Chemistry Commons^™

Novel Near-Infrared Cyanine Dyes For Fluorescence Imaging In Biological Systems, Nilmi T. Fernando

Chemistry Dissertations

Heptamethine cyanine dyes are attractive compounds for imaging purposes in biomedical applications because of their chemical and photophysical properties exhibited in the near-infrared region. A series of meso amino-substituted heptamethine cyanine dyes with indolenine, benz[e]indolenine and benz[c,d]indolenine heterocyclic moieties were synthesized and their spectral properties including fluorescence quntum yield were investigated in ethanol and ethanol/water mixture. Upon substitution with amines, the absorption maxima of the dyes shifted to the lower wavelength region (~600 nm), showed larger Stokes shifts and stronger fluorescence which can be attributed to an excited state intramolecular charge transfer (ICT). High quantum yields …

Nucleic Acid Substrates: Investigation Of Structural And Dynamic Features That Influence Enzyme Activity, Christopher N. Johnson

Chemistry Dissertations

The previous view of DNA as a linear sequence of bases is evolving to consider structure, topology and dynamics. Sequences surrounding damage lesions have been shown to effect enzyme recognition and processing. Here we present an in depth investigation of subtle structural and dynamical features imparted to nucleic acid duplexes by a designed modification or damage lesions. Highly restrained solution structures were generated and validated utilizing a range of NMR techniques. This allowed for the characterization of multiple features of the nucleic acid duplex; such as base pairing, backbone torsion angles, deoxyribose sugar pucker, and intra and inter nucleotide proton …

Transition Metal Complexes With Reactive Trimethylsilylchalcogenolate Ligands: Precursors For The Preparation Of Ternary Nanoclusters, Chhatra Bahadur Khadka

Electronic Thesis and Dissertation Repository

The Co²⁺ and Mn²⁺ complexes (N,N´-tmeda)Co(ESiMe₃)₂ (E = S, 1a; E = Se, 1b), (3,5-Me₂C₅H₃N)₂Co(ESiMe₃)₂ (E = S, 2a; E = Se, 2b), [Li(N,N´-tmeda)]₂[(N,N´-tmeda)Mn₅(μ-ESiMe₃)₂(ESiMe₃)₄(μ₄-E)(μ₃-E)₂] (E = S, 3a; E = Se, 3b), [Li(N,N´-tmeda)]₂[Mn(SSiMe₃)₄] (4), [Li(N,N´-tmeda)]4[Mn₄(SeSiMe₃)₄(μ_{3 …}

Affinity Chromatography In Environmental Analysis And Drug-Protein Interaction Studies, Efthimia Papastavros

Department of Chemistry: Dissertations, Theses, and Student Research

This dissertation will examine the use of novel affinity sorbents to extract emerging contaminants from water. These contaminants include carbamazepine, an anti-epileptic drug which is resistant to natural degradation in the environmental and to drinking water treatment procedures. This drug has been found in fish, drinking water, estuarine and coastal waters, and river sediment and has been used as a general marker of contaminants in wastewater. Carbamazepine was one of the most commonly detected compounds in surface-water and groundwater samples in a recent reconnaissance study of untreated drinking water sources in the U.S. Besides using this drug as a representative …

Synthesis And Characterization Of Highly Porous Borazine-Linked Polymers Via Dehydrogenation/Dehydrocoupling Of Borane-Amine Adducts And Their Applications To Gas Storage, Karl Jackson

Theses and Dissertations

A new class of porous polymers has been designed and successfully synthesized by thermal dehydrogenation of several polytopic arylamine-borane adducts and has been designated Borazine-Linked Polymers (BLPs). The polymers reported are constructed of linear, triangular, and tetrahedral amine building units to form 2D and 3D frameworks. The boron sites of the pores are aligned with hydrogen atoms contrasted with the recently reported halogenated BLPs which consist of pore channels aligned with bromine or chlorine atoms. One of the reported BLPs, BLP-2(H), was proven to be crystalline by PXRD, matching the experimental pattern to theoretical patterns calculated from modeled structures. BLPs …

Acrb Trimer Stability And Efflux Activity, Insight From Mutagenesis Studies, Linliang Yu, Wei Lu, Yinan Wei

Chemistry Faculty Publications

The multidrug transporter AcrB in Escherichia coli exists and functions as a homo-trimer. The assembly process of obligate membrane protein oligomers, including AcrB, remains poorly understood. In a previous study, we have shown that individual AcrB subunit is capable of folding independently, suggesting that trimerization of AcrB follows a three-stage pathway in which monomers first fold, and then assemble. Here we destabilized the AcrB trimer through mutating a single Pro (P223) in the protruding loop of AcrB, which drastically reduced the protein activity. We replaced P223 separately with five residues, including Ala, Val, Tyr, Asn, and Gly, and found that …

Development And Optimization Of Organic Based Monoliths For Use In Affinity Chromatography, Erika L. Pfaunmiller

Department of Chemistry: Dissertations, Theses, and Student Research

Affinity chromatography is an important and useful tool for studying biological interactions, such as the binding of an antibody with an antigen. Monolithic supports offer many advantages over traditional packed bed supports in affinity chromatography, including their ease of preparation, low back pressures and good mass transfer properties. Monoliths can be broken down into two basic categories: organic (polymer) and inorganic (silica) monoliths. There are many varieties of polymer based monoliths; however, a large focus has been on co-polymers of glycidyl methacrylate (a functional monomer) and ethylene dimethacrylate (a cross-linking agent). The solvents of choice for making this type of …

Designed Synthesis Of Halogenated Borazine-Linked Polymers And Their Applications In Gas Storage And Separation, Thomas Reich

Theses and Dissertations

The synthesis of highly porous organic polymers with predefined porosity has attracted considerable attention due to their potential in a wide range of applications. Of particular interest in porous organic polymers is their potential use in automotive applications as well as separation processes whereby advancements could result in a reduction in carbon dioxide emissions and the production of natural gas in a more economically friendly manner. Along these pursuits, seven borazine-linked polymers (BLPs) have been synthesized through the introduction of p-phenylenediamine, 1,3,5-tris-(4-aminophenyl)benzene, benzidine, or tetra-(4-aminophenyl)methane with boron tribromide or boron trichloride followed by the thermolysis reaction of the resulting in …

Polymer Nanocomposite Analysis And Optimization For Renewable Energy And Materials, Nathan Walter Henry

Doctoral Dissertations

Polymer nanocomposites are an important research interest in the area of engineering and functional materials, including the search for more environmentally materials for renewable energy and materials. The ability to analyze and optimize morphology is crucial to realizing their potential, since the distribution of materials in the composite strongly influences its properties. This dissertation presents research into three different polymer nanocomposite systems with three different applications that underscore the need to understand and control the composite morphology to succeed.

The first project details work on development of a copolymer compatibilizer to enhance the dispersion of the plant-derived biopolymer lignin in …

Adsorption Of Hydrogen Onto Bare And Metal Decorated Metal Oxides, Paige Elizabeth Landry

Doctoral Dissertations

Catalytically relevant metal clusters were deposited on metal oxide supports. Palladium and gold were deposited on mixed morphology ZnO, and palladium was deposited on MgO(100). The materials were characterized with electron microscopy, photoluminescent spectroscopy, and X-ray photoelectron spectroscopy. The behavior of hydrogen on these materials, as well as bare ZnO, was studied using volumetric isotherms. The isotherms were used to determine the monolayer gas coverage, surface

area, and heats of adsorption of hydrogen on these materials over the temperature range of approximately 8-13 K. At the temperatures and pressures studied, hydrogen physically adsorbed onto the materials. Additional investigations with inelastic …

Targeted Synthesis And Characterization Of Nanostructured Silicate Building Block Supports And Heterogeneous Catalysts With Tungsten(Vi) Or Zirconium(Iv) Centers, Michael Edward Peretich

Doctoral Dissertations

Catalysts play a vital role in almost every aspect of our lives and are used in the production of fuels, polymers, chemicals, foods, and pharmaceuticals. One challenge facing the heterogeneous catalysis community is the targeted synthesis of dispersed catalyst ensembles.

The Barnes research group has developed a general methodology for the synthesis of nanostructured silicate building block supports and heterogeneous catalysts. This methodology provides researchers with the ability to control the dispersion of surface functionality, the dispersion of metal cation centers, the number of linkages from the metal cation center to the support, the surface area of the support, and …

Development And Application Of Liquid Chromatography-Tandem Mass Spectrometry Methods To The Understanding Of Metabolism And Cell-Cell Signaling In Several Biological Systems, Jessica Renee Gooding

Doctoral Dissertations

Liquid chromatography tandem mass spectrometry has become a powerful tool for investigating biological systems. Herein we describe the development of both isotope dilution mass spectrometry methods and targeted metabolomics methods for the study of metabolic and cell-cell signaling applications.

A putative yeast enzyme was characterized by discovery metabolite profiling, kinetic flux profiling, transcriptomics and structural biology. These experiments demonstrated that the enzyme shb17 was a sedoheptulose bisphosphatase that provides a thermodynamically dedicated step towards riboneogenesis, leading to the redefinition of the canonical pentose phosphate pathway.

An extension of metabolic profiling and kinetic flux profiling methods was developed for a set …

Synthesis Of An Antimicrobial Textile Coating, William M. Morris

Chemistry and Biochemistry

A titania nanosol was synthesized and coated onto nylon/cotton blended textile substrates. The substrates were characterized via SEM for adhesion and nanoparticle formation, then subjected to antimicrobial efficacy tests. The titania nanosol was successfully coated on to textiles samples. Particles were observed to be around 2 by 3 micrometers and formed between the interstitial space of textile fibers. Although larger than typical nanoparticles, the coatings exhibited what seemed to be antimicrobial activity. Titania nanosol coated textile samples were subjected to Kirby Bauer Assay in the presence of S. aureus. The coated textile sample exhibited an inhibition of growth around its …

Method Development And Validation Of The Quantitation Of 19 Antipsychotics Using Deuterated Internal Standards, Anthony S. Epps

Chemistry Theses

Antipsychotic drugs or neuroleptics are used primarily for psychiatric disorders such as schizophrenia, psychosis, and bipolar disorder. In forensic science antipsychotics are drugs of considerable interest because of their potential abuse, involvement in suicides, and they are frequently associated with sudden death investigations. Well-characterized and fully validated analytical data is necessary to generate reproducible and reliable results. As a result, data can be correctly interpreted and objectively demonstrate in its applicability for the intended use. This research has developed and validated a method that is selective, sensitive and accurate using liquid chromatography–tandem mass spectrometry (LC–MS/MS) for the simultaneous determination of …

Organ-Distribution Of The Metabolite 2-Aminothiazoline-4-Carboxylic Acid In A Rat Model Following Cyanide Exposure, Ilona Petrikovics, David E. Thompson, Gary A. Rockwood, Brian A. Logue

Chemistry and Biochemistry Faculty Publications

The reaction of cyanide (CN⁻) with cystine to produce 2-aminothiazoline-4-carboxylic acid (ATCA) is one of the independent detoxification pathways of cyanide in biological systems. In this report, in vivo production of ATCA and its distributions in plasma and organs were studied after a subcutaneous sublethal dose of 4 mg/kg body weight potassium cyanide (KCN) administration to rats. At this sublethal dose of KCN, ATCA concentration was not significantly increased in the plasma samples, however, it was found significantly increased in liver samples. These results suggested that ATCA might not be a good diagnostic biomarker in plasma for sublethal …

Lectio Praecursoria, Kari Myöhänen

Kari Myöhänen

Lectio praecursoria: Modelling of combustion and sorbent reactions in three-dimensional flow environment of a circulating fluidized bed furnace

Development Of A Glycoconjugate Tool Set For The Assembly And Presentation Of Carbohydrate Ligands On Surfaces, Irene Esah Abia

Doctoral Dissertations

Carbohydrate and protein interactions are often essential in viral and bacterial infection, the immune response, cell differentiation and development, and the progression of tumor cell metastasis. Therefore, an understanding of carbohydrate–protein interactions at the molecular level would lead to a better insight into the biological process of living systems and assist in the development of therapeutic and diagnostic strategies. Our goal was to synthesize different mannose derivatives, immobilize them on nano-patterned surfaces and carry out binding studies with mannose-binding lectins in order to characterize carbohydrate–protein interactions.

Different derivatives of D-mannose (monosaccharide, (1→2)-linked disaccharide, (1→3)-linked disaccharide, and (1→2, 1→3)-linked trisaccharide) with …

Citrate Binding To The Membrane Protein Proteorhodopsin, Farhana F. Syed

Chemistry - Dissertations

Proteorhodopsin (pR) is an intrinsic membrane protein with an important role in solar-energy storage of the biosphere. Earlier work in our lab has shown that polyhistidine-tagged pR can be purified by means of selective precipitation with citrate under specific conditions, as can a number of mutants based on this His₆-tagged pR. Purification of a heterologously-expressed trans-membrane protein by a simple salt such as citrate is novel. However, such a phenomenon leads to several questions: How does citrate cause pR precipitation? Does the polyhistidine-tag assist in such a precipitation? Is this precipitation pH-specific? Does citrate affect the function of …

Controlling Biofouling By Surface Engineering And Molecular Inhibition, Debjyoti Bandyopadhyay

Chemistry - Dissertations

The common theme that binds together all the chapters in this dissertation is anti-biofouling chemistry. By utilizing tools of surface engineering and molecular inhibition, a hypothesis driven, systematic approach of controlling the different forms of biofoulings such as protein adsorption, mammalian cell adhesion and biofilm formation is presented. Chapter 1 provides a brief introduction about topics relevant for understanding the studies presented in subsequent chapters. Chapter 2 reports the synthesis of enantiomerically pure alkanethiols that terminate with different stereoisomer's of sugar alcohols, and the effect of chirality of these polyol-terminated self-assembled monolayers (SAMs) on resisting protein adsorption.

Chapter 3 …

The Tetrafluoroborate Salt Of 4-Methoxybenzyl N-2-(Dimethylamino)Ethyl-N-Nitrosocarbamate: Synthesis, Crystal Structure And Dft Calculations, Helene Hedian, Vladimir Benin

Chemistry Faculty Publications

The tetrafluoroborate salt of 4-methoxybenzyl N-2-(dimethylamino)ethyl-N-nitrosocarbamate was prepared in two steps, via the corresponding carbamate. Its crystal structure is monoclinic, space group P21/c. The unit cell dimensions are: a = 19.499(8) Å, b = 5.877(3) Å, c = 15.757(7) Å, α = 90°, β = 110.019(7)°, γ = 90°, V = 1696.5(12) Å3, Z = 4. The structure exhibits an unexpected, pseudo-gauche conformation with respect to the C2–C3 bond, due to a stabilizing hydrogen bond between the carbonyl oxygen (O1) and the hydrogen atom at the trialkylammonium center (H3n), with a distance between them of …

Gold Nanoparticle Generation Using In Situ Reduction On A Photoresist Polymer Substrate, Christopher J. Clukay

HIM 1990-2015

This report presents evidence that in-situ reduction of metal ions bound to a cross-linked polymer surface does not always result in nanoparticle formation solely at the interface, as is commonly assumed, but also as much as 40 nm deep within the polymer matrix. Tetrachloroaurate ions were bound using a variety of multi-functional amines to cured films of SU-8 -- a cross-linkable epoxide frequently used for micro- and nanofabrication -- and then treated using one of several reducing agents. The resulting gold-nanoparticle decorated films were examined by X-ray photoelectron spectroscopy and by plan-view and cross-sectional transmission electron microscopy. Reduction using sodium …

Synthesis And Characterization Of Catalysts For The Selective Transformation Of Biomass-Derived Materials, Isaac Tyrone Ghampson

Electronic Theses and Dissertations

The experimental work in this thesis focuses on generating catalysts for two intermediate processes related to the thermal conversion of lignocellulosic biomass: the synthesis and characterization of mesoporous silica supported cobalt catalysts for the Fischer-Tropsch reaction, and an exploration of the reactivity of bulk and supported molybdenum-based nitride catalysts for the hydrodeoxygenation (HDO) of guaiacol, a lignin model compound. The first section of the work details the synthesis of a series of silicasupported cobalt Fischer-Tropsch catalysts with pore diameters ranging from 2-23 nm. Detailed X-ray diffraction measurements were used to determine the composition and particle diameters of the metal fraction, …

Maxwell's Equations, Part Iv, David W. Ball

Chemistry Faculty Publications

In this column, we continue our explanation of Maxwell’s equations, the seminal classical explanation of electricity and magnetism (and, ultimately, light). For those of you new to the series, consider finding the last few appearances of this column to get caught up. Alternately, you should be able to find past columns on our website, www.spectroscopymag.com and look for “The Baseline” link. Words of warning: for my own reasons, the figures are being numbered sequentially through this series of columns, which is why the first figure in this column is numbered 26. Also, we’re going to get a bit mathematical. Unfortunately …

Synthesis And Biosynthesis Of Polyketide Natural Products, Atahualpa Pinto

Chemistry - Dissertations

Traditionally separate disciplines of a large and broad chemical spectrum, synthetic organic chemistry and biochemistry have found in the last two decades a fertile common ground in the area pertaining to the biosynthesis of natural products. Both disciplines remain indispensable in providing unique solutions on numerous questions populating the field. Our contributions to this interdisciplinary pursuit have been confined to the biosynthesis of polyketides, a therapeutically and structurally diverse class of natural products, where we employed both synthetic chemistry and biochemical techniques to validate complex metabolic processes. One such example pertained to the uncertainty surrounding the regiochemistry of dehydration and …

Studies Toward The Development Of A Microelectrode Array For Detection Of Dopamine Through Redox Cycling, Anupama Aggarwal

Graduate Theses and Dissertations

Redox cycling is an electrochemical technique that cycles the reversible redox species between its oxidative states repeatedly on generator and collector electrodes. Two or more individually-addressable microelectrodes located close to each other allow redox cycling to be possible. Electrochemical behavior of a biologically important molecule, dopamine is examined under redox cycling conditions. To our knowledge, this is the first report on detection of physiological concentration of dopamine in presence of up to 100 times excess ascorbate with the use of redox cycling, without the involvement of polymer coating such as Nafion®.

Microfabrication was used to produce different geometries (parallel bands …

Chemical Modification On Gold Slides To Gain Better Control Of Patterning Techniques, Ragini Vuppalapati

Masters Theses & Specialist Projects

Nanolithography is a rapidly evolving field that requires new combinations of techniques to improve patterning and to assist in fabricating electromechanical devices. An increasing number of applications require surfaces with defined regions of different chemical functionality. In our previous project optimum conditions for lithographic patterning were determined and potential blockers were identified to reduce force on the tip.

This work is focused on identifying good chemical modifications that will allow better control of basic patterning and to investigate the minimum force of patterning required while using each chemical system. The primary aim is to gain better control of basic pattern …

Prevention Of Iron- And Copper-Mediated Oxidative Dna Damage By Neurotransmmitters And Related Compounds: Evidence For Metal Binding As An Antioxidant Mechanism, Carla Garcia

All Theses

An array of health concerns have been attributed to oxidative DNA damage from the hydroxyl radical (*OH), and the presence of the most biologically available metals iron and copper perpetuate the production of this radical through the Fenton and Fenton-like reactions, respectively. The concentrations at which flavonol and polyphenol antioxidants prevent 50% of DNA damage (IC50) were measured using gel electrophoresis assays upon Fe(II)/H2O2- and Cu(I)/H2O2-mediated DNA damage (Chapter 2). Results show that catechol- and gallol-containing antioxidants differ greatly in preventing DNA damage by Cu(I)/H2O2, compared to Fe(II)/H2O2, behavior that was explained using electron paramagnetic resonance spectroscopy. Semiquinone and other …

Investigation Of A Novel Method For Polonium-210 Determination In Groundwater, Tara Matheny

All Theses

A novel method was investigated for the quantification of 210Po in water as an alternative to the standard method of spontaneous plating onto Ag disks followed by quantification with an alpha spectrometer. The novel method concentrated a 0.5L sample by MnO2 co-precipitation followed by dissolution of the precipitate into a solution. Polonium-210 was separated from the solution and quantified in a column containing a 50:50 by volume mixture of Pb resin (Eichrom Technologies, Inc.) mixed with granulated CaF2:Eu scintillator. The column containing 210Po is quantified on a liquid scintillation counter without the introduction of liquid cocktail. The minimum detectable concentration …

Quantum Mechanical And Molecular Mechanical Study Of Solvent Effects, Dejun Si

Department of Chemistry: Dissertations, Theses, and Student Research

Intermolecular interaction and solvent effects play important roles in determining physical and chemical properties of molecular systems, and must be considered in relevant quantum mechanical (QM) calculations. Due to the high computational cost, full and rigorous QM treatment of both solute and solvent molecules is impractical. Computationally efficient molecular mechanical (MM) methods can be used to describe solvent effects, and combined into QM methods to formulate QM/MM methods. Classical force field method and reaction-field method are the two most popular MM methods. However, the issue of effectively combining MM methods with high-level QM methods remains unsolved. This thesis presents several …

First-Principles Studies On Physical And Chemical Properties Of Nanostructures, Menghao Wu

Department of Physics and Astronomy: Dissertations, Theses, and Student Research

The physical and chemical properties of decorated graphene and graphene ribbons, single-layer III-V systems, three-dimensional carbon and BN foam, and transition-metal-molecular sandwich nanowires have been investigated by first-principle calculations and their potential applications have been predicted. First, it is shown that zigzag graphene nanoribbons (ZGNRs) can be converted into half metal when their edges are decorated by some chemical functional groups, and the half-metalicity is induced by chemical potential difference between two edges when one edge is decorated by electron-donating group like –OH and the other edge is decorated by electron-accepting group like –F, -NH₂, -N(CH₃) …