polyheterocycles, Teresa M. Cowger

Electronic Theses and Dissertations

Photoassisted diversity-oriented synthesis holds great promise in its ability to provide rapid access to complex and diverse molecular scaffolds. As it stands, while photochemical techniques have this potential, their implementation in the field of synthetic organic chemistry is very limited. The main goal of this project was to utilize photochemically assisted techniques in the synthesis of a variety of novel polyheterocycles.

Initially, we explored the how the strain installed in these polycycles could be harnessed to trigger cationic rearrangements in the framework of the system. This was achieved via the high yield and rapid assembly of a highly strained system …

Synthesis Of Fluorescent Molecules And Their Applications As Viscosity Sensors, Metal Ion Indicators, And Near-Infrared Probes, Mengyuan Wang

Electronic Theses and Dissertations

The primary focus of this dissertation is the development of novel fluorescent near-infrared molecules for various applications. In Chapter 1, a compound dU-BZ synthesized via Sonogashira coupling reaction methodology is described. A deoxyuridine building block was introduced to enhance hydrophilic properties and reduce toxicity, while an alkynylated benzothiazolium dye was incorporated for near-IR emission and reduce photodamage and phototoxicity that is characteristic of common fluorphores that are excited by UV or visible light. A 30-fold enhancement of fluorescence intensity of dU-BZ was achieved in a viscous environment. Values of fluorescence quantum yields in 99% glycerol/1% methanol (v/v) of varying temperature …

Degradation Of Hydrazine And Monomethylhydrazine For Fuel Waste Streams Using Alpha-Ketoglutaric Acid, Carolina Franco

Electronic Theses and Dissertations

Alpha-ketoglutaric acid (AKGA) is an organic acid important for the metabolism of essential amino acids as well as for the transfer of cellular energy. It is a precursor of glutamic acid which is produced by the human body during the Krebs Cycle. AKGA has a specific industrial interest as it can be taken as a dietary supplement and is also widely used as a building block in chemical synthesis. Collectively termed as hydrazine (HZs), hydrazine (HZ) and monomethylhydrazine (MMH) are hypergolic fuels that do not need an ignition source to burn. Because of the particular HZs' characteristics the National Aeronautics …

Novel Developments On The Extraction And Analysis Of Polycyclic Aromatic Hydrocarbons In Environmental Samples, Walter Wilson

Electronic Theses and Dissertations

This dissertation focuses on the development of analytical methodology for the analysis of polycyclic aromatic hydrocarbons (PAHs) in water samples. Chemical analysis of PAHs is of great environmental and toxicological importance. Many of them are highly suspect as etiological agents in human cancer. Among the hundreds of PAHs present in the environment, the U.S. Environmental Protection Agency (EPA) lists sixteen as "Consent Decree" priority pollutants. Their routine monitoring in environmental samples is recommended to prevent human contamination risks. A primary route of human exposure to PAHs is the ingestion of contaminated water. The rather low PAH concentrations in water samples …

Photo-Induced Protonation Of Polyaniline Composites And Mechanistic Study Of The Degradation Of Polychlorinated Biphenyls With Zero-Valent Magnesium, Candace Kirkland

Electronic Theses and Dissertations

As technology advances, a need for non-metal, conductive materials has arisen for several types of applications. Lithographic techniques are helpful to develop some of these applications. Such techniques require materials that are insulating and become conductive after irradiated. Composites of polyaniline in its emeraldine base form (PANI-EB) doped with photo-acid generators (PAG) become conductive upon photo-irradiation. This increase in conductivity is due to the protonation of PANI-EB. Such materials may be utilized to fabricate conducting patterns by photo-irradiation; however, the conductivity obtained by direct irradiation of PANI-EB/PAG composites is normally quite low (<10-3 S/cm) due to aggregation of highly loaded PAG. In this work, poly(ethylene glycol) (PEG), a proton transfer polymer, was added to PANI-EB/PAG. Results showed the addition of low molecular weight (MW) (550) PEG significantly enhanced the photo-induced conductivity to a level comparable to that of PANI-salt synthesized by oxidizing aniline in the presence of an acid. High MW (8000) PEG is less effective than PEG 550, and composites of PANI-EB and N-PEG-PANI showed conductivity as high as 102 S/cm after treatment with HCl vapor. The photo-induced conductivity of the N-PEG-PANI/PANI-EB/PAG composite reached 10-2-10-1 S/cm. Polychlorinated biphenyls (PCBs) are a class of chemicals with 209 different congeners, some of which are known carcinogens, and are persistent organic pollutants in the environment. After its synthesis, it was seen as a phenomenal additive in a multitude of different applications leading to the wide spread use of PCBs and a need for a safe, effective, and inexpensive remediation technique. While it is known that magnesium can degrade PCBs, the mechanism of this reaction was not well-understood. In order for magnesium to be broadly used as a remediation tool, it is necessary to fully understand how the reaction is taking place and if the PCBs are able to be fully dechlorinated into biphenyl. This research focuses on the hydrodechlorination of PCBs with zero-valent magnesium in acidified ethanol. The degradation pathways of 2, 2', 3, 5, 5', 6- hexachlorobiphenyl were investigated to determine the identity of the daughter PCBs produced, how and if they continue to be dechlorinated into biphenyl. The proton source for this hydrodehalogenation reaction was also studied using both deuterated solvent and acid to give more detail to the mechanism of this reaction.

Structural And Functional Studies Of Glycine Riboswitches And Development Of Fab Chaperone Assisted Rna Crystallography, Eileen Sherman

Electronic Theses and Dissertations

The glycine riboswitch is a structured RNA found upstream of genes in mRNA transcripts in many bacteria, functioning as a biofeedback gene regulator. Upon binding glycine, a complete RNA transcript including gene sequences is transcribed, effectively turning on gene expression. In an effort to understand the intricacies of its functioning, many mutants of the riboswitch were made and characterized during Ph. D. work, resulting in discovery of a P0 duplex/kink-turn motif involving a few nucleotides upstream of the established glycine riboswitch sequence which changed its ligand binding characteristics (Chapter 1). Previously, the two aptamers of the riboswitch were thought to …

Synthesis And Study Of Chemo-Hydrothermally Derived Water-Soluble Chitosan And Chiosan-Metal Oxide Composites, Srijita Basumallick

Electronic Theses and Dissertations

Chitosan (CS) is a man-made sugar based biopolymer derived from chitin, the second most abundant natural polymer after cellulose. Chitin is sourced from crustacean species such as shrimps and crabs. The chemical structure of chitin contains N-Acetyl D-glucosamine monomer units which forms CS upon deacetylation. In CS, ?-(1-4) linked D-glucosamine units are randomly distributed. Approximately 75% - 80% sugar units contains primary amine groups in commercially available low molecular weight CS. Biodegradability, low toxicity, mucoadhesive and transfecting properties of CS polymer are attractive for applications as oral and nasal drug delivery systems. Chitosan polymer is water insoluble at neutral pH. …

Application Of Two-Photon Absorbing Fluorene-Containing Compounds In Bioimaging And Photodyanimc Therapy, Xiling Yue

Electronic Theses and Dissertations

Two-photon absorbing (2PA) materials has been widely studied for their highly localized excitation and nonlinear excitation efficiency. Application of 2PA materials includes fluorescence imaging, microfabrication, 3D data storage, photodynamic therapy, etc. Many materials have good 2PA photophysical properties, among which, the fluorenyl structure and its derivatives have attracted attention with their high 2PA cross-section and high fluorescence quantum yield. Herein, several compounds with 2PA properties are discussed. All of these compounds contain one or two fluorenyl core units as part of the conjugated system. The aim of this dissertation is to discuss the application of these compounds according to their …

Action Potentials As Indicators Of Metabolic Perturbations For Temporal Proteomic Analysis, Aditya Reddy Kolli

Electronic Theses and Dissertations

The single largest cause of compound attrition during drug development is due to inadequate tools capable of predicting and identifying protein interactions. Several tools have been developed to explore how a compound interferes with specific pathways. However, these tools lack the potential to chronically monitor the time dependent temporal changes in complex biochemical networks, thus limiting our ability to identify possible secondary signaling pathways that could lead to potential toxicity. To overcome this, we have developed an in silico neuronal-metabolic model by coupling the membrane electrical activity to intracellular biochemical pathways that would enable us to perform non-invasive temporal proteomics. …

Noncovalent Interactions Involving Microsolvated Networks Of Trimethylamine N-Oxide, Kristina Andrea Cuellar

Electronic Theses and Dissertations

This thesis research focuses on the effects of the formation of hydrogen-bonded networks with the important osmolyte trimethylamine N-oxide (TMAO). Vibrational spectroscopy, in this case Raman spectroscopy, is used to interpret the effects of noncovalent interactions by solvation with select hydrogen bond donors such as water, methanol, ethanol and ethylene glycol in the form of slight changes in vibrational frequencies. Spectral shifts in the experimental Raman spectra of interacting molecules are compared to the results of electronic structure calculations on explicit hydrogen bonded molecular clusters. The similarities in the Raman spectra of microsolvated TMAO using a variety of hydrogen bond …

Probing Structure For Photophysical Properties Through Synthesis Of Novel Nucleosides, Brittney Jean Rodgers

Electronic Theses and Dissertations

A brief history of nucleosides and their photophysics provides the background information for the discussion of synthesis, photophysics and incorporation of fluorescent nucleotide analogs during enzymatic DNA synthesis. Through the use of nucleoside starting material, it is possible to synthesize a number of modified nucleotides for use as fluorescent probes in biochemical research. Synthetic endeavors into the synthesis of these and related molecules from nucleobase starting materials are also presented. The synthesis of these molecules involved re-development of the synthetic routes to broaden substrate scope by overcoming the changed reactivity resulting from the presence of additional functionality.

While many highly …

Degradation Of High Voltage Glass Fiber-Reinforced Polymer Matrix Composites By Aggressive Environmental Conditions, Tianyi Lu

Electronic Theses and Dissertations

Polymer matrix composites reinforced with either E glass or ECR glass fibers-reinforced are used in a variety of high voltage electrical applications because of their advantages like lower weight and cost. However, they can be damaged by aggressive in-service conditions such as high temperature, ultraviolet radiation, moisture, ozone and corrosive environments. Different degradation mechanisms can develop in high voltage PMCs under those extreme environments, which, in turn, can affect the long term structural durability of the composites. A set of PMCs reinforced with ECR-glass and E-glass fibers embedded in four different resins has been investigated in this study. In addition, …