Chemistry Commons^™

Promiscuous And Adaptable Enzymes Fill “Holes” In The Tetrahydrofolate Pathway In Chlamydia Species, Nancy E. Adams, Jennifer J. Thiaville, James Proestos, Ana L. Juárez-Vázquez, Andrea J. Mccoy, Francisco Barona-Gómez, Dirk Iwata-Reuyl, Valérie De Crécy-Lagard, Anthony T. Maurelli

Chemistry Faculty Publications and Presentations

Folates are tripartite molecules comprising pterin, para-aminobenzoate (PABA), and glutamate moieties, which are essential cofactors involved in DNA and amino acid synthesis. The obligately intracellular Chlamydia species have lost several biosynthetic pathways for essential nutrients which they can obtain from their host but have retained the capacity to synthesize folate. In most bacteria, synthesis of the pterin moiety of folate requires the FolEQBK enzymes, while synthesis of the PABA moiety is carried out by the PabABC enzymes. Bioinformatic analyses reveal that while members of Chlamydia are missing the genes for FolE (GTP cyclohydrolase) and FolQ, which catalyze the initial …

Mineralogical Transformation And Electrochemical Nature Of Magnesium-Rich Primers During Natural Weathering, Shashi S. Pathak, Michael D. Blanton, Sharathkumar K. Mendon, James W. Rawlins

Faculty Publications

Magnesium-rich primers (MgRP) have generated great interest as a promising alternative to chromium-based primers for the protection of aluminum substrates but their performance during exterior exposure has not been well documented. This paper focuses on the evaluation of MgRP during natural weathering to gain insight into its mineralogical phase transformation and electrochemical nature. Control studies were conducted on Mg and AA2024-T3 coupons. The results indicate that Mg particles in MgRP transform into a variety of hydroxide, carbonate, and hydroxy carbonates. During natural weathering, CO₂ inhibited the dissolution of both Mg and AA2024-T3 as a result of protective carbonate layer …

Synthesis Of [1,2,4]-Triazines As Kinase Inhibitors And Of Novel Fluorine Capture Reagents For Pet Probes, Fenger Zhou

USF Tampa Graduate Theses and Dissertations

ABSTRACT

Anaplastic lymphoma kinase (ALK) is a tyrosine kinase receptor, which plays a pivotal part in the development of the central nervous system. Aberrant expression of full-length ALK occurs in neuroblastoma and chromosomal translocation or inversion of the ALK gene can generate novel fusion-ALK proteins that possess constitutive kinase activity and contribute to oncogenic processes. One of the well-studied fusion proteins is nucleophosmin (NPM-ALK), which draws a lot of attention for medicinal chemists to design small molecules as kinase inhibitors for this target. In this dissertation, [1, 2, 4]-Dihydrotriazine dimers as competitors of the lead compound NVP-TAE684 targeting NPM-ALK have …

Fundamental Studies On Copper Zeolites For Catalytic No X Abatement, Anuj Arun Verma

Open Access Dissertations

Stringent regulations in mobile NOx emissions have resulted in the development of Standard Selective Catalytic Reduction (SCR) as the dominant NOx abatement technology in lean burn diesel engines. Standard SCR is a reaction of nitric oxide (NO) with ammonia (NH₃), in the presence of oxygen (O ₂) to form nitrogen (N₂) and water (H₂O). Copper containing zeolites show commercially viable SCR performance. Cu-SSZ-13 (CHA framework), a member of this family, is a preferred catalyst for SCR applications because it shows exceptional hydrothermal stability in addition to commercially viable SCR performance. Our work focuses …

Isolation And Screening Of Microalgae From Natural Habitats In The Midwestern United States Of America For Biomass And Biodiesel Sources, Keesoo Lee, Megan L. Eisterhold, Fabio Rindi, Swaminathan Palanisami, Paul Ki-Souk Nam

Chemistry Faculty Research & Creative Works

Native species of microalgae were isolated from natural water bodies in the Midwestern United States of America and were screened for the ultimate goal of mass cultivation in Missouri and the surrounding states, and for their potential as biomass and biodiesel sources. A number of different nutrient media recipes were utilized to isolate the maximum number of colonies from each field samples. These nutrient recipes were modified in order to optimize the isolation and growth dynamics of specific colonies. All of the isolates were categorized based on the morphological appearance of the culture and the microscopic cellular appearance of the …

Density Functional Theory Modeling Of It-Stacking And Electrophilic Donor-Acceptor Interactions With Application To Therapeutic Targeting Of Zinc-Finger Proteins, Patricia Beall Lutz

Chemistry & Biochemistry Theses & Dissertations

Several viruses, including viruses that cause cancer, contain conserved zinc finger (ZF) proteins that are essential for viral reproduction, making them attractive drug targets for cancer and viral treatment. ZFs are small protein domains that have Zn²⁺ tetrahedrally coordinated to at least 2 Cys and His. They form three classes of ZFs depending on the amino acid ligands, CCHH, CCCH, and CCCC. Zn²⁺ is stable towards redox reactions; however, the Cys thiolates are redox active. Oxidation of the Cys thiolates release Zn²⁺, and the ZF loses its tertiary structure and can no longer bind DNA or …

Determination Of Corrosion Inhibitor Lubricity Improver In Jet Fuel By Liquid Chromatography-Electrospray Ionization Mass Spectrometry, David W. Johnson, Milissa Flake, Ryan Adams

Chemistry Faculty Publications

Military jet fuel (JP-8) is very similar to commercial jet fuel (Jet A) except for the presence of three additives, fuel system icing inhibitor, corrosion inhibitor–lubricity improver (CI-LI), and antistatic additive, which are added to improve characteristics of JP-8. Of particular interest is the CI-LI additive; the most common active ingredient is a dimer of linoleic acid. This article focuses on quantification of the active ingredient in the CI-LI additive by liquid chromatography–mass spectrometry (LC–MS). This method will allow the determination of CI-LI content in military jet fuel samples.

Synthesis, Characterization And Reactivity Studies Of Fe(Ii) Complexes With Relevance To The Radical Sam Enzymes, Xixi Hong

Master's Theses (2009 -)

It is well-established that S-adenosylmethionine (SAM) serves as the methyl group donor in methylations of DNA, hormones, neurotransmitters and signal transduction systems. However, a new class of enzymatic reactions involving SAM has recently attracted considerable attention. In these systems, SAM initiates radical-based reactions at the active sites of enzymes via formation of an adenosyl radical, which further abstracts a H-atom from the substrate to initiate a radical-based mechanism. However, modeling studies of radical SAM enzymes have been hindered, by difficulties in preparing adequate synthetic [Fe4S4] clusters. We prepared a novel series of Fe(II) complexes with tripodal tris(2-hydroxybenzyl)amine ligands, which replicate …

Gas-Phase Ion/Ion Reactions Of Biomolecules: An Examination Of Carboxylate Reactivity And Arginine Based Non-Covalent Complexes, Nathan Zachary Barefoot

Open Access Theses

The advent of Electrospray Ionization with the ability to generate multiply charges ions has contributed significantly to the study of gas-phase ion/ion reactions. With the tools available in mass spectrometry it has been shown that these reactions are effective at transforming one type of gaseous ion into another through a series of reactions. This work examines some of these reactions and their application to field of proteomics specifically focusing on the amino acids of arginine and lysine. NHS reagents have been shown to react to both of these molecules with in the gas-phase under different conditions but have relies on …

Characterization Of Water-Solid Interactions In Crystalline Ingredients And Development Of Deliquescence Measurement Recommendations, Matthew C. Allan

Open Access Theses

There are five major mechanisms of water-solid interactions. The primary focus of this thesis was on two of these: deliquescence and hydrate formation. Many crystalline food ingredients are deliquescent compounds (e.g., NaCl, sucrose, and ascorbic acid) and some are both deliquescent and hydrate formers (e.g., glucose, thiamine HCl, citric acid). Deliquescence is the first order phase transformation of a crystalline solid to a solution above a critical relative humidity (RH) known as the deliquescence point (RH0). A crystalline hydrate is a pseudo-polymorph in which water is incorporated into the crystal structure, altering the molecular formula and the physical properties.^ To …

Physical And Chemical Attributes Of A Genetically Modified Fruit Pectin, Carl Patrick Littrell

Open Access Theses

Pectin is an important polymer used in the food industry as a thickening and gelling agent. Though pectin is ubiquitous in plants, chemical and structural differences among pectin molecules prevent most from being viable for industrial use. Enzymes found naturally in fruit cell walls during the ripening process impair many desirable attributes of fruit pectins, rendering them unsuitable for industrial applications. Pectin methylesterase (PME) is one such enzyme whose expression can be altered during ripening through the use of recombinant genetic engineering. Reduction in levels of PME results in increased degree of methylation and molecular size of pectin, greatly increasing …

Investigation Into The Control Of Melittin Secondary Structure And Antimicrobial Activity, Zachary B. Molinets

Open Access Theses

Antimicrobial resistance has been an exponentially growing problem since the discovery of antibiotics. Antibiotics have been misused for many years and this misuse has grown into a real problem for the medical community. While there are countless safeguards to prevent infection by a resistant strain of bacteria, there are still many plagued by it and must be treated with sometimes dangerous antibiotics. Melittin, along with many other peptides, contain potent antimicrobial properties, but are also toxic toward enthrocytes. The control of the secondary structure of peptides provides the key to adjusting their activity.

Preparation & Characterization Of High Purity Cu2 Znsn(Sxse1-X)4 Nanoparticles, Bethlehem G. Negash

Open Access Theses

Research in thin film solar cells applies novel techniques to synthesize cost effective and highly efficient absorber materials in order to generate electricity directly from solar energy. Of these materials, copper zinc tin sulfoselenide (Cu₂ZnSn(S_xSe_1-x) ₄) nanoparticles have shown great promise in solar cell applications due to optimal material properties as well as low cost & relative abundance of materials.^1,2 Sulfoselenide nanoparticles have also a broader impact in other industries including electronics³, LED ⁴, and biomedical research⁵. Of the many routes of manufacturing these class of semiconductors, …

Synthesis And Characterization Of Crystalline Iron Nanoparticles From Zerovalent Iron Sandwich Complexes, Anh Tue Nguyen

Open Access Theses

In this project we present a systematic study on the synthesis of crystalline iron nanocubes by thermal decomposition of an iron sandwich complex, ( π-C₅H₅)Fe⁰(π-C ₆H₇), in the presence of oleylamine and oleylamine.HCl as surfactants and n-decane as a solvent. The presence of oleylamine.HCl is essential for the reproducible formation of crystalline iron cores.^ Reaction parameters such as temperature, surfactant concentration, effect of counterion, and organoiron reagent structure were investigated in order to obtain iron nanoparticles with uniform size and shape. The nanoparticles, which were characterized by …

Student's Objectives And Achievement Strategies For Laborataory Work, Taylor M. Owings

Open Access Theses

In this study, we look at students' objectives and strategies for completing their objectives for undergraduate labs. Students across two universities and three levels of chemistry were surveyed at the beginning of the semester in the fall of 2012 using an open ended survey to identify the goals students had for the course. The students responses were coded and used to create a survey that went out to the same courses at the end of the fall semester. Using data from the fall of 2012, the survey was modified and data was collected in the fall of 2013 at one …

Abcb11 Functions With B1 And B19 To Regulate Rootward Auxin Transport, Jesica Elyse Reemmer

Open Access Theses

Auxin transport is essential for the architecture and development of erect plants. In a network of transporters directing auxin flows, ATP-Binding Cassette (ABC) transporters are a ubiquitous family of proteins that actively transport important substrates, including auxins, across the plasma membrane. ABCB1 and ABCB19 have been shown to account for the majority of rootward auxin transport, but residual fluxes to the root tip in Arabidopsis b1b19 double mutants implies the involvement of at least one additional auxin transporter in this process. Of specific interest, the severe dwarfism seen in abcb1abcb19 is strikingly reminiscent of that seen in mutants defective in …

Correlating Molecular Architecture Of A Radical Polymer Based Copolymer With Its Electrical Transport Properties, Holly Chan

Open Access Theses

The design and synthesis of electrically-conductive macromolecules can lead to significant improvements in the performance of polymer-based energy conversion devices (e.g., thermoelectric devices). For these organic electronic devices, conjugated polymers have dominated the area of conductive polymers; however, these materials are usually synthesized using conditions that lead to poorly-defined polymers. Furthermore, in these increasingly-standard polymers, the charge transport ability of the polymer thin films is largely affected by the degree of crystallinity, which is a difficult property to control in a reproducible fashion. Therefore, we seek to explore a new class of amorphous, non-conjugated polymers containing a stable radical …

Separation Of On-Column Labeled Model Proteins With Packed Capillary Electrophoresis, Yingxu Hao

Open Access Theses

Protein drugs are increasingly developed in the pharmaceutical company. Under the regulation of FDA, high purity of therapeutic proteins needs to be maintained. Before putting those drugs in the market, fast and efficient method is in need to achieve homogeneity. Traditionally, polyacrylamide gel electrophoresis (PAGE), capillary electrophoresis (CE), and size-exclusion chromatography (SEC) are used for the purification process. These methods have the disadvantages of low time and cost efficiency, and this quality assurance process has become the bottleneck of production. In our group, sub-micron silica colloidal particles with polyacrylamide layer on the surface are packed inside capillaries to increase the …

Synthesis And Dna-Binding Studies With Two Stericallyfriendly Porphyrin Frameworks, Srijana Ghimire

Open Access Dissertations

Peripheral substituents on cationic porphyrins play a significant role during binding with DNA hosts. Possible applications of these systems in photodynamic therapy as well as in anti-bacterial and anti-cancer therapies motivate the binding studies. For characterizing DNA binding motifs different methods are useful including absorption, emission, and circular dichroism spectroscopies, as well as viscometry and X-ray crystallography. With the classic H₂ T₄ porphyrin, or 5,10,15,20-tetra(N-methylpyridinium-4-yl)porphyrin, the mode of binding varies with the base composition of the DNA host. The porphyrin binds adenine-thymine rich sequences externally whereas intercalation occurs in guanine-cytosine rich sequences. The McMillin group has made some …

Metal-Protein Interactions For Proteomics Applications, Keerthi B Jayasundera

Open Access Dissertations

In the quest of deciphering biological mechanisms, the understanding of proteins and their functions is a vital component. However the complexity of the proteome poses an immense challenge for analytical chemists to explore it comprehensively. Currently mass spectrometry is at the forefront of proteome analysis, providing great capabilities to couple with modern separation techniques for wide applications. One major objective of current proteomic technologies is to identify proteins of interest among high background, in particular from complex biological samples. A variety of techniques have been developed over the years to simplify protein samples, which are broadly classified as enrichment, high …

Leucine Zipper Interacts Promiscuously? Analysis Of Leucine Zipper Specificity In The C-Protein Family., Evelyn Rebecca Yambay-Tilman

Electronic Theses & Dissertations

Heterogeneous nuclear ribonucleoprotein C is ubiquitous in vertebrates, and exists as two alternatively spliced isoforms, hnRNP C1 and hnRNP C2 (hnRNP C). hnRNP C has been associated with pre-mRNA packaging, pre-mRNA, splicing, mRNA stability, internal ribosome entry site medicated translation, and has even been reported to be an integral component of the telomerase enzyme. Two proteins, hRaly and hRalyl, exhibit a great deal of primary sequence similarity with the C proteins and also conserve structural and functional motifs that have been identified in hnRNP C. A leucine zipper motif has been shown to be the oligomerization domain of hnRNP C …

Biodegradable Electrospun Nanofibers Coated With Platelet-Rich Plasma For Cell Adhesion And Proliferation, Luis Diaz-Gomez, Carmen Alvarez-Lorenzo, Angel Concheiro, Maite Silva, Fernando Dominguez, Faheem A. Sheikh, Travis Cantu, Raj Desai, Vanessa L. Garcia, Javier Macossay-Torres

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Chemistry)

Biodegradable electrospun poly(ε-caprolactone) (PCL) scaffolds were coated with platelet-rich plasma (PRP) to improve cell adhesion and proliferation. PRP was obtained from human buffy coat, and tested on human adipose-derived mesenchymal stem cells (MSC) to confirm cell proliferation and cytocompatibility. Then, PRP was adsorbed on the PCL scaffolds via lyophilization, which resulted in uniform sponge-like coating of 2.85 (s.d. 0.14) mg/mg. The scaffolds were evaluated regarding mechanical properties (Young’s modulus, tensile stress and tensile strain), sustained release of total protein and growth factors (PDGF-BB, TGF-β1 and VEGF), and hemocompatibility. MSC seeded on the PRP-PCL nanofibers showed an increased adhesion and proliferation …

Investigations Of Synthetic Models Of Mononuclear Nonheme Iron Dioxygenases, Michael Bittner

Dissertations (1934 -)

Ring cleaving dioxygenases, such as o-aminophenol dioxygenase (APDO) and extradiol catechol dioxygenases (CatD), play an important role in human metabolism and the degradation of aromatic pollutants, yet questions still remain concerning the enzymatic mechanisms. One area of the catalytic cycle that remains controversial is the geometric and electronic structure of the intermediate formed after O₂ binding to the Fe(II) centers. Synthetic model systems can be useful for studying enzyme active sites, as they are easier to modify and characterize than the enzymes themselves. However, synthetic models of APDOs have been relatively rare thus far. We prepared several monoiron(II) complexes …

Discovery Of An Allosteric Site On Furin, Contributing To Potent Inhibition: A Promising Therapeutic For The Anemia Of Chronic Inflammation, Andrew Jacob Gross

Theses and Dissertations

Release Date: October 2017

Anemia of chronic inflammation (ACI) is a condition that develops in a setting of chronic immune activation. ACI is characterized and triggered by inflammatory cytokines and the disruption of iron homeostasis. Hepcidin, a small peptide hormone, is the master regulator of iron homeostasis, and rapidly responds to iron supply and demand. Under conditions of chronic inflammation, hepcidin is elevated, and alters the way that iron is absorbed and disrupted throughout the body, resulting in disrupted iron homeostasis through inhibition of the iron exporter protein ferroportin. Anemia arises when insufficient erythropoietic activity combined with inadequate iron supply …

Bioinformatic Solutions To Complex Problems In Mass Spectrometry Based Analysis Of Biomolecules, Ryan M. Taylor

Theses and Dissertations

Biological research has benefitted greatly from the advent of omic methods. For many biomolecules, mass spectrometry (MS) methods are most widely employed due to the sensitivity which allows low quantities of sample and the speed which allows analysis of complex samples. Improvements in instrument and sample preparation techniques create opportunities for large scale experimentation. The complexity and volume of data produced by modern MS-omic instrumentation challenges biological interpretation, while the complexity of the instrumentation, sample noise, and complexity of data analysis present difficulties in maintaining and ensuring data quality, validity, and relevance. We present a corpus of tools which improves …

Fluorescence2d: Software For Accelerated Acquisition And Analysis Of Two-Dimensional Fluorescence Spectra, Evgenii L. Kovrigin

Chemistry Faculty Research and Publications

The Fluorescence2D is free software that allows analysis of two-dimensional fluorescence spectra obtained using the accelerated “triangular” acquisition schemes. The software is a combination of Python and MATLAB-based programs that perform conversion of the triangular data, display of the two-dimensional spectra, extraction of 1D slices at different wavelengths, and output in various graphic formats.

Electrochemistry And Spectroelectrochemistry Of 1,4-Dinitrobenzene In Acetonitrile And Room-Temperature Ionic Liquids: Ion-Pairing Effects In Mixed Solvents, Abderrahman Atifi, Michael D. Ryan

Chemistry Faculty Research and Publications

Room-temperature ionic liquids (RTILs) have been shown to have a significant effect on the redox potentials of compounds such as 1,4-dinitrobenzene (DNB), which can be reduced in two one-electron steps. The most noticeable effect is that the two one-electron waves in acetonitrile collapsed to a single two-electron wave in a RTIL such as butylmethyl imidazolium-BF₄ (BMImBF₄). In order to probe this effect over a wider range of mixed-molecular-solvent/RTIL solutions, the reduction process was studied using UV–vis spectroelectrochemistry. With the use of spectroelectrochemistry, it was possible to calculate readily the difference in E°’s between the first and …

A New Silver Electrode Based On The Composite Silver Sulfide/Attapulgite As Ionophore, Wen-Zhuo Li, Ding-Jia Xu, Jun Wang, Jian-Long Wang

Journal of Electrochemistry

A novel silver ion selective electrode with its ionophore being a kind of organic/inorganic composite composed of silver sulfide and attapulgite has been prepared. Attapulgite is a type of natural inorganic polymer which has some properties similar to zeolite, such as a higher specific surface area and plenty of intercrystalline cavities. In this work, the silver ions were firstly adosrbed in the micropores of the attapulgite, then thioacetamidetiny was selected to mix with the prepared silver ions/ attapulgite composite. Owning to the existence of sulfur atoms in the structure of thioacetamide molecules, thioacetamide molecules can react with the silver ions/attapulgite …

Key Factors And Techno-Economic Analyses Of Manganese Electrolysis Process, Gui-Mei Han, Fu-Yuan Xu, Lin-Hua Jiang, Zhi-Gang Dan, Xiao-Juan Gao, Ning Duan

Journal of Electrochemistry

This paper first studied the key factors affecting the initial manganese electrolysis process, including concentration of Mn²⁺, electrolysis time, overpotential, and then optimized these processing parameters with the chronocoulometry method under a three-electrode system. The results showed that, during the initial manganese electrolysis process, hydrogen evolution occurred more significantly on the stainless steel surface. As electrolysis process continued, manganese covered the stainless steel surface gradually, and hydrogen evolution reaction restrained which all contributed to the higher current efficiency. Besides, the limiting current density appeared at high overpotential region, and the reaction was controlled by diffusion process. In 0.02 …

Surface Enhanced Raman Spectroscopic Studies Of Pyridine Adsorbed On Ti/Au@Sio2 Film Electrode, Min-Min Xu, Ke Liu, Qing-Hua Guo, Jian-Lin Yao

Journal of Electrochemistry

This study was performed based on shell-isolated nanoparticles-enhanced Raman spectroscopy (SHINERS) technology. The Au@SiO₂ nanoparticles were prepared and characterized by TEM and cyclic voltammetry. It was shown that the shell of SiO₂ was compact. The high quality signal measured by surface enhanced Raman spectroscopy (SERS) was obtained from the adsorbed pyridine on Ti/Au@SiO₂ electrode. The origin of the SERS signals was further confirmed by testing Pt and Ni electrodes. In addition, potential dependent adsorption behavior was investigated. It was found that pyridine was adsorbed parallel on the surface from -0.1 V to -0.6 V, and converted to …