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Polymerization Of Blocked Isocyanate Functional Polymer Surfaces And Post-Polymerization Modification By Thiol-Isocyanate Reactions, Chase A. Tretbar

Honors Theses

Direct polymerization of isocyanate-functional monomers has been achieved with controlled radical polymerizations (CRP) for precisely engineered modification platforms with highly reactive side chains. However, despite the success of these strategies, the inherent reactivity of isocyanates still leads to adverse side reactions, such as hydrolysis, that are difficult to suppress. Phenol, lactam, and oxime-based blocking agents have been used to limit the reactivity of isocyanates in applications such as multicomponent urethane coating systems. The reactivity of these blocked isocyanates can be restored by thermal deprotection of the blocking agent to achieve the desired reactions. In this work, we use blocked isocyanate-functional …

Computational Prediction And Rational Design Of Novel Clusters, Nanoparticles, And Solid State Materials, Alexander S. Ivanov

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The prediction of structure at the atomic level is one of the most fundamental challenges in materials science. Indeed, the structure is arguably the most important piece of information about a material, as it determines pretty much all properties of a material. Knowing the structure, one can analyze a large number of properties of a material, even before it is synthesized – the crucial importance of structure prediction for computational molecular design. This dissertation describes the technique of reliable theoretical predictions and presents the results on the successfully predicted unusual clusters, nanoparticles and solid state materials. The major part of …

Synthesis Of Fluorogenic Probes For Studying Biomass Degradation And Synthesis Of New Antifungal Aminoglycosides, Qian Zhang

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

For the first project, a library of fifteen commercially purchased and synthetic fluorogenic probes were employed for the investigation of biomass degradation using extract of white-rot fungi. These discoveries prove that it is possible to employ fungi for selective degradation or release of hemicelluloses from biomass. This work is supported by Sun Grant Western Regional Center/DOT "Bioprospecting for Enzymes to Break Lignin-Hemicellulose Bond" ($300,000,09/01/2011-08/31/2013)

The second project is focused on synthesizing new aminoglycoside analogs and exploring the potential to revive traditional antibacterial kanamycin as new type of antifungal agents. Although aminoglycosides antibiotics are mainly used as antibacterial agents, this project …

Relative Toxicity Of Select Dehydropyrrolizidine Alkaloids And Evaluation Of A Heterozygous P53 Knockout Mouse Model For Dehydropyrrolizidine Alkaloid Induced Carcinogenesis, Ammon W. Brown

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Dehydropyrrolizidine alkaloids (DHPAs) are toxins produced by approximately 3% of the world’s flowering plants that can be present naturally or as contaminants in animal feed and the human food supply. Many of these compounds have been determined to cause cancer in animals and probably also cause cancer in humans. Due to the difficulty in obtaining sufficient amounts of pure DHPAs most toxicity research has been done via injection of a small amount into the abdomen of a rodent, although natural exposure is exclusively oral. For the same reason, cancer research is limited to a handful of the hundreds of known …

Novel [3,3]- And [1,3]- Rearrangements Of Azole-Derived N,X-Ketene Acetals, Sefat A. Alwarsh

Graduate Theses and Dissertations

The formation of carbon-carbon bonds in organic chemistry is fundamentally important. One of the major reactions that chemists have widely investigated is the Claisen rearrangement. Based on the fundamental features of this rearrangement, chemists exploited the capability of the transformation and invented their own variations of Claisen-type rearrangements. Our goal in this project is to develop a novel variation of the Claisen rearrangement using azole compounds, which are common heteroaromatic ring systems that are present extensively in the biomedically important natural products. We propose here novel methodologies of preparing 2-substitution azole derivatives using aza-based Claisen rearrangement, N,X-ketene acetals that requires …

Applications Of Pure And Recycled Polymeric Micronanofiber For The Removal Of Oil Spills, Afra Gharib Khamis Al-Blooshi Al-Blooshi

Theses

Cleaning oil spills is a universal concern due to its environmental impact. The aim of this study is to study the effectiveness and applications of pure and recycled polymers in clean-up and the recovery of crude oil from oil spills. In this study, micro-nanofibers of analytical-grade and commercial polystyrene samples were prepared by electrospinning technique. Fiber size distribution was shown to vary with the electrospinning parameters and type of polymer. Fibrous sorbents prepare hereafter were investigated for their efficiency in removing oil spills. Results showed a variation in the sorption capacities of the fibers to various types of crude oils …

Adsorption Of Dyes On Activated Carbon From Agricultural Wastes, Maliha Parvin

Theses

Adsorption of dyes as a remediation technique for dye-loaded wastewater remains an area of interest. On the one hand, adsorption using bio-derived, renewable sorbent materials can be seen as environmentally friendly, on the other hand adsorption can provide us with a trouble-free, commercially cheap operation. The main objective of this thesis is adsorption of the dyes Crystal Violet (CV) and Nile Blue (NB) on activated carbon derived from date palm leaf wastes. For this purpose, activated carbon was prepared via chemical treatment of palm leaf wastes with sulfuric acid (H2SO4), phosphoric acid (H3PO4), and nitric acid (HNO3), respectively, with subsequent …

Applications Of Pure And Recycled Polymeric Micro-Nanofiber For The Removal Of Oil Spills., Afra Gharib Khamis Al Blooshi

Theses

Cleaning oil spills is a universal concern due to its environmental impact. The aim of this study is to study the effectiveness and applications of pure and recycled polymers in clean-up and the recovery of crude oil from oil spills. In this study, micro-nanofibres of analytical-grade and commercial polystyrene samples were prepared by electrospinning technique. Fiber size distribution was shown to vary with the electrospinning parameters and type of polymer. Fibrous sorbents prepared hereafter were investigated for their efficiency in removing oil spill. Results showed variation in the sorption capacities of the fibers to various types of crude oils with …

Heterogeneous Dynamics In Dna Site Discrimination By The Structurally Homologous Dna-Binding Domains Of Ets-Family Transcription Factors, Gaofei He, Ana Tolic, James Bashkin, Gregory Poon

Chemistry & Biochemistry Faculty Works

The ETS family of transcription factors exemplifies current uncertainty in how eukaryotic genetic regulators with overlapping DNA sequence preferences achieve target site specificity. PU.1 and Ets-1 represent archetypes for studying site discrimination by ETS proteins because their DNA-binding domains are the most divergent in sequence, yet they share remarkably superimposable DNA-bound structures. To gain insight into the contrasting thermodynamics and kinetics of DNA recognition by these two proteins, we investigated the structure and dynamics of site discrimination by their DNA-binding domains. Electrophoretic mobilities of complexes formed by the two homologs with circularly permuted binding sites showed significant dynamic differences only …

Whole Genome Comparison Of A Large Collection Of Mycobacteriophages Reveals A Continuum Of Phage Genetic Diversity, Welkin H. Pope, Charles A. Bowman, Daniel A. Russell, Deborah Jacobs-Sera, David J. Asai, Steven G. Cresawn, William R. Jacobs Jr, Roger W. Hendrix, Jeffrey G. Lawrence, Graham F. Hatfull, Dr. Kathleen Cornely

Chemistry & Biochemistry Faculty Publications

The bacteriophage population is large, dynamic, ancient, and genetically diverse. Limited genomic information shows that phage genomes are mosaic, and the genetic architecture of phage populations remains ill-defined. To understand the population structure of phages infecting a single host strain, we isolated, sequenced, and compared 627 phages of Mycobacterium smegmatis. Their genetic diversity is considerable, and there are 28 distinct genomic types (clusters) with related nucleotide sequences. However, amino acid sequence comparisons show pervasive genomic mosaicism, and quantification of inter-cluster and intra-cluster relatedness reveals a continuum of genetic diversity, albeit with uneven representation of different phages. Furthermore, rarefaction analysis shows …

Unraveling Structures Of Protection Ligands On Gold Nanoparticle Au68(Sh)32, Wen Wu Xu, Yi Gao, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

New low-energy atomic structures of the thiolate-protected gold nanoparticle Au₆₈(SH)₃₂ are uncovered, where the atomic positions of the Au atoms are taken from the recent single-particle transmission electron microscopy measurement by Kornberg and co-workers, whereas the pattern of thiolate ligands on the gold core is attained on the basis of the generic formulation (or rule) of the “divide and protect” concept. Four distinct low-energy isomers, Iso1 to Iso4, whose structures all satisfy the generic formulation, are predicted. Density-functional theory optimization indicates that the four isomers are all lower in energy by 3 to 4 eV than the …

Toward The Measurement Of Biodistribution Of 18F-Labeled Industrial Chemicals With Positron Emission Tomography (Pet), Katelyenn S. Mccauley

Department of Chemistry: Dissertations, Theses, and Student Research

Plasticizers are added to polymeric materials to increase flexibility and durability, thus they constitute a common, and widely used class of industrial chemicals. Plasticizers have been suspected of a number of adverse health effects including the interference with the endocrine system.¹ These substances have the tendency to migrate to the surfaces of materials, where they can be absorbed, ingested, or inhaled. ⁵ The iniquitousness of plasticizers and the daily contact with polymeric materials has given rise to concern about the toxicity and health effects of these substances. Many long-term and excessive-dose studies have been conducted on many of these …

The 8-Silyloxyquinoline Scaffold As A Versatile Platform For The Sensitive Detection Of Aqueous Fluoride, Xinqi Zhou

Department of Chemistry: Dissertations, Theses, and Student Research

As one of the most essential elements in nature, fluoride has been well known and extensively studied since the 16^th century. Since then the two-edged nature of fluoride in biological systems has been well described. Specifically, moderate fluoride exposure can aid in tooth and bone development, while fluoride overexposure results in the depilating disease known as fluorosis. Because of the side effects upon overexposure of fluoride, there is a need to develop fast and straight forward methods to sensitively and selectively detect and quantify fluoride concentration in drinking water. With this goal in mind and by taking advantage of …

A Maltose-Binding Protein Fusion Construct Yields A Robust Crystallography Platform For Mcl1, Matthew C. Clifton, David M. Dranow, Alison Leed, Ben Fulroth, James W. Fairman, Jan Abendroth, Kateri A. Atkins, Ellen Wallace, Dazhong Fan, Guoping Xu, Z. J. Ni, Douglas S. Daniels, John Van Drie, Guo Wei, Alex B. Burgin, Todd R. Golub, Brian K. Hubbard, Michael H. Serrano-Wu

Chemistry Faculty Publications

Crystallization of a maltose-binding protein MCL1 fusion has yielded a robust crystallography platform that generated the first apo MCL1 crystal structure, as well as five ligand-bound structures. The ability to obtain fragment-bound structures advances structure-based drug design efforts that, despite considerable effort, had previously been intractable by crystallography. In the ligand-independent crystal form we identify inhibitor binding modes not observed in earlier crystallographic systems. This MBP-MCL1 construct dramatically improves the structural understanding of well-validated MCL1 ligands, and will likely catalyze the structure-based optimization of high affinity MCL1 inhibitors.

Synthesis Of 1, 2 Amino Alcohols Through Arbuzov Method, Brianne Gibson

Celebrating Scholarship & Creativity Day (2011-2017)

This research involves the synthesis of one diethyl amino-dihydroxy butyl phosphonate which hold characteristics shown to serve as an anti-fungal and anti-microbial agent. The first step of this research involves epoxidation of the phosphonate-containing olefin made using the Arbuzov procedure with crotonaldehyde. The second step synthesizes an oxazolidone using benzyl isocyanate to open the epoxide and cyclize the compound. Hydrolysis of the oxazolidone is performed for the production of the 1, 2 amino-alcohols in the third stage. This step synthesizes the amino-phosphonates. The first and second steps have been completed. Upon successful retrieval of the oxazolidones, the alcohol can be …

On The Mechanism Of Rna Phosphodiester Backbone Cleavage In The Absence Of Solvent, Christian Riml, Heidelinde Glasner, M T. Rodgers, Ronald Micura, Kathrin Breuker

Chemistry Faculty Research Publications

Ribonucleic acid (RNA) modifications play an important role in the regulation of gene expression and the development of RNA-based therapeutics, but their identification, localization and relative quantitation by conventional biochemical methods can be quite challenging. As a promising alternative, mass spectrometry (MS) based approaches that involve RNA dissociation in ‘top-down’ strategies are currently being developed. For this purpose, it is essential to understand the dissociation mechanisms of unmodified and posttranscriptionally or synthetically modified RNA. Here, we have studied the effect of select nucleobase, ribose and backbone modifications on phosphodiester bond cleavage in collisionally activated dissociation (CAD) of positively and negatively …

Synthesis Of Β-Triphosphotriester Pronucleotides, Yousef Beni, Chandravanu Dash, Keykavous Parang

Chemistry Faculty Research

Dinucleoside phosphorochloridite was synthesized from phosphorus trichloride and three nucleoside analogs, 3′-fluoro-2′,3′-dideoxythymidine (FLT), 2′,3′-dideoxy-5-fluoro-3′-thiacytidine (FTC), and 2′,3′-dideoxy-3′-thiacytidine (3TC), in a multistep synthesis. Polymer-bound N-Boc p-acetoxybenzyl 5′-O-2′-deoxythymidine was reacted with dinucleoside phosphorochloridite in the presence of 2,6-lutidine, followed by the reaction with dodecyl alcohol and 5-(ethylthio)-1H-tetrazole, oxidation with tert-butyl hydroperoxide, and acidic cleavage, respectively, to afford the β-triphosphotriester derivatives containing three different nucleosides.

Novel Photodynamic Therapy Agents: Biochemical Analysis, Eboni D. Pullen

Honors College Theses

Bioinorganic photochemistry is a rapidly advancing research area in the field of bioinorganic chemistry. This project seeks to build upon the growing field by synthesizing and analyzing new photodynamic therapy (PDT) agents. There are three major generations of PDT agents. The first generation consists of chemically modified natural hematoporphyrins, which are not of great interest in the phototherapeutic field due to their low distinguishability between tumor cells and healthy cells, and extended skin photosensitivity in patients. The second generation consists of organic dyes, aromatic hydrocarbons, polypyrolics complexes, and semi-conductors, but is also not of much interest due to the same …

The Synthesis And Biological Activity Of Iron Binding Motifs, Rachel Burke

Honors College Theses

Iron is an essential mineral that plays a key role in the oxygen transporting molecule hemoglobin. Iron also helps muscles store and use oxygen. Excess iron in the body can attract electrons, creating harmful oxygen radicals. Iron overload can be caused by several factors such as genetics, age, gender, and having received multiple red blood cell transfusions. Excess iron can lead to many diseases, such as arthritis, liver cirrhosis, heart disease, and several forms of cancer. Iron-chelating therapies work by binding free iron in the bloodstream and by reducing the amount of iron bound in transferrin, the iron transporting molecule. …

Mechanism Of Assembly Of The Bardet-Biedel Syndrome (Bbs) Complex, Barry M. Willardson

Journal of Undergraduate Research

1. Devon Blake. Devon was the most productive student I have had in my 18 years at BYU. The MEG award helped support his work from January 2013 through May 2014. During this time, Devon co-authored two papers on the effects of cell-type specific deletion of phosducinlike protein 1 (PhLP1) in rod and cone photoreceptor cells (Lai et al. (2013) J. Neurosci. 33, 7941-7951, selected by the Faculty of 1000 as a high-impact paper and Tracy et al. (2014) PLOS One in press). He reported this work in poster form at an international meeting of the Federation of American Society …

Urine Proteomics Identifies Preeclampsia Subphenotypes, Michelle R. Axe

Undergraduate Honors Thesis Projects

Preeclampsia is a perinatal complication of unknown etiology, resulting in 76,000 maternal deaths and 500,000 infant deaths annually₁. The Nationwide Children’s Center for Perinatal Research was the first cohort to propose that preeclampsia is rooted in protein misfolding. We aimed to characterize the misfolded protein components of maternal urine samples and to determine if distinct molecular profiles exist for clinical preeclampsia phenotypes. A total of 86 maternal urine samples from Yale-New Haven Hospital were analyzed for this study, from six clinical preeclampsia subphenotypes- pregnant control (n=10), idiopathic proteinuria (n=15), mild preeclampsia (n=14), superimposed preeclampsia (n=12), typical severe preeclampsia …

Development And Application Of Web-Based Open Source Drug Discovery Platforms, Yuri Pevzner

USF Tampa Graduate Theses and Dissertations

Computational modeling approaches have lately been earning their place as viable tools in drug discovery. Research efforts more often include computational component and the usage of the scientific software is commonplace at more stages of the drug discovery pipeline. However, as software takes on more responsibility and the computational methods grow more involved, the gap grows between research entities that have the means to maintain the necessary computational infrastructure and those that lack the technical expertise or financial means to obtain and include computational component in their scientific efforts. To fill this gap and to meet the need of many, …

Laboratory And Field Studies Of Chemical Processes Of Atmospheric Relevance, Bryant N. Fong

Student Theses and Dissertations

Atmospheric processes such as surface absorption and reflectance are dependent on aerosol composition and aging processes. Our studies examined four atmospheric processes. First, mole ratio effects on deliquescence of mixed binary particles were analyzed. Experimental mole ratio results match established atmospheric model calculations and show that binary component concentrations affect the deliquescence relative humidity (DRH). Second, hydrogen chloride (HCl) gas formation as a function of humidity was investigated. HCl production influences pH of aerosols and was found to be independent of humidity conditions. Third, particles collected in Northeast Arkansas were found to be indicative of urban or rural point sources. …

Essential Oils From Apple Mint (Mentha Suaveolens) And Passionflower Fruit (Passiflora Incarnata): Studies On Cognition, Coordination, And Chemical Components., Evelyn F. Patrick *, Jessie Bowers *, Shannon Read *, Brett R. Lackey, Christine Murphy, Sandra L. Gray

Journal of the South Carolina Academy of Science

Plant essential oils (EO) are used as perfumes, lotions and air fresheners because of their pleasant aromas, but EO also have the ability to elicit changes in mood and behavior. These activities are influenced by the mode of administration and by multiple signaling pathways. The EO aromas from organically grown apple mint (Mentha suaveolens) and passionflower fruit (Passiflora incarnata) were assessed for their effects on cognition and coordination. Participants completed two tasks designed to test working memory and bimanual task efficiency in rooms infused with apple mint, passionflower fruit or control EO. Bimanual coordination was assessed using the Intercept2 program …

The Rise Of Carbon Nanoscience In South Carolina, Apparao M. Rao

Journal of the South Carolina Academy of Science

No abstract provided.

On The Influence Of Ionic Strength On Radium And Strontium Sorption To Sandy Loam Soils, Brian A. Powell, Todd Miller, Daniel I. Kaplan

Journal of the South Carolina Academy of Science

Models which can estimate environmental transport of radioactive contaminants in natural and engineered systems are required to 1) deploy effective remediation strategies for contaminated sites, 2) design waste repositories for future waste streams, and 3) ensure protection of human and environmental health in all cases. These models require accurate transport parameters in order to correctly predict how these contaminants will move in the subsurface. This work aimed to determine more accurately the distribution coefficients for radium and strontium sorption to Savannah River Site (SRS) soils. Radium and strontium sorption to the soils was found to be highly dependent upon ionic …

Application And Development Of Computational Methods In Conformational Studies Of Bio-Molecules, Aleksandra Karolak

USF Tampa Graduate Theses and Dissertations

The work presented in my dissertation focuses on the conformational studies of bio-molecules including proteins and DNA using computational approaches. Conformational changes are important in numerous molecular bioprocesses such as recognition, transcription, replication and repair, etc. Proteins recognize specific DNA sequences and upon binding undergo partial or complete folding or partial unfolding in order to find the optimal conformational fit between molecules involved in the complex. In addition to sequence specific recognition, proteins are able to distinguish between subtle differences in local geometry and flexibility associated with DNA that may further affect their binding affinities. Experimental techniques provide high-resolution details …

Use Of Assessments In College Chemistry Courses: Examining Students' Prior Conceptual Knowledge, Chemistry Self-Efficacy, And Attitude, Sachel M. Villafañe-García

USF Tampa Graduate Theses and Dissertations

Students' retention in STEM-related careers is of great concern for educators and researchers, especially the retention of underrepresented groups such as females, Hispanics, and Blacks in these careers. Therefore it is important to study factors that could potentially influence students' decision to stay in STEM. The work described in this dissertation involved three research studies where assessments have been used in college chemistry courses to assess students' prior content knowledge, chemistry-self-efficacy, and attitude toward science. These three factors have been suggested to have an influence on students' performance in a course and could eventually be a retention factor.

The first …

Investigation Of Bioactive Metabolites From The Antarctic Sponge Dendrilla Membranosa And Marine Microorganisms, Chris G. Witowski

USF Tampa Graduate Theses and Dissertations

Natural products continue to be a valuable source of compounds in research involving chemical ecology and drug discovery. Secondary metabolites are biosynthesized to benefit the host organism in its environment (feeding deterrence from predators, antibiotic properties to avoid infection, etc.) but these compounds also serve as useful scaffolds in drug discovery applications. The research herein describes both aspects of these two branches of natural products chemistry. The Antarctic sponge Dendrilla membranosa produces diterpenes, of which membranolide A, deters feeding of the predatory amphipod Gondogenia antarctica. A metabolomic study of several sponges was undertaken to determine environmental factors that govern …

Reagent Pencils: A New Technique For Solvent-Free Deposition Of Reagents Onto Paper-Based Microfluidic Devices, Haydn T. Mitchell, Isabelle C. Noxon, Cory A. Chaplan, Samantha J. Carlton, Cheyenne H. Liu, Kirsten A. Ganaja, Nathaniel W. Martinez, Chad Immoos, Philip Costanzo, Andres W. Martinez

Chemistry and Biochemistry

Custom-made pencils containing reagents dispersed in a solid matrix were developed to enable rapid and solvent-free deposition of reagents onto membrane-based fluidic devices. The technique is as simple as drawing with the reagent pencils on a device. When aqueous samples are added to the device, the reagents dissolve from the pencil matrix and become available to react with analytes in the sample. Colorimetric glucose assays conducted on devices prepared using reagent pencils had comparable accuracy and precision to assays conducted on conventional devices prepared with reagents deposited from solution. Most importantly, sensitive reagents, such as enzymes, are stable in the …