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Understanding The Influence Of Interfacial Chemistry In Core, Core/Shell And Core/Shell/Shell Quantum Dots On Their Fluorescence Properties, Omondi Bernard Omogo

Graduate Theses and Dissertations

Colloidal semiconductor nanocrystals (quantum dots) have received a great deal of attention due to their superior size tunable properties and promising applications in many areas. Some of the most practical areas of their applications include light emitting diodes (LED), photovoltaic and biological studies. Synthetic methods of these crystals is becoming more established with new strategies being reported every now and then. However, quantitative studies connecting the processes at the interface, namely core-ligand, core-shell and shell-shells, to the overall quantum dots fluorescence properties are not well understood. Specifically for cores, relating surface-atoms interactions, solvents, ligands nature, density and functional groups on …

Redox Active Motifs In Selenoproteins, Fei Li, Yuliya Pepelyayeva, Elias S. J. Arner, Craig A. Bayse, Sharon Rozovsky

Chemistry & Biochemistry Faculty Publications

Selenoproteins use the rare amino acid selenocysteine (Sec) to act as the first line of defense against oxidants, which are linked to aging, cancer, and neurodegenerative diseases. Many selenoproteins are oxidoreductases in which the reactive Sec is connected to a neighboring Cys and able to form a ring. These Sec-containing redox motifs govern much of the reactivity of selenoproteins. To study their fundamental properties, we have used Se-77 NMR spectroscopy in concert with theoretical calculations to determine the conformational preferences and mobility of representative motifs. This use of Se-77 as a probe enables the direct recording of the properties of …

Structure And Multi-Center Bonding: From Atomic Clusters To Solid Phase Materials, Timur R. Galeev

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The work presented in this dissertation has been focused on structure, stability, and chemical bonding of atomic clusters and solid-state compounds. The common thread was development of theoretical models and methods capable of interpreting bonding and hence, structures of these species. A major part of this work presents joint experimental and theoretical studies of a large series of doped boron clusters. The dissertation introduces a new theoretical tool for interpretation of bonding of solid phase materials in chemically intuitive terms of localized and multi-center bonds. Understanding how interactions between atoms in sub-nano clusters and solid-state compounds determine their structures, physical …

Purple Urine Bag Syndrome: Regulation Of Pyrimidine Enzymes, Ashley N. Broadway

Honors Theses

Purple Urine Bag Syndrome, PUBS, is a unique condition that shows an interesting discoloration of the urine from women who have a chronic catheter. This study focused on the regulation of enzyme activities to determine the effects that may create an environment where PUBS is seen in patients with catheters. In this study, the reductive pyrimidine pathway was used to read out the bacteria Pseudomonas aeruginosa ATCC 15692. This microorganism expresses a pathway that synthesizes indoxyl from tryptophan. The bacteria strains were grown using various carbon and nitrogen sources. Concentrations of acetonitrile at 2 mM and 10 mM, concentrations of …

Biogeochemistry Of Trace Elements In The Mixing Zone Of The Mississippi And Atchafalaya Rivers And Chemical Distributions As Affected By The Deepwater Horizon Blowout, Dongjoo Joung

Dissertations

Selected trace elements (TEs), dissolved organic carbon, and nutrients were studied in Louisiana Shelf waters including the Mississippi (MR) and Atchafalaya (AR) River plumes during periods of high, intermediate, and low river discharges. Seasonal variations in TEs were observed at low salinity, reflecting seasonal changes in the river water endmembers. Shelf surface water dissolved Mo, Cs, U, Ni, and Cu showed conservative behavior with minor scattering in some high salinity waters. Based on associated mixing experiments, nutrient and chlorophyll distributions, as well as surface-bottom concentration contrasts, the non-conservative behavior of TEs was variously related to colloidal flocculation (Fe, Cr), biological …

Metal Stopping Reagents Facilitate Discontinuous Activity Assays Of The De Novo Purine Biosynthesis Enzyme Pure, Kelly L. Sullivan, Loredana C. Huma, Elwood Mullins, Michael E. Johnson, T. Joseph Kappock

Department of Biochemistry Faculty Publications

The conversion of 5-aminoimidazole ribonucleotide (AIR) to 4-carboxy-AIR (CAIR) represents an unusual divergence in purine biosynthesis: microbes and nonmetazoan eukaryotes use class I PurEs while animals use class II PurEs. Class I PurEs are therefore a potential antimicrobial target; however, no enzyme activity assay is suitable for high throughput screening (HTS). Here we report a simple chemical quench that fixes the PurE substrate/product ratio for 24 h, as assessed by the Bratton-Marshall assay (BMA) for diazotizable amines. The ZnSO₄ stopping reagent is proposed to chelate CAIR, enabling delayed analysis of this acid-labile product by BMA or other HTS methods

A Screening Platform For Identification Of Compounds That Inhibit Protein Synthesis In Pseudomonas Aeruginosa, Yanmei Hu

Theses and Dissertations - UTB/UTPA

Pseudomonas aeruginosa is a Gram-negative pathogenic bacteria and a common cause of nosocomial infections. This pathogen has recently garnered attention due to its pan-resistance. We have developed a poly(U) mRNA-directed aminoacylation/translation (A/T) protein synthesis system from P. aeruginosa. The concentration of each component of the system has been arrived at through multiple rounds of optimization. Poly-phenylalanine synthesis in the system was monitored using scintillation proximity assays (SPA). This system has been used to screen two natural compound libraries (>1100) and a number of the compounds that inhibit greater than 50% of the activity of the system have been identified. …

Monitoring Citrus Nutrition In The Rio Grande Valley For Fertilizer Recommendations, Iram Lopez

Theses and Dissertations - UTB/UTPA

Soil fertility and plant nutrition is crucial for a better yield and consistent harvest in the Rio Grande Valley for local farmers growing citrus trees. A field of oranges and a field of grapefruits were monitored and nutrition deficiencies were noticed that played an important role during fruit set. Soil samples that were taken throughout the year were analyzed via a carbon dioxide extraction method that mimics the way plants naturally take up nutrients or extract nutrients from every soil type. Macronutrients such as the N, P, K, Na, Ca, Mg and some of the micronutrients (Zn, Fe, Mn, and …

The Impact Of Surface Ligands And Synthesis Method On The Toxicity Of Glutathione-Coated Gold Nanoparticles, Bryan Harper, Federico Sinche, Meenambika Gowrishankar, Grant Marquart, Marilyn R. Mackiewicz, Stacey L. Harper

Chemistry Faculty Publications and Presentations

Gold nanoparticles (AuNPs) are increasingly used in biomedical applications, hence understanding the processes that affect their biocompatibility and stability are of significant interest. In this study, we assessed the stability of peptide-capped AuNPs and used the embryonic zebrafish (Danio rerio) as a vertebrate system to investigate the impact of synthesis method and purity on their biocompatibility. Using glutathione (GSH) as a stabilizer, Au-GSH nanoparticles with identical core sizes were terminally modified with Tryptophan (Trp), Histidine (His) or Methionine (Met) amino acids and purified by either dialysis or ultracentrifugation. Au-GSH-(Trp)2 purified by dialysis elicited significant morbidity and mortality at …

Initial Characterization Of A Conserved Active Site Residue For The Cdc34 Ubiquitin Conjugating Enzyme, Arvin Akoopie

Honors College Theses

Ubiquitin-conjugating enzymes (E2s) covalently modify protein substrates with ubiquitins. The active site cysteine residues on E2s are essential for catalyzing the transfer of ubiquitin from the E2 active site onto the protein substrate, however there is a limited amount of information available concerning additional active site residues for E2s that may also participate in catalysis. Cdc34 is an essential E2 that has merited the lion’s share of attention for biochemical analysis of the E2 family. Previous phylogenetic analysis of Cdc34 amino acid sequences has identified an invariably conserved histidine residue close to the active site cysteine in the primary structure, …

A Fluidic Fiber Platform Modified For The Selective Extraction And On Fiber Fluorescence Detection Of Proteins And Nucleic Acids, Natasha Khan

All Theses

Solid phase extraction has become a popular tool for analytical method development as a sample preparation technique. Solid phase sorbents can generally extract analytes based on polarity or selectively based on highly specific interactions between the analyte and an immobilized surface molecule. Biomolecular recognition based solid phases utilize antibodies, nucleic acids, and proteins as a secondary affinity layer on a solid phase support for selective analyte extractions and have been used for sample preparation, purification, separations, bioassays, and molecular diagnostics. Polymer supports for solid phase extraction are desirable for their low cost, abundance, chemical inertness, and pH stability. This thesis …

A Facile Route To Tailoring Peptide-Stabilized Gold Nanoparticles Using Glutathione As A Synthon, Rosina Ho Wu, Tan P. Nguyen, Grant W. Marquart, Thomas J. Miesen, Theresa Mau, Marilyn R. Mackiewicz

Chemistry Faculty Publications and Presentations

The preparation of gold nanoparticles (AuNPs) of high purity and stability remains a major challenge for biological applications. This paper reports a simple synthetic strategy to prepare water-soluble peptide-stabilized AuNPs. Reduced glutathione, a natural tripeptide, was used as a synthon for the growth of two peptide chains directly on the AuNP surface. Both nonpolar (tryptophan and methionine) and polar basic (histidine and dansylated arginine) amino acids were conjugated to the GSH-capped AuNPs. Ultracentrifugation concentrators with polyethersulfone (PES) membranes were used to purify precursor materials in each stage of the multi-step synthesis to minimize side reactions. Thin layer chromatography, transmission electron …

Miniaturization Of Chemical Analysis Tools: Micro-Solid Phase Extraction Tips For Protein Extractions And Development Of A Miniaturized Glow Discharge Source For Elemental Analysis, Benjamin Manard

All Dissertations

An increased interest has been placed on the miniaturization of chemical processes. Focus is placed on rapid chemical analysis, decreased operation cost, minimal generation of chemical waste, and reduced sample size. Presented here is an approached the goal of 'miniaturization' through two distinct areas of analytical chemistry: 1) employing capillary-channeled polymer (C-CP) fibers as a stationary phase in micro-SPE (solid phase extraction) tips for the extraction of proteins from buffered solutions (i.e. biofluids) with analysis by mass spectrometry (MS) and 2) the development of the liquid sampling-atmospheric pressure glow discharge (LS-APGD) as an excitation source for elemental analysis. Determination of …

Building Chemistry One Atom At A Time: An Investigation Of The Effects Of Two Curricula In Students' Understanding Of Covalent Bonding And Atomic Size, Barbara Bull

All Dissertations

Chemists have to rely on models to aid in the explanation of phenomena they experience. Instruction of atomic theory has been used as the introduction and primary model for many concepts in chemistry. Therefore, it is important for students to have a robust understanding of the different atomic models, their relationships and their limitations. Previous research has shown that students have alternative conceptions concerning their interpretation of atomic models, but there is less exploration into how students apply their understanding of atomic structure to other chemical concepts. Therefore, this research concentrated on the development of three Model Eliciting Activities to …

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.

The Dimerization Domain In Dape Enzymes Is Required For Catalysis, Boguslaw Nocek, Anna Starus, Magdalena Makowska-Grzyska, Blanca Gutierrez, Stephen Sanchez, Robert Jedrzejczak, Jamey C. Mack, Kenneth W. Olsen, Andrzej Joachimiak, Richard C. Holz

Chemistry: Faculty Publications and Other Works

The emergence of antibiotic-resistant bacterial strains underscores the importance of identifying new drug targets and developing new antimicrobial compounds. Lysine and meso-diaminopimelic acid are essential for protein production and bacterial peptidoglycan cell wall remodeling and are synthesized in bacteria by enzymes encoded within dap operon. Thereforedap enzymes may serve as excellent targets for developing a new class of antimicrobial agents. The dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE) convertsN-succinyl-L,L-diaminopimelic acid to L,L-diaminopimelic acid and succinate. The enzyme is composed of catalytic and dimerization domains, and belongs to the M20 peptidase family. To understand the specific role …

Porphyrin Cross-Linkers For Generating Soluble Molecularly Imprinted Polymers From Polyethyleneimine, Mohammed R. Elshaer

Seton Hall University Dissertations and Theses (ETDs)

Molecular recognition is vital to many biochemical processes and is at the heart of promising bio-medically related technologies. Molecular imprinting has a long-standing history as a successful method for mimicking the molecular recognition phenomena exhibited by nature, whereby artificial receptors are prepared for a given target molecule based on synthetic polymers. The molecularly imprinted polymer (MIP) contains a three dimensional network with a memorized cavity specific to the shape and functionality of the templated target molecule. The utility of traditional MIPs has been limited due to an inherent lack of solubility. We have worked toward developing a system that allows …

A Synthesis Approach Of Trp-Like Primary Amine Peptoid Side Chains Used In Cyclic Beta-Hairpin - Like Scaffolds, Josanne-Dee Woodroffe

USF Tampa Graduate Theses and Dissertations

In recent studies it was reported that the D-amino acid containing peptide HYD1 was used in the treatment of necrotic cell death in multiple myeloma cell lines and showed promising biological activity and in vivo activity. It was meaningful to explore strategies for increasing the therapeutic efficacy of HYD1, a linear peptide. These efforts led to the development of MT1-101 (cyclized peptidomimetics), a lead compound that showed increased in vitro activity and in vivo activity. MTI-101 was found to bind the cell adhesion molecule CD44 and induce programmed necrosis in myeloma cell lines. It was important to improve on the …

Homochiral Metal-Organic Materials: Design, Synthetic And Enantioseletive Separation, Shi-Yuan Zhang

USF Tampa Graduate Theses and Dissertations

Owing to the growing demand for enantiopurity in biological and chemical processes, tremendous efforts have been devoted to the synthesis of homochiral metal-organic materials (MOMs) because of their potential applications in chiral separation and asymmetric catalysis. In this dissertation, the synthetic strategies for homochiral MOMs are discussed keeping the focus on their applications. Two distinct approaches have been taken to synthesize chiral structures with different topologies and accessible cavities. The chiral MOMs have been utilized in enantioselective separation of racemates.

Chiral variants of the prototypal metal-organic framework MOF-5, δ-CMOF-5 and [lambda]-CMOF-5, have been synthesized by preparing MOF-5 in the presence …

Interfacial Rheology Of Bacterial Biofilms At Air/Water And Oil/Water Interfaces, Patrick Rühs, R. Inglis, Peter Fischer

Biology Department Faculty Works

No abstract provided.

Interpretation Of Chemical Environments By Rna And The Implications To The Origins Of Life, Brian Larson

Dissertations and Theses

We describe the initial realization of behavior in the biosphere, which we term behavioral chemistry. If molecules are complex enough to attain a stochastic element to their structural conformation in such a way as to radically affect their function in a biological (evolvable) setting, then they have the capacity to behave. This circumstance is described here as behavioral chemistry, unique in its definition from the colloquial chemical behavior. This transition between chemical behavior and behavioral chemistry need be explicit when discussing the root cause of behavior, which itself lies squarely at the origins of life and is the foundation of …

Implementation And Application Of The Mmff94 Force Field, Hongbo Zhu

Department of Chemistry: Dissertations, Theses, and Student Research

MMFF94 is implemented for molecular mechanics calculation in the quantum chemistry polarizable force field program (QuanPol). As a general force field for organic molecules, the availability of MMFF94 expends the capability of the QuanPol program. The MMFF94 force field atom type determination and parameter matching methods are established and corresponding program routines are written in the FORTRAN language. In this implementation, the MMFF94 atom types can be determined automatically from the connectivity of the input atoms with no or minimum information of formal charges. This implementation of MMFF94 is validated using the 761 standard tests, thus is a complete implementation. …

Electro-Catalytic Oxidation Of Hydrogen Peroxide On Au/ L-Methionine /Gc Electrode, Jian-Feng Fan, Xue-Mei Luo, Jing Li, Lou-Zhen Fan

Journal of Electrochemistry

The modified electrodes have been fabricated by generation of Au nanoparticle chains, which was produced by reaction between HAuCl4 and sodium citrate without any additional capping agents or surfactants. The self-assembled Au nanoparticles were attached to the surface of glassy carbon electrode (GCE) layer by layer, using L-methionine (L-Met), thiourea (TU), allyl thiourea (ATU) and polyvinylpyrrolidone (PVP) as a crosslinking agent, respectively. The experimental results showed that the electrochemical performance of the different modified electrodes varied in [Fe(CN)₆]^3-/4- solution. The Au/L-Met/GCE exhibited an excellent electrochemical property, which is superior to other modified electrodes. In addition, the catalysis …

Polyethylene Glycol Containing Rompolymers For The Modification Of Neuro-Protective Hemoglobin, Andrea L. Mccollum

Honors College Theses

Polyethylene glycol (PEG) has shown the ability to improve compatibility when used in combination with cell-free hemoglobin in the treatment of traumatic brain injuries. It has been demonstrated that the covalently bonded PEG increases the hydrodynamic radius of the hemoglobin and hence generates a physical barrier while slowing down the oxygen delivery of the strongly oxidative hemoglobin. In this context, I have been working on the development of synthetic pathways to incorporate PEG into monomers and polymers through both direct modification of (7-oxa)norbornene derivatives and post polymerization modification. Starting from the (7-oxa)norbornene anhydride derivatives, we have developed pathways to cationic …

Antimicrobial And Antiinsectan Phenolic Metabolites Of Dalea Searlsiae, Gil Belofsky, Mario Aronica, Eric Foss, Jane Diamond, Felipe Santana, Jacob Darley, Patrick F. Dowd, Christina M. Coleman, Daneel Ferreira

All Faculty Scholarship for the College of the Sciences

Continued interest in the chemistry of Dalea spp. led to investigation of Dalea searlsiae, a plant native to areas of the western United States. Methanol extractions of D. searlsiae roots and subsequent chromatographic fractionation afforded the new prenylated and geranylated flavanones malheurans A–D (1–4) and known flavanones (5 and 6). Known rotenoids (7 and 8) and isoflavones (9 and 10) were isolated from aerial portions. Structure determination of pure compounds was accomplished primarily by extensive 1D- and 2D-NMR spectroscopy. The absolute configurations of compounds 1–5, 7 …

Effect Of Sulfuric Acid Exposure On Common Mineral Dust Particles, Miguel D. Mendoza

Celebrating Scholarship & Creativity Day (2011-2017)

Mineral dust has a large effect on cloud formation and ultimately the climate. Several studies have shown the addition of acid to these mineral dust particles decreases their ability to nucleate ice. This study explores what chemistry occurs between common components of mineral dust particles and sulfuric acid. Hematite (Fe₂O₃), calcite (CaCO₃), and quartz (SiO₂) were exposed to sulfuric acid, and then analyzed using a combination of Attenuated Total Reflectance-FTIR, Diffuse Reflectance-FTIR Spectroscopy, X-Ray Diffraction, and Inductively Coupled Plasma Atomic Emission Spectroscopy to identify functional groups, mineral species, and aqueous phase elements. …

The Fenzian Unit: Applications To Physical Therapy And Beyond, Jeshua Paul Spadino Mr.

Senior Honors Theses

The field of physical therapy includes many different treatment options in the form of exercises and modalities. The development of a low electrical stimulation signal through the Fenzian unit has provided a new outlook on healing. This device gives information to and receives information from the central nervous system (CNS) through electro-biofeedback and is separated into its own category of modalities. The device can be used to treat a wide range of ailments, all with no adverse effects. This makes it a promising tool in the medical field. It is currently being validated as an authentic medical device through clinical …

Synthesis Of A Soluble Thiopheneanthrone Organic Semiconductor: Thiopheneanthrone-1-Thioglycoliccarboxylic Acid, Denise M. Page

Senior Honors Theses

Organic semiconductors are currently being researched for various uses, both electronic and biologic. They are less expensive than current inorganic semiconductors and do not require doping. They are useful in many areas including thin film transistors, photovoltaic cells, and Light Emitting Diodes (LED). However, synthesizing soluble organic semiconductors has been difficult. As a result, this study undertakes the synthesis of a specific organic semiconductor aiming at increased solubility following an adapted literature protocol. Tests for solubility, fluorescence, and conductivity potential will be used to assess the potential of this molecule as a semiconductor. Synthesis of anthraquinone-1,8-bisthioglycoliccarboxylic acid as an intermediate …

Computational Study Of The Nitric Oxide Autoxidation Mechanism Using Quantum Chemistry Methods, Yazen Abusad

Collection of Engaged Learning

Nitric oxide (NO) is a critical cell-signaling messenger in the immune, cardiovascular, and nervous systems. It is linked to several diseases, and due to its high reactivity, and toxicity as a free radical, NO possesses a controversial effect on cell viability. The S-nitrosylation of protein thiol groups is a key mechanism in NO redox signal transduction, and lends a mechanistic basis for NO as a cell regulator. Numerous experiments have shown that the rate-limiting step of S-nitrosylation is NO autoxidation, independent of thiol concentration. Due to the transient nature, and structural variety of reactive nitrogen species, very little is known …