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A Study Of The Degradative Capabilities Of The Bimetallic System: Mg(Pd/C) As Applied In The Destruction Of Decafluoropentane, An Environmental Contaminant, Douglas Tomlin

Electronic Theses and Dissertations

Pollution from hydrofluorocarbons (HFC) poses a serious challenge to the environmental community. Released from industrial operations, they have contaminated both the atmosphere and groundwater and are considered persistent in both media.1 For over the past 20 years, the practice of synthesizing hydrofluorocarbons as alternatives to chlorofluorocarbons (CFC) has been conducted in an effort to reverse the effects of stratospheric ozone layer depletion. 2,3 However, in doing so these new fluorinated compounds exhibited an unexpected property as a potent global warming greenhouse gas (GHG) with radiative forcing potentials in the range of 100 to 10,000 equivalents greater than carbon dioxide.4 Conversely, …

Assessment Of Molecular Interactions Via Magnetic Relaxation: A Quest For Inhibitors Of The Anthrax Toxin, Oscar Santiesteban

Electronic Theses and Dissertations

Anthrax is severe disease caused by the gram-positive Bacillus anthracis that can affect humans with deadly consequences. The disease propagates via the release of bacterial spores that can be naturally found in animals or can be weaponized and intentionally released into the atmosphere in a terrorist attack. Once inhaled, the spores become activated and the anthrax bacterium starts to reproduce and damage healthy macrophages by the release of the anthrax toxin. The anthrax toxin is composed of three virulent factors: (i) anthrax protective antigen (APA), (ii) anthrax lethal factor (ALF), and (iii) anthrax edema factor (AEF) that work in harmony …

Nmr Line Shapes And Multi-State Binding Equilibria, Evgenii L. Kovrigin

Chemistry Faculty Research and Publications

Biological function of proteins relies on conformational transitions and binding of specific ligands. Protein-ligand interactions are thermodynamically and kinetically coupled to conformational changes in protein structures as conceptualized by the models of pre-existing equilibria and induced fit. NMR spectroscopy is particularly sensitive to complex ligand-binding modes—NMR line-shape analysis can provide for thermodynamic and kinetic constants of ligand-binding equilibria with the site-specific resolution. However, broad use of line shape analysis is hampered by complexity of NMR line shapes in multi-state systems. To facilitate interpretation of such spectral patterns, I computationally explored systems where isomerization or dimerization of a protein (receptor) molecule …

How A Silent Mutation Suppresses The Activity And Iron Incorporation In Superoxide Dismutase, Xiaonan Mei

Theses and Dissertations--Chemistry

A mutation (CTG to TTG) of FeSOD gene was found in Escherichia coli. Since they both encode leucine, it is a silent mutation. Site-­‐directed mutagenesis was applied to correct the mutation, and the mutant FeSOD (before gene correction) and wild type FeSOD (after gene correction) were purified. The FeSODs from the two genes were Characterized using different assays and spectroscopic methods including EPR and CD. The requirement for the rare codon TTG may result in slowed translation and heavy demand on a scarce tRNA. Cultures expressing wild type FeSOD are better able to grow for long times after addition of …

Investigations Into Modulation Of Brain Oxidative Stress By Various Interventions, Jessica Lynn Harris

Theses and Dissertations--Chemistry

In this thesis study we examined glycogen synthase kinase-3β (GSK-3β) and its effects over Nrf2 and Pin 1 as it relates to Alzheimer’s disease (AD). AD is a neurodegenerative disease characterized by a prolonged high oxidative environment. Transcription factor Nrf2 is vital in the brain’s defense against oxidative insults through its up-regulation of over 100 antioxidants. Depletion of the brain’s antioxidant defense system results in intolerance to an oxidative environment, contributing to the progression of AD. The regulatory Pin 1 protein promotes cellular homeostasis, and when down-regulated results in increased deposits of neurofibrillary tangles (NFTs) and amyloid-β (Aβ) plaques, the …

Bifunctional Bisphosphonates For Delivering Biomolecules To Bone, Jivan N. Yewle

Theses and Dissertations--Chemistry

Active targeting with controlled delivery of therapeutic agents to bone is an ideal approach for treatment of several bone diseases. Since bisphosphonates (BPs) are known to have high affinity to bone mineral and are being widely used in treatment of osteoporosis, they are well-suited for drug targeting to bone. For this purpose, bifunctional hydrazine-bisphosphonates (HBPs) with spacers of various lengths and lipophilicity were synthesized and studied. Crystal growth inhibition assays demonstrated that the HBPs with shorter spacers bound more strongly to bone mineral, hydroxyapatite (HA), than did alendronate. HBPs were also demonstrated to be non-toxic to MC3T3-E1 pre-osteoblasts. The targeted …

Investigations Of Oxidative Stress Effects And Their Mechanisms In Rat Brain After Systemic Administration Of Ceria Engineered Nanomaterials, Sarita S. Hardas

Theses and Dissertations--Chemistry

Advancing applications of engineered nanomaterials (ENM) in various fields create the opportunity for intended (e.g. drug and gene delivery) or unintended (e.g. occupational and environmental) exposure to ENM. However, the knowledge of ENM-toxicity is lagging behind their application development. Understanding the ENM hazard can help us to avoid potential human health problems associated with ENM applications as well as to increase their public acceptance. Ceria (cerium [Ce] oxide) ENM have many current and potential commercial applications. Beyond the traditional use of ceria as an abrasive, the scope of ceria ENM applications now extends into fuel cell manufacturing, diesel fuel additives …

Removal Of Arsenic(Iii) From Water With A New Solid-Supported Thiol, Partha Jana

Theses and Dissertations--Chemistry

Arsenic is a highly toxic, easily transportable and widespread contaminant in groundwater throughout the world. Arsenic causes acute toxicity by disrupting biological functions. In groundwater arsenic concentrations can reach up to a few milligrams per liter. Current regulations on arsenic content in drinking water are becoming more stringent and require the standard to be reduced to a few parts per billion. Arsenic exists as oxyanions in aqueous solution in either trivalent or pentavalent oxidation states depending on the oxidation-reduction potential and pH of the medium. Several treatment methods are available for removing arsenic from water. However, cost, operational complexity of …

Biosensing Systems For The Detection Of Bacterial Quorum Sensing Molecules: A Tool For Investigating Bacteria-Related Disorders And Food Spoilage Prevention, Nilesh G. Raut

Theses and Dissertations--Chemistry

Quorum sensing enables bacteria to communicate with bacteria of the same or different species, and to modulate their behavior in a cell-density dependent manner. Communication occurs by means of small quorum sensing signaling molecules (QSMs) whose concentration is proportional to the population size. When a QSM threshold concentration is reached, certain genes are expressed, thus allowing control of several processes, such as, virulence factor production, antibiotic production, and biofilm formation. Not only many pathogenic bacteria are known to produce QSMs, but also QSMs have been identified in some bacteria-related disorders. Therefore, quantitative detection of QSMs present in clinical samples may …

Novel Aromatic Ion–Pairs: Synergy Between Electrostatics And Π-Face Aromatic Interactions, Pramod Prasad Poudel

Theses and Dissertations--Chemistry

This dissertation focuses on the design and study of charged aromatic molecules where weak π-π interactions synergize with electrostatic interactions to enhance the overall interaction between aromatic moieties. Each chapter investigates some aspect of this hypothetical synergy between electrostatics and π-face aromatic cohesion.

The first chapter unveiled the importance of electrostatics in the intramolecular stacking of flexible aromatic molecular templates 1-2Br and 2a. While our previous studies found dicationic molecular template 1-2Br to have intramolecular π-stacking between electron poor pyridinium and electron rich xylylene moieties, no such stacking interaction was observed in the neutral analog 2a.

Chapter two systematically …

Development Of Novel Chemical Tools For Proteasome Biology & A New Approach To 1-Azaspirocyclic Ring System, Lalit Kumar

Theses and Dissertations--Chemistry

The proteasome, a multiprotease complex, is clinically validated as an anticancer target by the FDA approval of bortezomib and carfilzomib for the treatment of multiple myeloma. The emergence of resistance to proteasome inhibitors however remains a major clinical challenge. Recently, distinct types of proteasomes termed ‘intermediate proteasomes’, which contain unconventional mixtures of catalytic subunits, have been implicated with drug resistance of tumor cells. In elucidating the role of intermediate proteasomes in drug resistance, a crucial step is to unequivocally determine the subunit composition of intermediate proteasomes in cells. With this in mind, the goal of the studies reported in this …

Recent Applications Of The Simple Hydrocarbon Cyclooctatetrene As A Starting Material For Complex Molecule Synthesis, Kevin W. Glaeske, William A. Donaldson

Chemistry Faculty Research and Publications

Cyclooctatetraene [COT], a simple non-aromatic cyclic polyene, is capable of undergoing a variety of oxidation and cycloaddition reactions to afford polycyclic structures. In addition, complexation of COT or the cycloaddition products with transition metals facilitates bond formation. Recent developments in the reactivity of COT and application to the synthesis of naturally occurring and non-naturally occurring compounds is reviewed.

Effects Of Activated Carbon Surface Chemistry Modification On The Adsorption Of Mercury From Aqueous Solution, Emily K. Faulconer

Publications

Mercury (Hg), a naturally occurring element, is toxic and can lead to negative health impacts for humans and ecosystems. Activated carbon adsorption is effective in treating Hg-laden aqueous effluent for safe discharge. Two modifications of commercially available activated carbon were investigated: iron impregnation to allow for magnetic sorbent recapture and wet chemical oxidation to enhance aqueous Hg capture. The modified carbons were characterized by nitrogen adsorption-desorption, XRD, pHpzc, vibrating sample magnetometry, elemental analysis, and total acidity titration. The 3:1 C:Fe magnetic powdered activated carbon (MPAC) retained a high surface area of 790 m2 /g and was 95% magnetically recoverable, with …

Part I: Quantitative Determination Of Total Corrosive Sulfur In Mineral Insulating Oils And Technical Liquids; Part Ii: Development And Validation Of A Broad Spectrum Microbial Disinfectant, Kyle Rodney Anderson

Doctoral Dissertations

"Part one of this dissertation deals with the development and validation of a test method for determination of total corrosive sulfur in mineral insulating oils other technical oils. The method involved reaction of corrosive sulfur compounds in oils with finely divided copper at temperatures ≥ 110 °C. The reaction yielded cuprous sulfide (Cu₂S), Cu₂S was then oxidized to cupric sulfate (CuSO₄), which was determined as sulfate with ion chromatography. The method offers a quantitative assessment of corrosive sulfur compounds in oils and eliminates ambiguities associated with the international standard methods for corrosive sulfur in mineral insulating oils and other technical …

X-Ray Crystallography For The Study Of Nickel And Iron Salicylaldimines, Carla Schmiesing Eribal

Doctoral Dissertations

"X-ray diffraction of single crystals has developed dramatically over the last century by combining fundamental theories of light, diffraction, and statistics to generate the complete, geometric structure of molecules. The quality of the resulting X -ray structure data are reported in R₁ < 5%, wR2 < 12% and a goodness of fit value of one. This technique was applied specifically to the evaluation of the spin crossover (SCO) compound [Fe(salpm)₂]BF₄ʺ0.5EtOH and how the molecule's geometry changed during a two-step thermal LS-HS conversion. The crystal structure was measured at 100,175,225, and 296 K to yield final R₁ values of 0.047, 0.054, 0.051, and 0.058, respectively. The coordination bond lengths show the spin transitions occur between 100-175K at one crystallographically unique Fe and between 175-225K at the other Fe site. No strong long range interactions are found, suggesting a gradual spin transition. Reaction ofNi(Nalkyl-sal)₂ complexes with Ni(N0₃)₂ form either nickel dimeric, [Ni₃(Rsal)(N0₃)(MeOH)]₂ or trinuclear complexes, Ni₃(Rsal)₄(N0₃)₂. The binuclear complexes, with orthogonal bridging ligands, show overall ferromagnetic interactions. The crystal structures for Ni₃(Rsal)₄(N0₃)₂ from methyl to benzyl were solved and indicate no steric restriction on formation for the series. The trinuclear compounds form an isosceles triangle of metal atoms with the isopropyl analog showing an overall antiferromagnetic interaction with J=+11.386 and J23=-13.891. Lastly, xanthene spirolactam derivatives were structurally analyzed to determine binding modes for their selective and sensitive (µM) detection of metals Cr³⁺, Fe³⁺, Ni²⁺, Co²⁺ and the nerve gas mimic, dichlorophosphate"--Abstract, page iii.

Nano-Particles Induced Oxidative Stress In Immortalized Human Brain Endothelial Cells, Xinsheng Zhang

Doctoral Dissertations

"Nanoparticles are engineered structure with at least one dimension of 100 nanometers or less. These materials are increasingly being used for commercial purposes such as catalyst, semiconductor, cosmetics, microelectronic, and drug carrier. However, the toxicological impact of these materials has not yet been studied in detail, thereby limiting their use. In our present study, we use human brain endothelial cell line as a blood-brain barrier (BBB) model to investigate if two kinds of nanoparticles [ 1). Diesel exhaust particles (DEPs) and 2). single wall carbon nanotube (CNT) ] induced oxidative stress in cell model. Our studies showed that DEPs or …

A Simple Approach For Synthesis, Characterization And Bioactivity Of Bovine Bones To Fabricate The Polyurethane Nanofiber Containing Hydroxyapatite Nanoparticles, Faheem A. Sheikh, M. A. Kanjwal, Javier Macossay-Torres, N. A. M. Barakat, H. Y. Kim

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

In the present study, we had introduced polyurethane (PU) nanofibers that contain hydroxyapatite (HAp) nanoparticles (NPs) as a result of an electrospinning process. A simple method that does not depend on additional foreign chemicals had been employed to synthesize HAp NPs through the calcination of bovine bones. Typically, a colloidal gel consisting of HAp/PU had been electrospun to form nanofibers. In this communication, physiochemical aspects of prepared nanofibers were characterized by FE-SEM, TEM and TEM-EDS, which confirmed that nanofibers were well-oriented and good dispersion of HAp NPs, over the prepared nanofibers. Parameters, affecting the utilization of the prepared nanofibers in …

Bismuth Nitrate-Induced Microwave-Assisted Expeditious Synthesis Of Vanillin From Curcumin, Debasish Bandyopadhyay, Bimal K. Banik

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

Background: Curcumin and vanillin are the two useful compounds in food and medicine. Bismuth nitrate pentahydrate is an economical and ecofriendly reagent.

Method: Bismuth nitrate pentahydrate impregnated montmorillonite KSF clay and curcumin were subjected to microwave irradiation.

Results: Microwave-induced bismuth nitrate-promoted synthesis of vanillin from curcumin has been accomplished in good yield under solvent-free condition. Twenty-five different reaction conditions have been studied to optimize the process.

Conclusion: The present procedure for the synthesis of vanillin may find useful application in the area of industrial process development.

Evaluation Of The Performance Of Non-Covalent Molecular Mechanical Models For Zn2+ And Mg2+ Metal Ions, Maria Magdalena Kamm

Master's Theses

Computer simulations using molecular dynamics (MD) on classical molecular mechanical

(MM) interatomic potentials can provide valuable information and quantitative

predictions about these systems. In MD calculations binding free energies of ions to

host molecules can be studied if correct ion solvation free energies in aqueous solution

are obtained. However, no MM models exist that parametrize various Zn2+ and

transition metals consistently and consider both structural and thermodynamic data

simultaneously.

The first part of our work focused on MD free energy perturbation (FEP) simulations

to derive MM interaction parameters for Zn2+ and Mg2+ ions in aqueous

solution. To obtain these parameters …

A Chemical Proteomic Probe For Detecting Dehydrogenases: Catechol Rhodanine, Xia Ge, Daniel S. Sem

Chemistry Faculty Research and Publications

The inherent complexity of the proteome often demands that it be studied as manageable subsets, termed subproteomes. A subproteome can be defined in a number of ways, although a pragmatic approach is to define it based on common features in an active site that lead to binding of a common small molecule ligand (ex. a cofactor or a cross-reactive drug lead). The subproteome, so defined, can be purified using that common ligand tethered to a resin, with affinity chromatography. Affinity purification of a subproteome is described in the next chapter. That subproteome can then be analyzed using a common ligand …

Chyd1 Solution Phase Synthesis Optimization And The Development Of A Novel Human Growth Hormone Antagonist And Agonist, Philip Murray

USF Tampa Graduate Theses and Dissertations

Inhibiting protein-protein interactions to achieve a therapeutically desired effect has been a goal in the field of drug discovery for decades. Recently, advances in peptidomimetics have led researches to the use of cyclized peptides to achieve this goal. Cyclization of linear peptides restricts the number of conformations of the peptide, increasing the peptide's affinity to binding to the desired target. Cyclization also stabilizes the peptide, allowing the peptide to be resistant to proteases. This study explores the optimization of solution phase synthesis of an important integrin-mediated cell adhesion cyclic peptide for the therapeutic inhibition of multiple myeloma, cHYD1. cHYD1 was …

Asymmetric Intra- And Intermolecular Cyclopropanation By Co(Ii)- Based Metalloradical Catalysis, Xue Xu

USF Tampa Graduate Theses and Dissertations

Metal-catalyzed cyclopropanation of olefins with diazo reagents has attracted research interest because of its fundamental and practical importance. The resulting cyclopropyl units are recurrent motifs in biologically important molecules and can serve as versatile precursors in organic synthesis. Since they were first introduced in 2004, Co(II) complexes of D₂-symmetric chiral amidoporphyrins [Co(D₂-Por*)] have emerged as a new class of catalysts for asymmetric cyclopropanation. These metalloradical catalysts have been shown to be highly effective for asymmetric intermolecular cyclopropanation of a broad scope of substrates with different classes of carbene sources, particularly including electron-deficient olefins and acceptor/acceptor-substituted …

Drug Discovery From Floridian Mangrove Endophytes, Jeremy Beau

USF Tampa Graduate Theses and Dissertations

A significant challenge of the 21st century is the growing health threat stemming from drug-resistant infectious diseases. There is an undeniable need to discover new, safe and effective drugs with novel mechanisms of action to combat this threat. A study of drugs currently on the market showed that natural products account for approximately 75% of new anti-infective drugs, either as new agents or analogs based upon their structure. Unfortunately, major pharmaceutical companies have cut back tremendously in natural products research in part due to the frustrating obstacle of frequent rediscovery of compounds. Fungi in particular are difficult to work with …

Synthesis And Anti-Mrsa Activity Of Hydrophilic C3-Acylated N-Thiolated Β-Lactams And N-Acyl Ciprofloxacin-N-Thiolated Β-Lactam Hybrids, Biplob Bhattacharya

USF Tampa Graduate Theses and Dissertations

The Turos laboratory has been working with N-thiolated β-lactams for years trying to understand the mode of action and structural features it needs to have biological activity. Over the years new data has shown promising inhibitory activity against various microbes.

In this dissertation, a review of the vast amount of work carried out on N-thiolated β-lactams in Turos laboratory has been done and their novelty, in terms of structure and mechanism has been discussed. A complete outline of our work in the discovery and ongoing development of these compounds, starting from our initial, unexpected finding of antimicrobial activity for one …

Chiral Binol Metal Phosphate/Phosphoric Acid Catalyzed Enantioselective Addition Of Phosphorus And Sulfur Nucleophiles To Imines And Epoxides, Gajendrasingh Ingle

USF Tampa Graduate Theses and Dissertations

The research presented in this dissertation focuses on chiral BINOL metal phosphatephosphoric acid catalyzed enantioselective additions of phosphorus and sulfur nucleophiles to imines and epoxides. In chapter 2, we reported a new method to synthesize chiral amino phosphine oxides. The reaction combines N-substituted imines and diphenylphosphine oxide catalyzed by chiral magnesium 9-antryl phosphate. A wide variety of aliphatic and aromatic aldimines substituted by electron neutral benzhydryl or dibenzocycloheptene groups were excellent substrates for the addition reaction. The imines protected with dibenzocycloheptene protecting group provided better enantioselectivity than those protected with benzhydryl group, while both imines gave comparable yields. Also, …

Development And Optimization Of Kinetic Target-Guided Synthesis Approaches Targeting Protein-Protein Interactions Of The Bcl-2 Family, Sameer Shamrao Kulkarni

USF Tampa Graduate Theses and Dissertations

Kinetic target-guided synthesis (TGS) and in situ click chemistry are among unconventional discovery strategies having the potential to streamline the development of protein-protein interaction modulators (PPIMs). In kinetic TGS and in situ click chemistry, the target is directly involved in the assembly of its own potent, bidentate ligand from a pool of reactive fragments. Herein, we report the use and validation of kinetic TGS based on the sulfo-click reaction between thio acids and sulfonyl azides as a screening and synthesis platform for the identification of high-quality PPIMs. Starting from a randomly designed library consisting of nine thio acids and nine …

Design Of Colloidal Composite Catalysts For Co2 Photoreduction And For Co Oxidation, Bijith D. Mankidy

USF Tampa Graduate Theses and Dissertations

In this doctoral dissertation, novel colloidal routes were used to synthesize nanomaterials with unique features. We have studied the impact of nanoparticle size of catalyst, role of high surface area of a photocatalyst, and the effect of varying elemental composition of co-catalytic nanoparticles in combination with core-shell plasmonic nanoparticles. We have demonstrated how physical and chemical characteristics of nanomaterials with these unique features play a role in catalytic reactions, specifically the oxidation of CO and the photoreduction of CO2. The first objective of this doctoral dissertation involved the preparation of CoO nanoparticles with discrete nanoparticles sizes (1-14 nm) using a …

Enantioselective Brønsted And Lewis Acid-Catalyzed Reaction Methodology: Aziridines As Building Blocks For Catalytic Asymmetric Induction, Shawn E. Larson

USF Tampa Graduate Theses and Dissertations

Chiral molecules as with biological activity are plentiful in nature and the chemical literature; however they represent a smaller portion of the pharmaceutical drug market. As asymmetric methodologies grow more powerful, the tools are becoming available to synthesize chiral molecules in an enantioselective and efficient manner.

Recent breakthroughs in our understanding of phosphoric acid now allow for Lewis acid catalysis via pairing with alkaline earth metals. Using alkaline earth metals with chiral phosphates is an emerging approach to asymmetric methodology, but already has an influential record.

The development of new conditions for the phosphoric acid-catalyzed highly enantioselective ring-opening of meso-aziridines …

Development Of A Bio-Molecular Fluorescent Probe Used In Kinetic Target-Guided Synthesis For The Identification Of Inhibitors Of Enzymatic And Protein-Protein Interaction Targets, Katya Pavlova Nacheva

USF Tampa Graduate Theses and Dissertations

Abstract

Fluorescent molecules used as detection probes and sensors provide vital information about the chemical events in living cells. Despite the large variety of available fluorescent dyes, new improved fluorogenic systems are of continued interest. The Diaryl-substituted Maleimides (DMs) exhibit excellent photophysical properties but have remained unexplored in bioscience applications. Herein we present the identification and full spectroscopic characterization of 3,4-bis(2,4-difluorophenyl)-maleimide and its first reported use as a donor component in Forster resonance energy transfer (FRET) systems. The FRET technique is often used to visualize proteins and to investigate protein-protein interactions in vitro as well as in vivo. The analysis …

Design Of Novel Inhibitors For Infectious Diseases Using Structure-Based Drug Design: Virtual Screening, Homology Modeling And Molecular Dynamics, Divya Ramamoorthy

USF Tampa Graduate Theses and Dissertations

The main aim of the study in this thesis was to use structure-based protocols to design new drugs for enzymes, DXS and DXR in the non mevalonate pathway. Another aim of this study was to identify the dimer interface in E.coli FabH as an allosteric binding site for designing new class of anti-infective drugs. We have attempted to identify potential inhibitors for DXS by docking the NCI Diversity set compounds, compound libraries available from GSK-MMV and St. Jude's Children's research center. FabH dimer interface has been identified as a potential target using SiteMap, Alanine mutagenesis and docking studies.

The first …