Chemistry Commons^™

The Spectrophotometric Analysis Of Lead Carbonate Complexation And Carbonate Saturation States In Seawater, Regina Anita Easley

USF Tampa Graduate Theses and Dissertations

The carbon dioxide (CO₂) system is the primary buffer in seawater which controls oceanic pH. Changes in the marine CO₂ system affect a number of processes such as metal speciation, mineral saturation states, auditory responses in fish, and primary productivity rates. Increased atmospheric concentrations of CO₂ from human activities (e.g. burning of fossil fuels, deforestation, and cement production) has led to a global decrease in surface ocean pH termed anthropogenic ocean acidification. One particular concern in response to increased oceanic CO₂ is a substantial decrease in the calcium carbonate (CaCO₃) saturation states, Ω …

Virtual Screening For Inhibitors Of Anti-Apoptotic Proteins: Dck, Bcl-Xl, Mcl-1, Mdmx, And Mdm2, Courtney Jerome Du Boulay

USF Tampa Graduate Theses and Dissertations

←Within this dissertation the topic of virtual screening is discussed with regard to three different cancer targets and also a brief introduction of the tools used in virtual screening. In Chapter 1, the reader will be introduced to virtual screening and the programs that are used in virtual screening. In Chapter 2, the first of three projects are discussed. This project consists of the work that was done to find inhibitors of the P53 binding domain of MDMX. In this project the mobility of residues within the binding site of MDMX are discussed and the ways in which we attempted …

Argumentation As A Lens To Examine Student Discourse In Peer-Led Guided Inquiry For College General Chemistry, Ushiri Kumarihamy Kulatunga

USF Tampa Graduate Theses and Dissertations

This dissertation work entails three related studies on the investigation of Peer-Led Guided Inquiry student discourse in a General Chemistry I course through argumentation. The first study, Argumentation and participation patterns in general chemistry peer-led sessions, is focused on examining arguments and participation patterns in small student groups without peer leader intervention. The findings of this study revealed that students were mostly engaged in co-constructed arguments, that a discrepancy in the participation of the group members existed, and students were able to correct most of the incorrect claims on their own via argumentation.

The second study, Exploration of peer leader …

Anti-Parasitic And Anti-Bacterial Agents: Studies On 1,4-Dihydropyridines And 2,4-Diaminoquinazolines, Kurt Steven Van Horn

USF Tampa Graduate Theses and Dissertations

Thirty-three 1,4-dihydropyridine diastereomeric pairs were synthesized and the structure-activity relationship studied in a Plasmodium falciparum in vitro model. Twenty-nine of these derivatives contained a 6-position oxygen, with 2.31, 2.32, 2.52 and 2.53 having single and double digit nanomolar activities. This SAR study revealed some insightful information about the 1,4-dihydropyridine substitution pattern. Substitution at the 7-position other than 3,4-dimethoxy severely reduced the activity. 4-phenyl substitution with 2- or 4- halo or methyl formed active compounds while substitution at the 3-position or with methoxy or conjugated aryl systems resulted in inactive compounds. The 2-position was found to majorly affect the activity, with …

Optimization, Modification And Application Of Gold Nanoparticles As The Substrates Of Surface Enhanced Raman Spectroscopy, Seongmin Hong

USF Tampa Graduate Theses and Dissertations

SERS

A Polarizable And Transferable Carbon Dioxide Potential For Materials Simulation, Ashley Lynn Mullen

USF Tampa Graduate Theses and Dissertations

Intermolecular potential energy functions for CO₂ have been developed from first principles for use in heterogeneous systems, including one with explicit polarization. The intermolecular potentials have been expressed in a transferable form and parameterized from nearly exact electronic structure calculations. Models with and without explicit many-body polarization effects, known to be important in simulation of interfacial processes, are constructed. The models have been validated on pressure-density isotherms of bulk CO₂ and adsorption in three metal-organic framework (MOF) materials. The present models appear to offer advantages over high quality fluid/liquid state potentials in describing CO₂ interactions in interfacial …

Synthesis Of Amphiphilic Α- And Γ-Aapeptides For Antimicrobial, Self-Assembly, And Mineralization Studies, Mohamad N. Amin

USF Tampa Graduate Theses and Dissertations

Seven novel, amphiphilic AApeptides were prepared. Two cationic, lipo-α-AApeptides, NA-75 and NA-77 were found to possess potent antimicrobial activity against Gram-positive bacteria, with almost no hemolytic activity. In addition to NA-75 and 77, four amphiphilic, γ-AApeptides, NA-133, 135, 137, and 139, and one anionic lipo-α-AApeptide, NA-81, were prepared for molecular self-assembly studies, with several interesting nanostructures observed by TEM. Mineralization of calcium carbonate from gaseous CO2 and Ca2+ in the presence of the 7 AApeptide amphiphiles was also observed by optical microscopy. Several AApeptides were found to be able to influence CaCO3 crystal morphology. Another α-AApeptide, NA-63, was synthesized by …

Development Of Improved Models For Gas Sorption Simulation, Keith Mclaughlin

USF Tampa Graduate Theses and Dissertations

Computational chemistry offers one the ability to develop a better understanding of the complex physical and chemical interactions that are fundamental to macro- and mesoscopic processes that are seen in laboratory experiments, industrial processes, and ordinary, everyday life. For many systems, the physics of interest occur at the molecular or atomistic levels, and in these cases, computational modeling and two well refined simulation techniques become invaluable: Monte Carlo (MC) and molecular dynamics (MD). In this work, two well established problems were tackled. First, models and potentials for various gas molecules were produced and refined from first principles. These models, although …

Design, Synthesis, Processing, And Thermal Analysis Of Nanocomposites With Tunable Properties, Mu Seong Kim

USF Tampa Graduate Theses and Dissertations

Polymer composites containing nanosized fillers have generated explosive interest since the early 1980's. Many recent studies have been conducted incorporating nano-fillers into polymer matrices to design and synthesize materials with tunable mechanical, thermal, and optical properties. Conventional filled polymers, where the reinforcement is on the order of microns, have been replaced by composites with discrete nanosized fillers. Gradually, theories that predicted that composite properties are independent of particle size in the micron range were challenged by nanocomposites. Rather, nanocomposite properties are greatly influenced by the surface area of the. All of this is complicated by the fact that nanoparticles are …

Design, Synthesis And Evaluation Of Novel Diazirine Photolabels With Improved Ambient Light Stability And Fluorous-Based Enrichment Capacity, Arun Babu Kumar

USF Tampa Graduate Theses and Dissertations

Photoaffinity labeling is a quintessential technique in studying and analyzing the interaction between a ligand and receptor. Diazirines are one of the important photo-labile moieties used in photoaffinity labeling due to their superior photo labeling characteristics. Herein, we report the investigations we conducted with diazirine photolabels on (a) photochemical aspects leading to enhancement of their ambient light stability and (b) equipping them with fluorous tags to enable fluorous enrichment of labeled proteins. Furthermore, we report a pilot study to develop BACE-1 inhibitors, which have potential to be developed into photoaffinity probes.

3-Trifluoromethyl-3-phenyldiazirine offers good selectivity and protection against pseudolabeling but …

N-Acyl Ciprofloxacins: Synthesis, Antibacterial Activity And Effects On Molecular Loading Of Poly(Vinyl Benzoate) Nanoparticles, Ryan Cormier

USF Tampa Graduate Theses and Dissertations

Bacterial infections are becoming progressively more difficult to treat due to antibiotic resistance and the decreasing rate at which new antibiotics are brought to market. The Turos laboratory has attempted to tackle this problem for the last 15 years with the discovery of N-thiolated β-lactams leading to the design of polyacrylate nanoparticles to deliver these and other drugs. Chapter 1 discusses many reported instances of utilizing different types of polymeric nanoparticles to deliver antibiotics. Poly(lactic-co-glycolic acid) (PLGA), poly(alkyl cyanoacrylate) (PACA), poly(styrene-co-butylacrylate), and chitosan are the main polymers used to make nanoparticles. Chapter 2 describes the synthesis, antibacterial activity, and mechanism …

Production Of Bioactive Secondary Metabolites By Florida Harmful Bloom Dinoflagellates Karenia Brevis And Pyrodinium Bahamense, Cheska Burleson

USF Tampa Graduate Theses and Dissertations

Despite the critical role algae serve as primary producers, increases or accumulation of certain algae may result in Harmful Algal Blooms (HABs). Algal toxins from these blooms contribute significantly to incidences of food borne illness, and evidence suggests HABs are expanding in frequency and distribution. Mitigation of these HABs without knowledge of the ecological purpose and biochemical regulation of their toxins is highly unlikely. The production, function, and potential of secondary metabolites produced by the dinoflagellates Karenia brevis and Pyrodinium bahamense, were investigated.

Brevetoxins were demonstrated by two different methods to localize within the cytosol of Karenia brevis. …

Design And Synthesis Of Protein-Protein Interaction Inhibitor Scaffolds, David B. Badger

USF Tampa Graduate Theses and Dissertations

Many currently relevant diseases such as cancer arise from altered biological pathways that rely on protein-protein interactions. The proteins involved in these interactions contain certain functional domains that are responsible for the protein's biological activities. These domains consist of secondary structural elements such as α-helices and Β-sheets which are at the heart of the protein's biological activity. Therefore, designing drugs that inhibit protein-protein interactions by binding to these key secondary structural elements should provide an effective treatment for many diseases. Presented in this dissertation are the designs, syntheses, and biological evaluations for both novel α-helix and novel Β-sheet mimics.

The …

Hierarchy Of Supramolecular Synthons In The Of Design Multi-Component Crystals, Padmini Kavuru

USF Tampa Graduate Theses and Dissertations

Most of the biological systems in nature are sustained by molecular self-assemblies which are the finest examples of supramolecular architectures. Non-covalent interactions are key concepts which govern these molecular assemblies. Inspired by these examples crystal engineering emerged as an important tool in supramolecular chemistry which aids in the invention of new molecular structures with desired properties. Understanding of how the molecules interact at the molecular levels enables one to rationally design novel solid forms with modulated physicochemical properties. This feature of crystal engineering has heightened its position in materials chemistry and is currently one of the most well studied fields …

The Role Of Hsp70 In Cancer: A Study Of The Hsp70 / Akt Relationship, John Koren

USF Tampa Graduate Theses and Dissertations

The Hsp70 family of molecular chaperones is essential for

protein folding, re-folding misfolded client proteins, clearance

of aberrant client proteins, and can also inhibit programmed

cell death. There are two major cytosolic members of this

family: the constitutive Hsc70, and the inducible Hsp72. Under

stress conditions the Hsp70 family protects the cell from

protein related damage by the induction of Hsp72. Hsc70 and

Hsp72 are highly homologous with minor differences in

substrate binding. In cancers, Hsp72 is commonly induced and

this induction is thought to aid in cancer cell survival. In these

studies we demonstrate the differential regulation of the …

Hydrophilic Polymers Of Poly (2-Hydroxy Ethyl Methacrylate) With Tunable Properties For Drug Release, Sequestration Of Blistering Agent, Preparation Of Ultra-Strong Hydrogels & Thermal Stability Of Various Organic Azides, Ramakanth Ananthoji

USF Tampa Graduate Theses and Dissertations

The design and synthesis of new finely tunable porous materials has spurred interest in developing novel uses in a variety of systems. Zeolites, inorganic materials with high thermal and mechanical stability, in particular, have been widely examined for use in applications such as catalysis, ion exchange and separation. A relatively new class of inorganic-organic hybrid materials known as metal-organic frameworks (MOFs) has recently surfaced, and many have exhibited their efficiency in potential applications such as ion exchange and drug delivery. A more recent development is the design and synthesis of a subclass of MOFs based on zeolite topologies (i.e. ZMOFs), …

Protein Profiling Of Adenine Nucleoside And Nucleotide Analogs Binding Proteins Using N6-Biotinylated-8-Azidoadenosine Analogs As Affinity Based Protein Profiling Probes, Shikha Mahajan

USF Tampa Graduate Theses and Dissertations

Identification of differential expressions of proteins in proteomic profiles of biological samples shows great potential as a valuable technique for the early diagnosis of various diseases. An important challenge in modern protein profiling approaches is to reduce the complexity of the samples by limiting the number of proteins that need to be evaluated for distinction in the expression between normal and deceased cells. In this research, an affinity based approach for the enrichment of nucleotide and nucleoside binding proteins from a complex cell proteome has been developed. To achieve this goal, new N6-biotinylated-8-azido-adenosine probes (AdoRs) have been designed and synthesized …

Crystal Engineering Of Multi-Component Crystal Forms: The Opportunities And Challenges In Design, Heather Dawn Marie Clarke

USF Tampa Graduate Theses and Dissertations

There is heightened interest to diversify the range of crystal forms exhibited by active pharmaceutical ingredients (APIs) in the pharmaceutical industry. The crystal form can be regarded as the Achilles' heel in the development of an API as it directly impacts the physicochemical properties, performance and safety of the API. This is of critical importance since the crystal form is the preferred method of oral drug delivery by industry and regulatory bodies. The ability to rationally design materials is a lucrative avenue towards the synthesis of functional molecular solids with customized physicochemical properties such as solubility, bioavailability and stability. Pharmaceutical …

Investigation And Synthesis Of Novel Graphene-Based Nanocomposites For Hydrogen Storage, Anthony Joseph D'Angelo

USF Tampa Graduate Theses and Dissertations

It is of great interest to develop and utilize a high surface area material with optimized hydrogen sorption properties. The need for a renewable energy source to replace automobile gasoline has become more critical in the past decade. Hydrogen is a viable fuel source for automobile usage; however, the question of how hydrogen will be safely and efficiently stored still remains. Critical factors for optimum hydrogen storage include ambient conditions and low activation temperature for adsorption and desorption phenomena. In order for optimum hydrogen adsorption to be achieved, the properties of (1) high surface area, (2) optimum hydrogen adsorption energy, …

Design And Construction Of Functional Metal-Metalloporphyrin Frameworks, Le Meng

USF Tampa Graduate Theses and Dissertations

Porous metal-organic frameworks are a new type of functional materials with potential applications for gas storage, gas separation, catalysis, biomedical and chemical sensors. This thesis describes several porous metal-metalloporphyrin frameworks (MMPFs), which were synthesized with a series of transition metals and 5,15-bis(3,5-dicarboxyphenyl)-10,20-bis(2,6-dibromophenyl)porphine. Among these MMPFs, the cobalt MMPF (CoBrPTC) has a fcu structure, which represents the first porphyrin-based MOF with this topology. CoBrPTC was evaluated as heterogeneous catalyst and demonstrated interesting catalytic performances.

Removal Of Bisphenol A Model Compounds And Related Substances Using Octolig®, Rachael Josephine Alessio

USF Tampa Graduate Theses and Dissertations

Bisphenol A used in the production of polycarbonate plastics and epoxy resins is ubiquitous in the environment. The raw material is released to the environment during the manufacturing process and by leaching from consumer products. Recent studies are suggesting that low-dose amounts of Bisphenol A may have adverse health effects on humans. The possibility of removing Bisphenol A from natural water sources or from solvents used to extract the material from consumer products before they enter the market has been studied. The use of model compounds and related substances (4-isopropylphenol, 4-(t-butyl) phenol, and nitrophenols) have been used to study their …

Compound-Specific Stable Isotopic Analysis Of Protein Amino Acids: Ecological Applications In Modern And Ancient Systems, Greg Ellis

USF Tampa Graduate Theses and Dissertations

Stable isotopic analysis of the major biochemically important elements is an increasingly utilized tool in the study of ecology. Patterns of isotopic fractionation in carbon and nitrogen are used to determine trophic linkages, nutrient pathways, and sources of primary production in numerous contexts. Traditional techniques rely on measurements made of bulk samples such as tissue, but emerging methods using individual chemical compounds provide a means of achieving deeper understanding in a variety of inquiries.

Amino acids, as the building blocks of proteins, are the dominant nitrogen-bearing biomolecules and are a major constituent of all life. Patterns of isotopic fractionation during …

Comparisons Of Observed And Modeled Oh And Ho2 Concentrations During The Ambient Measurement Period Of The Ho(X)Comp Field Campaign, Y. Kanaya, A. Hofzumahaus, H. -P. Dorn, T. Brauers, H. Fuchs, F. Holland

USF St. Petersburg Campus Faculty Publications

A photochemical box model constrained by ancillary observations was used to simulate OH and HO2 concentrations for three days of ambient observations during the HO(x)Comp field campaign held in Julich, Germany in July 2005. Daytime OH levels observed by four instruments were fairly well reproduced to within 33% by a base model run (Regional Atmospheric Chemistry Mechanism with updated isoprene chemistry adapted from Master Chemical Mechanism ver. 3.1) with high R-2 values (0.72-0.97) over a range of isoprene (0.3-2 ppb) and NO (0.1-10 ppb) mixing ratios. Daytime HO2(*) levels, reconstructed from the base model results taking into account the sensitivity …

The Kamlet Laboratories Collection At The University Of South Florida, Dean F. Martin, Karina Bidani

Chemistry Faculty Publications

Jonas Kamlet (1914-1960) and his wife Edna (1915- 2011) founded the Kamlet Laboratory (as it was then called) in 1941 (I). It was in many ways a pioneering consulting laboratory that was unique for its approach and creativity. In 2006, the collected papers of the Kamlet Laboratories that were housed in two storage units in Sarasota, Florida, were donated to the University of South Florida (USF) Library, Tampa Campus, as noted elsewhere (I). This paper describes the background of the laboratory and indicates the potential value of the material in the Kamlet Chemical Laboratories Collection. The collection came to USF …

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 …

Novel Blends Of Sulfur-Tolerant Water-Gas Shift Catalysts For Biofuel Applications, Timothy Michael Roberge

USF Tampa Graduate Theses and Dissertations

As traditional sources of energy become depleted, significant research interest has gone into conversion of biomass into renewable fuels. Biomass-derived synthesis gas typically contains concentrations of approximately 30 to 600 ppm H2S in stream. H2S is a catalyst poison which adversely affects downstream processing of hydrogen for gas to liquid plants. The water-gas shift reaction is an integral part of converting CO and steam to H2 and CO2. Currently, all known water-gas shift catalysts deactivate in sulfur concentrations typical of biomass-derived synthesis gas. Novel catalysts are needed to remain active in the presence of sulfur concentrations in order to boost …

Molecular Dynamics Of The Rna Binding Cavity Of Influenza A Non-Structural Protein 1 (Ns1) Rna Binding Domain, Christi Leigh Whittington

USF Tampa Graduate Theses and Dissertations

Molecular dynamics simulations were performed on the influenza A non-structural protein 1 (NS1) RNA binding domain (RBD), a homodimer. Fourteen simulations were performed at 298K, nine ionized with 0.1M KCl and five with no ions. Several analysis techniques were employed to study RBD residue flexibility. The focus of the study was the RNA binding cavity formed by side chains of helix 2 (chain A) and helix 2’ (chain B) and cavity intermonomeric salt bridges. Opening of the salt bridges D29–R46’ and D29’–R46 was observed in several of the trajectories. The RNA binding cavity has large flexibility, where the dimension and …

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 …