Other Chemistry Commons^™

Exploring Computational Chemistry On Emerging Architectures, David Dewayne Jenkins

Doctoral Dissertations

Emerging architectures, such as next generation microprocessors, graphics processing units, and Intel MIC cards, are being used with increased popularity in high performance computing. Each of these architectures has advantages over previous generations of architectures including performance, programmability, and power efficiency. With the ever-increasing performance of these architectures, scientific computing applications are able to attack larger, more complicated problems. However, since applications perform differently on each of the architectures, it is difficult to determine the best tool for the job. This dissertation makes the following contributions to computer engineering and computational science. First, this work implements the computational chemistry variational …

The Effects Of Color Concentrates On The Rheology Of Tint Bases, Doug James Herrick

Master's Theses

ABSTRACT

THE EFFECTS OF COLOR CONCENTRATES ON THE RHEOLOGY OF TINT BASES

Douglas James Herrick

Waterborne coatings are formulated with a number of different ingredients; water, latex polymers, pigments, surfactants, dispersants, defoamers, biocides, coalescing aids, and rheology modifiers or thickeners. Rheology modifiers are necessary in order to improve the physical properties of the coating before, during, and after application to a substrate. There are two kinds of rheology modifiers used in waterborne coatings; associative thickeners and non-associative thickeners. Coatings formulated with associative thickeners are quite sensitive to coating variations; the slightest change in the formulation has profound effects on the …

Reactions Of Methyl Perfluoroalkyl Ethers With Isopropyl Alcohol: Experimental And Theoretical Studies, Howard Knachel, Vladimir Benin, Chadwick Barklay, Janine C. Birkbeck, Billy D. Faubion, William E. Moddeman

Chemistry Faculty Publications

The reaction of an isomeric mixture of the methyl perfluoroalkyl ether, C4F9OCH3 (Novec-7100), in the presence of isopropyl alcohol (IPA) and/or water has been studied by measuring the rate of product formation using an ion-selective electrode (ISE) for fluoride ion, Karl Fisher coulometric titrations for water, and 1H and 19F NMR spectroscopy for product identification and rate studies. The results showed the methyl perfluoroalkyl ether to be very stable with products forming at the rate of ∼1 ppm per year at a laboratory temperature of 20 °C. Measurements over the temperature range of 6° to 100 °C were made on …

A Reduced Model Of Cavitation Physics For Use In Sonochemistry, Brian Storey, Andrew Szeri

Brian Storey

Sonochemistry involves focusing acoustic energy through cavitation bubbles to increase chemical activity. The violent bubble collapses lead to temperatures of several thousand kelvin, which drive chemical reactions. In previous work, we gave a detailed computational model of a single bubble collapse, taking into account phase change, mass diffusion, heat diffusion and chemical reactions. All of these phenomena are important in determining the conditions at collapse. The present work involves development of a much simpler model that includes all the physics relevant to the determination of the reaction products. Comparisons with the more detailed computations are made; the reduced model is …

Water Vapour, Sonoluminescence And Sonochemistry, Brian Storey, Andrew Szeri

Brian Storey

Sonoluminescence is the production of light from acoustically forced bubbles; sonochemistry is a related chemical processing technique. The two phenomena share a sensitive dependence on the liquid phase. The present work is an investigation of the fate and consequences of water vapour in the interior of strongly forced argon micro–bubbles. Due to the extreme nonlinearity of the volume oscillations, excess water vapour is trapped in the bubble during a rapid inertial collapse. Water vapour is prevented from exiting by relatively slow diffusion and non–equilibrium condensation at the bubble wall. By reducing the compression heating of the mixture and through primarily …

Double Layer In Ionic Liquids: Overscreening Versus Crowding, Martin Z. Bazant, Brian D. Storey, Alexei A. Kornyshev

Brian Storey

We develop a simple Landau-Ginzburg-type continuum theory of solvent-free ionic liquids and use it to predict the structure of the electrical double layer. The model captures overscreening from short-range correlations, dominant at small voltages, and steric constraints of finite ion sizes, which prevail at large voltages. Increasing the voltage gradually suppresses overscreening in favor of the crowding of counterions in a condensed inner layer near the electrode. This prediction, the ion profiles, and the capacitance-voltage dependence are consistent with recent computer simulations and experiments on room-temperature ionic liquids, using a correlation length of order the ion size.

Mixture Segregation Within Sonoluminescence Bubbles, Brian D. Storey, Andrew J. Szeri

Brian Storey

This paper concerns a relaxation of the assumption of uniform mixture composition in the interior of sonoluminescence bubbles. Intense temperature and pressure gradients within the bubble drive relative mass diffusion which overwhelms diffusion driven by concentration gradients. This thermal and pressure diffusion results in a robust compositional inhomogeneity in the bubble which lasts several orders of magnitude longer than the temperature peak or light pulse at the main collapse of the bubble. This effect has important consequences for control of sonoluminescence, gas dynamics, sonochemistry, and the physics of light production.

Patent: Methods Of Treating Fgf21-Associated Disorders, Brian R. Boettcher, Shari L. Caplan, Douglas S. Daniels, Bernhard Hubert Geierstanger, Norio Hamamatsu, Stuart Licht, Andreas Loew, Stephen Craig Weldon

Chemistry Faculty Publications

The invention relates to the identification of new polypeptide and protein variants of fibroblast growth factor 21 (FGF21) that have improved pharmaceutical properties. Also disclosed are methods for treating FGF21-associated disorders, includ ing metabolic conditions.

Heme Binding And Transfer In The Isd Heme Scavenging Pathway Of Staphylococcus Aureus, Michael T. Tiedemann

Electronic Thesis and Dissertation Repository

The antibiotic resistant bacterium Staphylococcus aureus is a significant problem in hospitals and communities worldwide. Survival of the bacterium in the host is reliant on iron scavenging. Staphylococcus aureus has adopted specialized mechanisms for scavenging iron from the host. The cell wall and membrane-associated iron regulated surface determinant (Isd) proteins allow Staphylococcus aureus to scavenge iron from the heme in hemoglobin. There are nine Isd proteins (IsdH, IsdB, IsdA, IsdC, IsdE, IsdD, IsdF, IsdG and IsdI) located at different depths in the cell wall and membrane. Magnetic circular dichroism (MCD) spectroscopy and electrospray ionization mass spectrometry (ESI-MS) have been used …

Improving Analytical Utility Of Surface Enhanced Raman Spectroscopy Through Unique Lithographic Substrate Development, Sabrina Marie Wells

Doctoral Dissertations

Surface enhanced Raman spectroscopy (SERS) has the potential to be a useful analytical technique due to large signal enhancements. Unfortunately, SERS has several drawbacks, including a lack of reproducibility, which inhibits it from being a practical option. These large signals often arise from “hot spots” of extremely high enhancement on nanofeatured metallic substrates, the most common being comprised of aggregated silver colloid. It is difficult to reproducibly create these hot spots due to the randomness of the colloid substrates. However, through controlled substrate fabrication, many problems associated with SERS analysis can be overcome. Electron beam lithography (EBL) combined with reactive-ion …

Synthesis Of Novel Alkaline Earth Tosylate Complexes Through Donor Studies, Adam J. Brooks

Honors Capstone Projects - All

Salt metathesis has become a critical reaction pathway in organometallic chemistry; however, for alkaline earth metals this process is hindered by the need of highly pure and expensive metal iodides as starting materials. This contribution highlights recent attempts to identify inexpensive reagents for salt metathesis. Alkaline earth-tosylates can be prepared cost effectively using p-toluenesulfonic acid in one-pot reactions in water. The coordinated water molecules can be removed by gentle heating under vacuum. The anhydrous tosylates, however, have major solubility limitations as the result of extensive aggregation networks. The goal of this study was to increase the solubility of the tosylates …

Computational Studies Of The N2-H2 Interaction-Induced Dipole Moment, Hailey R. Bureau

Chancellor’s Honors Program Projects

No abstract provided.

Identification And Analysis Of Stereoselective Drug Interactions With Low Density Lipoprotein By High-Performance Affinity Chromatography, Matt Sobansky, David S. Hage

Chemistry Department: Faculty Publications

Columns containing immobilized low density lipoprotein (LDL) were prepared for the analysis of drug interactions with this agent by high-performance affinity chromatography (HPAC). R/SPropranolol was used as a model drug for this study. The LDL columns gave reproducible binding to propranolol over 60 h of continuous use in the presence of pH 7.4, 0.067 M potassium phosphate buffer. Experiments conducted with this type of column through frontal analysis indicated that two types of interactions were occurring between R-propranolol and LDL, while only a single type of interaction was observed between S-propranolol and LDL. The first type …

Quantifying Factors That Influence Metal Ion Release In Photocaged Complexes Using Zincast Derivatives, Shawn Burdette

Shawn C. Burdette

Two generations of nitrobenzhydrol-based photocages for Zn2+ have been prepared and characterized. The first series includes the tridentate ZinCast-1 utilizes a bis-pyridin-2-ylmethyl-aniline ligand that forms a 5,5-chelate ring upon metal binding. The related photocages ZinCast-2 with a N-[2-(pyridine-2-yl)ethyl]-N-(pyridine-2-ylmethyl)aniline (5,6-chelate ring) and ZinCast-3 with a N,N-bis[2-(pyridine-2-yl)ethyl]aniline (6,6-chelate ring) were synthesized for comparative studies. The complexes formed by the ions Cu2+, Zn2+ and Cd2+ with three ZinCast and their photoproducts (ZinUnc) were interrogated by UV-Vis spectroscopy. The studies indicate that ZinCast-1 forms complexes of the highest stability and ZinCast-3 exhibits the most significant changes in metal affinity upon uncaging. These results suggest …

Unusual Activities Of The Thioesterase Domain For The Biosynthesis Of The Polycyclic Tetramate Macrolactam Hsaf In Lysobacter Enzymogenes C3, Lili Lou, Haotong Chen, Ronald Cerny, Yaoyao Li, Yuemao Shen, Liangcheng Du

Ronald Cerny Publications

HSAF is an antifungal natural product with a new mode of action. A rare bacterial iterative PKSNRPS assembles the HSAF skeleton. The biochemical characterization of the NRPS revealed that the thioesterase (TE) domain possesses the activities of both a protease and a peptide ligase. Active site mutagenesis, circular dichroism spectra and homology modeling of the TE structure suggested that the TE may possess uncommon features that may lead to the unusual activities. The iterative PKS-NRPS is found in all polycyclic tetramate macrolactam gene clusters, and the unusual activities of the TE may be common to this type of hybrid PKS-NRPS.

Ccpa Regulates Arginine Biosynthesis In Staphylococcus Aureus Through Repression Of Proline Catabolism, Austin S. Nuxoll, Steven M. Halouska, Marat R. Sadykov, Mark L. Hanke, Kenneth W. Bayles, Tammy Kielian, Robert Powers, Paul D. Fey

Chemistry Department: Faculty Publications

Staphylococcus aureus is a leading cause of community-associated and nosocomial infections. Imperative to the success of S. aureus is the ability to adapt and utilize nutrients that are readily available. Genomic sequencing suggests that S. aureus has the genes required for synthesis of all twenty amino acids. However, in vitro experimentation demonstrates that staphylococci have multiple amino acid auxotrophies, including arginine. Although S. aureus possesses the highly conserved anabolic pathway that synthesizes arginine via glutamate, we demonstrate here that inactivation of ccpA facilitates the synthesis of arginine via the urea cycle utilizing proline as a substrate. Mutations within putA, rocD, …

Crystalline Nano Structures, Barry Chin Li Cheung, Joseph Reese Brewer, Nirmalendu Deo

Chemistry Department: Faculty Publications

The present invention comprises nano obelisks and nanostructures and methods and processes for same. The nano obelisks of the present invention are advantageous structures for use as electron source emitters. For example, the ultra sharp obelisks can be used as an emitter source to generate highly coherent and high energy electrons with high current.

Silica As A Matrix For Encapsulating Proteins:Surface Effects On Protein Structure Assessed By Circular Dichroism Spectroscopy, Daryl K. Eggers, P. J. Calabretta, M. C. Chancellor, C. Torres, G. R. Abel Jr., C. Neihaus, N. J. Birtwhistle, N. M. Khouderchah, G. H. Zemede

Faculty Publications, Chemistry

The encapsulation of biomolecules in solid materials that retain the native properties of the molecule is a desired feature for the development of biosensors and biocatalysts. In the current study, protein entrapment in silica-based materials is explored using the sol-gel technique. This work surveys the effects of silica confinement on the structure of several model polypeptides, including apomyoglobin, copper-zinc superoxide dismutase, polyglutamine, polylysine, and type I antifreeze protein. Changes in the secondary structure of each protein following encapsulation are monitored by circular dichroism spectroscopy. In many cases, silica confinement reduces the fraction of properly-folded protein relative to solution, but addition …

Cbe5e− (E = Al, Ga, In, Tl): Planar Pentacoordinate Carbon In Heptaatomic Clusters, Abril C. Castro, Gerarso Martinez-Guajardo, Thomas Johnson, Jesus M. Ugalde, Yan-Bo Wu, Jose M. Mercero, Thomas Heine, Kelling J. Donald, Gabriel Merino

Chemistry Faculty Publications

A series of clusters with the general formula CBe₅E^- (E = Al, Ga, In, Tl) are theoretically shown to have a planar pentacoordinate carbon atom. The structures show a simple and rigid topological framework—a planar EBe4 ring surrounding a C center, with one of the ring Be–Be bonds capped in-plane by a fifth Be atom. The system is stabilized by a network of multicenter σ bonds in which the central C atom is the acceptor, and π systems as well by which the C atom donates charge to the Be and E atoms that encircle it.

Plane And Simple: Planar Tetracoordinate Carbon Centers In Small Moleculesw, Chad Crigger, Bernard K. Wittmaack, Marina Tawfik, Gabriel Merino, Kelling J. Donald

Chemistry Faculty Publications

A class of neutral 18-electron molecules with planar tetracoordinate carbon (ptC) centers is introduced. We show computationally that when n = 3 the neutral singlet molecule C(BeH)_n(BH₂)_4-n and other isoelectronic (18-valence electron) molecules of main group elements collapse from locally tetrahedral arrangements at the C-center to (near) planar tetracoordinate structures. For C(BeH)₃BH₂ and C(CH₃)(BH₂)Li₂, for example, the tetrahedral type conformation is not even a minimum on the potential energy surface at the B3PW91, MP2(full), or CCSD levels of theory. The Mg analogue C(MgH)₃BH_{2 …}

Unraveling The Structural Complexity In A Single-Stranded Rna Tail: Implications For Efficient Ligand Binding In The Prequeuosine Riboswitch, Catherine D. Eichhorn, Jun Feng, Krishna C. Suddala, Nils G. Walter, Charles L. Brooks Iii, Hashim M. Al-Hashimi

Chemistry Department: Faculty Publications

Single-stranded RNAs (ssRNAs) are ubiquitous RNA elements that serve diverse functional roles. Much of our understanding of ssRNA conformational behavior is limited to structures in which ssRNA directly engages in tertiary interactions or is recognized by proteins. Little is known about the structural and dynamic behavior of free ssRNAs at atomic resolution. Here, we report the collaborative application of nuclear magnetic resonance (NMR) and replica exchange molecular dynamics (REMD) simulations to characterize the 12 nt ssRNA tail derived from the prequeuosine riboswitch. NMR carbon spin relaxation data and residual dipolar coupling measurements reveal a flexible yet stacked core adopting an …

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 …

Use And Development Of Computational Tools In Drug Discovery: From Small Molecules To Cyclic Peptides, Daniel Navarrete Santiago

USF Tampa Graduate Theses and Dissertations

The scope of this work focuses on computationally modeling compounds with protein structures. While the impetus of drug discovery is the innovation of new therapeutic molecules, it also involves distinguishing molecules that would not be an effective drug. This can be achieved by inventing new tools or by refining old tools. Virtual screening (VS, also called docking), the computational modeling of a molecule in a receptor structure, is a staple in predicting a molecule's affinity for an intended target. In our Virtual Target Screening system (also called inverse-docking), VS is used to find high-affinity targets, which can potentially explain absorption, …

A New, Simple, Green And One-Pot Four-Component Synthesis Of Bare And Poly(Α, Γ, L-Glutamic Acid) Capped Silver Nanoparticles, Magdalena Stevanović, Igor Savanović, Vuk Uskoković, Srečo D. Škapin, Ines Bračko, Uroš Jovanović, Dragan Uskoković

Pharmacy Faculty Articles and Research

A simple and green chemical method has been developed to synthesize stable bare and capped silver nanoparticles based on the reduction of silver ions by glucose and capping by poly(α,γ,Lglutamic acid) (PGA). The use of ammonia during synthesis was avoided. PGA has had a dual role in the synthesis and was used as a capping agent to make the silver nanoparticle more biocompatible and to protect the nanoparticles from agglomerating in the liquid medium. The synthesized PGA-capped silver nanoparticles in the size range 5–45 nm were stable over long periods of time, without signs of precipitation. Morphological examination has shown …

Short-Term Associations Between Pm2.5, Black Carbon, Delta-C, And Cardiovascular Diseases In A Large Developing Megacity, Daniel Malashock

Legacy Theses & Dissertations (2009 - 2024)

Introduction: Association between ambient air pollution and cardiovascular disease (CVD) have been demonstrated by many epidemiological studies in developed countries, however few studies have been performed in developing countries of Asia.

An Application Of Camx Process Analysis Tools : Exploring Process Contributions To Extreme Ozone, Nitrogen Oxides And Sulfur Dioxide, David-Anthony Murray

Legacy Theses & Dissertations (2009 - 2024)

The University at Albany Air Quality Forecasting Modeling System (AQFMS) is a state-of-the-art model that generates reliable daily and "day-ahead" air quality forecasts for the Northeastern United States. The three major categories of processes which dictate regional air quality are production from emission sources, horizontal and vertical transport driven by the prevailing meteorology, and chemical transformations. The Advanced Research WRF (ARW) produces meteorological fields. The Sparse Matrix Operator for Kernel Emissions (SMOKE) processes available emission inventories for air quality modeling. The Comprehensive Air Quality Model with extension (CAMx) handles both chemical processes and the integration of ARW-WRF and SMOKE in …

Quantitative Analysis Of Some Important Metals And Metalloids In Tobacco Products By Inductively Coupled Plasma-Mass Spectrometry (Icp-Ms), Syed Ghulam Musharraf, Muhammad Shoaib, Amna Jabbar Siddiqui, Muhammad Najam-Ul-Haq, Aftab Ahmed

Pharmacy Faculty Articles and Research

Background: Large scale usage of tobacco causes a lot of health troubles in human. Various formulations of tobacco are extensively used by the people particularly in developing world. Besides several toxic tobacco constituents some metals and metalloids are also believed to pose health risks. This paper describes inductively coupled plasma-mass spectrometric (ICP-MS) quantification of some important metals and metalloids in various brands of smoked, sniffed, dipped and chewed tobacco products.

Results: A microwave-assisted digestion method was used for sample preparation. The method was validated by analyzing a certified reference material. Percentage relative standard deviation (% R.S.D.) between recovered …

Silica As A Matrix For Encapsulating Proteins:Surface Effects On Protein Structure Assessed By Circular Dichroism Spectroscopy, Daryl K. Eggers, P. J. Calabretta, M. C. Chancellor, C. Torres, G. R. Abel Jr., C. Neihaus, N. J. Birtwhistle, N. M. Khouderchah, G. H. Zemede

Daryl K. Eggers

The encapsulation of biomolecules in solid materials that retain the native properties of the molecule is a desired feature for the development of biosensors and biocatalysts. In the current study, protein entrapment in silica-based materials is explored using the sol-gel technique. This work surveys the effects of silica confinement on the structure of several model polypeptides, including apomyoglobin, copper-zinc superoxide dismutase, polyglutamine, polylysine, and type I antifreeze protein. Changes in the secondary structure of each protein following encapsulation are monitored by circular dichroism spectroscopy. In many cases, silica confinement reduces the fraction of properly-folded protein relative to solution, but addition …

Biosynthesis Of Marineosin, A Spiroaminal Undecylprodiginine Natural Product, Shaimaa Mohamed Salem

Dissertations and Theses

Marineosins A and B are two spiroaminal-ring containing tripyrrole compounds isolated from the marine actinomycete, Streptomyces CNQ-617, and were found to possess potent and selective cytotoxic activity against leukemia and melanoma. Marineosins belong to the prodiginines class of natural products, examples of which are undecylprodiginine and streptorubin B. Unlike marineosins, prodiginines structures are characterized by the presence of fully conjugated tripyrrole nucleus linked to an alkyl chain (that lacks any oxygen). Cyclic prodiginines arise from an oxidative cyclization of the alkyl chain onto the tripyrrole, a step catalyzed by Rieske-oxygenase like enzymes such as RedG. The biosynthesis of prodiginines is …

Pegylated Silicon Nanowire Coated Silica Microparticles For Drug Delivery Across Intestinal Epithelium, Vuk Uskoković, Phin-Peng Lee, Laura Walsh, Kathleen Fischer, Tejal Dasai

Pharmacy Faculty Articles and Research

Composite particles made by growing nanoscopic silicon wires from the surface of monodispersed, microsized silica beads were tested in this study for their ability to affect the integrity and permeability of an epithelial cell layer. Polyethylene glycol (PEG) is known to sterically stabilize particles and prevent protein binding; as such, it is a routine way to impart in vivo longevity to drug carriers. The effect of the silica beads, both with and without silicon nanowires and PEG, on the disruption of the tight junctions in Caco-2 cells was evaluated by means of: (a) analysis of the localization of zonula occludens-1 …