Chemistry Commons^™

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 …

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 …

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.

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 …

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 …

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 …

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 …

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 …

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 …

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 …

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.

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 …

Applications Of Epr With An Emphasis On Tau Fibril Structure, Virginia Meyer

Electronic Theses and Dissertations

Substances containing unpaired electrons have been studied by electron paramagnetic resonance (EPR) for nearly 70 years. With continual development and enhancement of EPR techniques, questions have arisen regarding optimum method selection for a given sample based on its properties. In this work, radiation defects, natural lattice defects, solid organic radicals, radicals in solution, and spin-labeled proteins were analyzed using CW, pulse, and rapid scan EPR to compare methods. Studies of solid BDPA, E' in quartz, N_s⁰ in diamond, and a-Si:H, showed that rapid scan could overcome many obstacles presented by other techniques, cementing rapid scan as an effective …

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, …

In Actu Et In Silicio: Linear And Nonlinear Photophysical Characterization Of A Novel Europium Complex, And Incorporating Computational Calculations In The Analysis Of Novel Organic Compounds, Adam Woodward

Electronic Theses and Dissertations

Despite not being a tangible substance, light is becoming an increasingly valuable tool in numerous areas of science and technology: the use of laser excitation of a fluorescent probe can generate incredibly detailed images of cellular structures without the need for large amounts of dissection; new types of solar cells are being produced using organic dyes to harvest light; computer data can be stored by inducing a chemical change in a compound through irradiation with light. However, before any of these materials can be applied in such a way, their properties must first be analyzed for them to be deemed …

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 …

Photoactivatable Organic And Inorganic Nanoparticles In Cancer Therapeutics And Biosensing, Mona Mathew

Electronic Theses and Dissertations

In photodynamic therapy a photosensitizer drug is administered and is irradiated with light. Upon absorption of light the photosensitizer goes into its triplet state and transfers energy or an electron to oxygen to form reactive oxygen species (ROS). These ROS react with biomolecules in cells leading to cell damage and cell death. PDT has interested many researchers because of its non-invasiveness as compared to surgery, it leaves little to no scars, it is time and cost effective, it has potential for targeted treatment, and can be repeated as needed. Different photosensitizers such as porphyrines, chlorophylls, and dyes have been used …

1, 2, And 3 Dimension Carbon/Silicon Carbon Nitride Ceramic Composites, Flores Jean Calderon

Electronic Theses and Dissertations

Polymer-derived ceramics (PDCs) are exceptional ultra-high temperature and stable multifunctional class of materials that can be synthesized from a polymer precursor through thermal decomposition. The presented research focuses on 1-D nanofibers, 2-D films and 3-D bulk, carbon-rich silicon carbon nitride (SiCN) ceramics. 1-D nanofibers were prepared via electrospinning for light weight, flame retardant and conductive applications. The commercially available CerasetTM VL20, a liquid cyclosilazane pre-ceramic precursor, was mixed with polyacrylonitrile (PAN) in order to make the cyclosilazane electrospinnable. Carbon-rich PDC nanofibers were fabricated by electrospinning various ratios of PAN/cyclosilazane solutions followed by pyrolysis. Surface morphology of the electro spun nanofibers …

Atmospheric Mercury Species In Northern Mississippi: Concentrations, Sources, Temporal Patterns, And Soil-Air Exchange, Yi Jiang

Electronic Theses and Dissertations

Mercury is a highly toxic element that is found both naturally and as an introduced contaminant in the environment. The majority of Mercury released to the environment is into the atmosphere, where because of its high volatility and long residence time is dispersed globally. In order to better understand the factors controlling the distribution and temporal patterns of atmospheric Mercury species, as well as the sources of airborne Mercury in the mid-south region, concentrations of gaseous elemental mercury (gem), gaseous oxidized mercury (gom), and particulate-bound mercury (pbm), along with meteorological parameters and other ancillary data, were collected for more than …

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 …

Structural Analysis Of Bulky Thiolate-Protected Gold Nanomolecules, David Walton Crasto

Electronic Theses and Dissertations

Routine preparation of thiolate-protected gold nanomolecules involves, most commonly, straight-chain organic thiolate ligands for which the sulfhydryl `head' group is bound to a primary carbon atom. The primary connectivity of these sulfur atoms, such as for the case of n-hexanethiol and phenylethanethiol, allows for even packing, and the relative ease of formation of gold-thiolate oligomers about the surface monolayer in the formation of Au-SR bonds. Moreover, these straight-chain ligands routinely support the formation of an icosahedron-based series of core-size gold nanomolecules. Within this series of nanoparticles, Au25(SR)18 and Au38(SR)24 are among the most commonly studied core-sizes; Au25(SR)18 is situated upon …

Synthesis, Characterization And Electrochemical Properties Of Gold Nanomolecules, Vijay Bhaskar Reddy Jupally

Electronic Theses and Dissertations

Chapter 1 gives a brief introduction to the field of gold nanomolecules. Various synthetic protocols and analytical techniques used through out this dissertation are discussed in detail. Size dependent properties of the gold nanomolecules are described. The structure of gold nanomolecules is explained based on the crystal structure of Au25(SCH2CH2Ph)18. The theoretical basis for the stability of the gold nanomolecules is explained using the super atom complex model and geometric parameters. Chapter 2 includes ligand exchange experiments on gold nanomolecules. Ligand exchange experiments are used to modify the monolayer of nanomolecules after synthesis. Ligand exchange reactions are monitored by mass …

Characterizing Non-Covalent Interactions And Peptide Bond Formation With Electronic Structure Theory, Eric Van Dornshuld

Electronic Theses and Dissertations

The development and application of quantum mechanics has exploded in the past century. The rules of classical mechanics were found to be completely insufficient when applied to a universe that operates on the scale of atomic and subatomic particles. The advancement of quantum theory and computer technology has driven quantum mechanical analyses toward routine in the chemist's laboratory. Chapter 1 briefly outlines some comfailures of classical mechanics from a historical standpoint. Chapter 2 provides a mathematical overview to quantum chemistry including a brief presentation of the analytic solutions to the schrã¶dinger equation for some model systems. Chapter 3 and chapter …

Fluorescence Off-On Sensors For F-, K+, Fe3+, And Ca2+ Ions, Binglin Sui

Electronic Theses and Dissertations

Fluorescence spectroscopy has been considered to be one of the most important research techniques in modern analytical chemistry, biochemistry, and biophysics. At present, fluorescence is a dominant methodology widely used in a great number of research domains, including biotechnology, medical diagnostics, genetic analysis, DNA sequencing, flow cytometry, and forensic analysis, to name just a few. In the past decade, with the rapid development of fluorescence microscopy, there has been a considerable growth in applying fluorescence technique to cellular imaging. The distinguished merits of fluorescence techniques, such as high sensitivity, non-invasiveness, low cytotoxicity, low cost, and convenience, make it a promising …

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. …