Chemistry Commons^™

Inhibitors Of NΑ-Acetyl-L-Ornithine Deacetylase: Synthesis, Characterization And Analysis Of Their Inhibitory Potency, J. Hlavacek, J. Picha, V. Vanek, J. Jiracek, J. Slaninova, V. Fucik, M. Budesinsky, Danuta M. Gillner, Richard C. Holz

Chemistry Faculty Research and Publications

A series of N ^α-acyl (alkyl)- and N ^α-alkoxycarbonyl-derivatives of l- and d-ornithine were prepared, characterized, and analyzed for their potency toward the bacterial enzyme N ^α-acetyl-l-ornithine deacetylase (ArgE). ArgE catalyzes the conversion of N ^α-acetyl-l-ornithine to l-ornithine in the fifth step of the biosynthetic pathway for arginine, a necessary step for bacterial growth. Most of the compounds tested provided IC₅₀ values in the μM range toward ArgE, indicating that they are moderately strong inhibitors. N ^α-chloroacetyl-l-ornithine (1g) was the best inhibitor tested toward ArgE providing an IC₅₀ value of 85 …

Conformational Change And Topological Stability Of Proteins, Jeffrey Andrew Tibbitt

Chemistry & Biochemistry Theses & Dissertations

The conformation and topology of a protein changes when stabilizing forces are absent, but the mechanisms by which these changes occur remains elusive. This dissertation aims to broaden the understandings. On the conformational level, the M20 loop conformers of E. coli dihydrofolate reductase are interrogated to identify factors responsible for their stability as well as to determine how one conformer might change into another. Molecular dynamics is used to simulate the open, closed and occluded conformers (observed in X-ray crystal structures) under a series of different single ligand conditions. Analysis shows that all open conformers move to a similar new …

Molecular Characterization Of The Soluble Fraction Of Atmospheric Particulate Matter Obtained By Chemical Oxidation With Nitric Acid, Amanda Susan Priest

Chemistry & Biochemistry Theses & Dissertations

The availability of information regarding the composition of ambient atmospheric particulate matter and the transformations that these compounds may undergo upon atmospheric transit is surprisingly absent. Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry is used in this study to rapidly evaluate the composition of the water-soluble organic fraction of standard and collected atmospheric particulate matter samples, and the changes that these mixtures undergo upon oxidation with nitric acid. The standard samples include representative particulate matter collected over the course of a year in Washington, D.C. and particulate matter from the exhaust of a diesel-powered engine. The collected sample …

Guest-Free Monolayer Clathrate And Its Coexistence With Two-Dimensional High-Density Ice, Jaeil Bai, C. Austen Angell, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

Three-dimensional (3D) gas clathrates are ice-like but distinguished from bulk ices by containing polyhedral nano-cages to accommodate small gas molecules. Without space filling by gas molecules, standalone 3D clathrates have not been observed to form in the laboratory, and they appear to be unstable except at negative pressure. Thus far, experimental evidence for guest‐free clathrates has only been found in germanium and silicon, although guest‐free hydrate clathrates have been found, in recent simulations, able to grow from cold stretched water, if first nucleated. Herein, we report simulation evidence of spontaneous formation of monolayer clathrate ice, with or without gas molecules, …

Electrodeposited Silica Thin Films, Debbie Campbell-Rance

Theses and Dissertations

Sol-gel derived silica thin film synthesis has gained prominence because of the mild processing conditions and widespread understanding of the chemistry of the process. Traditionally, silicate films are prepared by spin- and dip-coating but these materials lack the desired porosity for sensing, separations and catalysis applications. Electrochemical deposition was proposed to improve the porosity of silicate films. The main aims of this work were threefold. First we wanted to elucidate what parameters influenced film formation during electrodeposition. Then we wanted to understand how these parameters affected the morphology of the materials prepared. These films were characterized by profilometry, AFM, and …

Solid-Phase Synthesis Of Peptide−Viologen Conjugates, Joseph J. Reczek, Elisa Rebolini, Adam R. Urbach

Chemistry Faculty Research

This paper presents a robust method for the conjugation of viologens to peptides using an amide coupling strategy that is compatible with standard Fmoc solid-phase peptide synthesis. Methodology is presented for monitoring the milligram scale process quantitatively by UV spectroscopy. This chemistry enables the synthesis of a broad range of asymmetric viologens in high yield at room temperature and is compatible with a wide range of functional groups, including amine, guanidinyl, thiol, carboxylic acid, phenol, and indole.

Metal-Organic Materials: From Design Principles To Practical Applications, Mohamed H. Alkordi

USF Tampa Graduate Theses and Dissertations

The works presented herein outline rational design approaches towards construction of solid state materials with great potentials to answer some of current demanding applications. Specifically, the materials targeted are metal−organic materials with desirable structural features and functional properties. Metal−organic materials are constructed from organic linker molecules and metal ions under relatively mild solvothermal reaction conditions that preserve the structural features of the relatively simple building blocks. Therefore, it is feasible to conceive a retrospective pathway of the reaction and thus deconstruct the desirable structures into simple, chemicallyrelevant, building blocks in an approach known as the molecular building block approach. Due …

Effects Of Uvb-Induced Oxidative Stress On Protein Expression And Specific Protein Oxidation In Normal Human Epithelial Keratinocytes: A Proteomic Approach, Marzia Perluigi, Fabio Di Domenico, Carla Blarzino, Cesira Foppoli, Chiara Cini, Alessandra Giorgi, Caterina Grillo, Federico De Marco, D. Allan Butterfield, Maria E. Schininà, Raffaella Coccia

Chemistry Faculty Publications

BACKGROUND: The UVB component of solar ultraviolet irradiation is one of the major risk factors for the development of skin cancer in humans. UVB exposure elicits an increased generation of reactive oxygen species (ROS), which are responsible for oxidative damage to proteins, DNA, RNA and lipids. In order to examine the biological impact of UVB irradiation on skin cells, we used a parallel proteomics approach to analyze the protein expression profile and to identify oxidatively modified proteins in normal human epithelial keratinocytes.

RESULTS: The expression levels of fifteen proteins - involved in maintaining the cytoskeleton integrity, removal of damaged proteins …

Crossed-Beams And Theoretical Studies Of Hyperthermal Reactions Of O(3P) With Hcl†, Jianming Zhang, Amy L. Brunsvold, Hari P. Upadhyaya, Timothy K. Minton, Jon P. Camden, Sophya V. Garashchuk, George C. Schatz

Faculty Publications

The reaction of O(3 P) with HCl at hyperthermal collision energies (45-116 kcal mol-1 ) has been investigated with crossed-molecular beams experiments and direct dynamics quasi-classical trajectory calculations. The reaction may proceed by two primary pathways, (1) H-atom abstraction to produce OH and Cl and (2) H-atom elimination to produce H and ClO. The H-atom abstraction reaction follows a stripping mechanism, in which the reagent O atom approaches the HCl molecule at large impact parameters and the OH product is scattered in the forward direction, defined as the initial direction of the reagent O atoms. The H-atom elimination reaction is …

Electrospray Ionization Mass Spectrometry For The Characterization Of Covalent And Noncovalent Polynuclear Platinum Compounds Interacting With Bio-Molecules, John Mangrum

Theses and Dissertations

Polynuclear platinum compounds represent a new class of potential platinum anticancer therapeutics. Derived from the most widely used platinum anticancer drug, cisplatin, these novel compounds are distinct in their interactions with bio-molecules. The effectiveness of platinum anticancer agents is influenced by three pharmacological factors: (i) their resistance to deactivating sulfur nucleophiles, (ii) the ability to gain cellular entry and efficient cellular uptake, and (iii) the ability to form stable and specific complexes with DNA. BBR 3464, the first multinuclear platinum compound to reach phase II clinical trials, has created a new approach to cancer drug design. Large, highly charged platinum …

Effect Of Nanoscale Confinement On Glass Transition Of Polystyrene Domains From Self-Assembly Of Block Copolymers, C. G. Robertson, T. E. Hogan, M. Rackaitis, Judit D. Puskas, X. Wang

Chemical, Biomolecular, and Corrosion Engineering Faculty Research

The understanding of size-dependent properties is key to the implementation of nanotechnology. One controversial and unresolved topic is the influence of characteristic size on the glass transition temperature (T(g)) for ultrathin films and other nanoscale geometries. We show that T(g) does depend on size for polystyrene spherical domains with diameters from 20 to 70 nm which are formed from phase separation of diblock copolymers containing a poly(styrene-co-butadiene) soft block and a polystyrene hard block. A comparison of our data with published results on other block copolymer systems indicates that the size dependence of T(g) is a consequence of diffuse interfaces …

Investigation Of The Thermal Degradation Of Polyurea: The Effect Of Ammonium Polyphosphate And Expandable Graphite, Walid Awad, Charles A. Wilkie

Chemistry Faculty Research and Publications

Polyurea was compounded with ammonium polyphosphate and expandable graphite and the morphology was studied by atomic force microscopy. The thermal degradation of polyurea and polyurea compounded with the additives has been investigated using thermogravimetry coupled with Fourier Transform infrared spectroscopy and mass spectrometry. The study of the thermal degradation and the parameters affecting the thermal stability of PU is essential in order to effectively design flame retarded polyurea. In general, thermal decomposition of polyurea occurs in two steps assigned to the degradation of the hard segment and soft segment, respectively. Adding these additives accelerates the decomposition reaction of polyurea. However, …

Role Of Members Of The Phosducin Gene Family In Protein Translation And Folding, Nana Sono-Koree

Theses and Dissertations

G proteins regulate various physiological processes by way of transducing a wide variety of signals ranging from hormonal to sensory stimuli. Malfunctions in G protein signaling lead to numerous diseases. G protein signaling begins with binding of a ligand to a G protein-coupled receptor resulting in a conformational change that leads to the exchange of a GDP for a GTP on G α. The GTP bound α subunit dissociates for its stable Gβγ dimer partner. G α-GTP and Gβγ control the activity of effector enzymes and ion channels that ultimately orchestrate the cellular response to stimulus. Current reports have shown …

Improved Modeling Of Midlatitude D-Region Ionospheric Absorption Of High Frequency Radio Signals During Solar X-Ray Flares, Evelyn A. Schumer

Theses and Dissertations

The purpose of this research was to improve modeling of midlatitude D-region ionospheric absorption of high frequency radio signals during solar X-ray flares through analysis of HF propagation data obtained during the HF Investigation of D-region Ionospheric Variation Experiment (HIDIVE) and obtained at the Canadian Space Agency NORSTAR riometer in Pinawa, Manitoba, Canada and X-ray flux data, as reported by GOES satellites. The findings of the data analysis were then used to validate and suggest improvements for two existing HF absorption models, the operational Space Weather Prediction Center (SWPC) D-region Absorption model and the physical AbbyNormal model. Analysis of the …

Three Dimensional Positron Annihilation Momentum Measurement Technique (3dpamm) Applied To Measure Oxygen-Atom Defects In 6h Silicon Carbide, Christopher S. Williams

Theses and Dissertations

A three-dimensional Positron Annihilation Spectroscopy System (3DPASS) capable to simultaneously measure three-dimensional electron-positron (e--e+) momentum densities measuring photons derived from e--e+ annihilation events was designed and characterized. 3DPASS simultaneously collects a single data set of correlated energies and positions for two coincident annihilation photons using solid-state double-sided strip detectors (DSSD). Positions of photons were determined using an interpolation method which measures a figure-of-merit proportional to the areas of transient charges induced on both charge collection strips directly adjacent to the charge collection strips interacting with the annihilation photons. The subpixel resolution was measured for both double-sided strip detectors (DSSD) and …

Optical Properties Of Si, Ge, Gaas, Gasb, Inas, And Inp At Elevated Temperatures, Thomas R. Harris

Theses and Dissertations

Investigation of the optical and electrical behavior of some semiconductors at very high temperatures has not been an area of much study, at least not experimentally. The importance of such research becomes obvious due to the effects of high temperatures on semiconductor devices such as infrared detectors and light emitters. Besides the destructive effects of thermal stress and melting, changes in the optical properties of the material can greatly affect device performance. In this research, the infrared absorption of Si, Ge, GaAs, GaSb, InAs, and InP was measured from 0.6 to 25 μm at temperatures ranging from 295 up to …

Experimental Validation Techniques For The Heleeos Off-Axis Laser Propagation Model, John D. Haiducek

Theses and Dissertations

The High Energy Laser End-to-End Operational Simulation (HELEEOS) off-axis scattering algorithm is designed to predict the irradiance that will be detected at a given off-axis location due to atmospheric scattering of a high-energy laser. The HELEEOS system models the propagation of the laser through the atmosphere, accounting for such effects as turbulence, thermal blooming, and atmospheric absorption. The HELEEOS off-axis scattering algorithm uses the scattering phase functions of the Mie scattering models to predict the amount of radiation that will be scattered toward a particular observation location from each point along the beam path, and the total irradiance that will …

Changes To Electrical Conductivity In Irradiated Carbon-Nickel Nanocomposites, David F. Coy

Theses and Dissertations

Pre and post irradiation resistivity and XAFS measurements have been conducted to examine the effects of 0.5 MeV electron irradiations on nickel-carbon composites. Results showed a decrease in surface resistivity in all sample types of 14-30% following irradiation with a total electron exposure of 4 x 10^-16 cm^-2. Results also showed a corresponding decrease in NiO content for the irradiated samples as compared to measurements of non-irradiated samples. Surface resistivity measurement capabilities were established and measurement techniques refined to produce repeatable results of sufficient precision to discern changes in resistivity for an exposure of 2 x 10 …

In-Situ, Gate Bias Dependent Study Of Neutron Irradiation Effects On Algan/Gan Hfets, Janusz K. Mikina

Theses and Dissertations

AlGaN/GaN Heterostructure Field Effect Transistors (HFETs) have come under increased study in recent years due to their highly desirable material and electrical properties and survivability even during and after exposure to extreme temperature and radiation environments. In this study, unpassivated and SiN passivated Al_0.27Ga_0.73N/GaN HFETs were subjected to neutron radiation at 120 K. The primary focus of the research was the effects of neutron irradiation on drain current, gate leakage current, threshold voltage shift, gate-channel capacitance, and the effects of biasing the gate during irradiation. In-situ measurements were conducted on transistor current, gate-channel capacitance, and gate …

The Material Properties Of Cssnbr3 And Csbr:Sn-1% And Their Potential As Scintillator Detector Material, Neal B. Kleinschmidt

Theses and Dissertations

The search for superior nuclear radiation detection materials is ongoing. Current scintillator materials using Thallium doped Sodium Iodide or Cesium Iodide are the benchmarks for ease of use and quick identification of isotope species. This research aims to explore Cesium Bromide doped with 1% molar tin (CsBr:Sn-1%) and Cesium Tin Bromide (CsSnBr₃) as candidate materials for a new scintillator. The techniques of Extended X-Ray Absorption Fine Structure (EXAFS), X-Ray Absorption Near Edge Structure (XANES) and Cathodoluminescence are used to determine the suit- ability of CsSnBr3 and CsBr:Sn-1% with Sn⁴⁺ as a potential scintillator materials and explore their …

The Asymmetric Phase-Transfer Catalyzed Alkylation Of Imidazolyl Ketones And Aryl Acetates And Their Applications To Total Synthesis, Michael Andrew Christiansen

Theses and Dissertations

Phase-transfer catalysts derived from the cinchona alkaloids cinchonine and cinchonidine are widely used in the asymmetric alkylation of substrates bearing moieties that resonance stabilize their enolates. The investigation of α-oxygenated esters revealed decreased α-proton acidity, indicating the oxygen's overall destabilizing effect on enolates by electron-pair repulsion. Alkylation of α-oxygenated aryl ketones with various alkyl halides proved successful with a cinchonidine catalyst, giving products with high yield and enantioselectivity. The resulting compounds were converted to esters through modified Baeyer-Villiger oxidation. Alkylation with indolyl electrophiles gave products that underwent decomposition under Baeyer-Villiger conditions. Alternative N-methylimidazolyl ketones were explored. Alkylated imidazolyl ketones, obtained …

Calculation Of Collisional Cross Sections For The ²P3/2 > ²P1/2 Transition In Alkali-Noble Gas Systems, Samuel D. Butler

Theses and Dissertations

Collisional cross sections were calculated as a function of energy for two coupled one dimensional, spherically symmetric potentials. The Split Operator Method was used to propagate an initial Moller state, chosen to be a Gaussian in the asymptotic limit, through a potential. The correlation between the wave packet and Moller final state was calculated at each time step. Using the Channel Packet Method, the correlation function was used to obtain scattering matrix elements. From scattering matrix elements for several different effective potential values and using the Method of Partial Waves, the collisional cross section is calculated for the transition from …

Atomic Details Of Near-Transition State Conformers For Enzyme Phosphoryl Transfer Revealed By Mgf3− Rather Than By Phosphoranes, Nicola J. Baxter, Matthew W. Bowler, Tooba Alizadeh, Matthew J. Cliff, Andrea M. Hounslow, Bin Wu, David B. Berkowitz, Nicholas H. Williams, G. Michael Blackburn, Jonathan P. Waltho

David Berkowitz Publications

Prior evidence supporting the direct observation of phosphorane intermediates in enzymatic phosphoryl transfer reactions was based on the interpretation of electron density corresponding to trigonal species bridging the donor and acceptor atoms. Close examination of the crystalline state of β-phosphoglucomutase, the archetypal phosphorane intermediate-containing enzyme, reveals that the trigonal species is not PO−3 , but is MgF−3 (trifluoromagnesate). Although MgF−3 complexes are transition state analogues rather than phosphoryl group transfer reaction intermediates, the presence of fluorine nuclei in near-transition state conformations offers new opportunities to explore the nature of the interactions, in particular the independent measures of local electrostatic and …

Depositional Ice Nucleation On Solid Ammonium Sulfate And Glutaric Acid Particles, K. J. Baustian, M. E. Wise, M. A. Tolbert

CUP Faculty Research

Heterogeneous ice nucleation on solid ammonium sulfate and glutaric acid particles was studied using optical microscopy and Raman spectroscopy. Optical microscopy was used to detect selective nucleation events as water vapor was slowly introduced into an environmental sample cell. Particles that nucleated ice were dried via sublimation and examined in detail using Raman spectroscopy. Depositional ice nucleation is highly selective and occurred preferentially on just a few ammonium sulfate and glutaric acid particles in each sample. For freezing temperatures between 214 K and 235 K an average ice saturation ratio of S = 1.10±0.07 for solid ammonium sulfate was observed. …

Reactive Layer-By-Layer Assembly Of Suspended Thin Films And Semipermeable Membranes At Interfaces Created Between Aqueous And Organic Phases, Maren E. Buck, David M. Lynn

Chemistry: Faculty Publications

Thin films of polymer suspended across the openings of pores, channels, and microcavities are of interest in a broad range of fundamental and applied contexts. A "reactive" layer-by-layer approach Is demonstrated for the fabrication of suspended thin films and semipermeable membranes that makes use of liquid/ liquid interfaces created between immiscible aqueous and organic phases as templates for film fabrication (see image). (Figure Presented).

Time-Resolved Infrared Spectroscopy And Density Functional Theory Study Of Weak Interactions Of Metal Carbonyls And Organic Solvents, Carolyn Evans Sheffield

Theses and Dissertations

Pulsed laser flash photolysis of M(CO)6 (M = Cr, W) in cyclohexane with a small amount of benzene results in three sequential reactions. The first is the photodissociation of the parent to yield a M(CO)5:C6H12 complex, which takes place faster than the time resolution of our experiments. The second reaction is the replacement of the cyclohexane ligand with benzene to form a M(CO)5:C6H6 complex, in which benzene is coordinated to the metal via one side of the ring. This complex then falls apart in solution as M(CO)5 coordinates with a trace impurity in the solution that is likely water. Kinetic …

An Electrochemical Cell For The Efficient Turn Around Of Wafer Working Electrodes, Nicholas Wozniak, Alyssa Frey, Lucas Osterbur, Timothy Boman, Jennifer R. Hampton

Faculty Publications

We present a new design for an electrochemical cell for use with wafer working electrodes. The key feature of the design is the use of half turn thumb screws to form a liquid-tight seal between an o-ring and the sample surface. The assembly or disassembly of the cell requires a half turn of each thumb screw, which facilitates the quick turn around of wafer samples. The electrochemical performance of the cell is demonstrated by cyclic voltammetry and double step chronoamperometry measurements of the ferricyanide/ferrocyanide couple.

Utilizing Service Learning In The Analytical Chemistry Classroom, Kimberly D. Chichester, Colleen Dugan, Amanda Lewis, Maryann Herman, Irene Kimaru

Chemistry Faculty/Staff Publications

Service learning has been incorporated into the Analytical Chemistry Laboratory to give students a real world sampling experience including both soil and water, alongside professionals in their fields. Analysis of the soil and water includes metals, suspended solids, phosphorus and nitrogen containing compounds requiring knowledge of several different instrumental and wet chemical techniques. Most educational experiences do not afford students the chance to see the real world applications of their classroom knowledge, but with the service learning aspects this deficiency has been resolved. In the soil experience, students provide homeowners from the Highland Park and South Wedge neighbors with lead …

Quasispecies-Like Behavior Observed In Catalytic Rna Populations Evolving In A Test Tube, Carolina Diaz Arenas, Niles Lehman

Chemistry Faculty Publications and Presentations

Background: During the RNA World, molecular populations were probably very small and highly susceptible to the force of strong random drift. In conjunction with Muller's Ratchet, this would have imposed difficulties for the preservation of the genetic information and the survival of the populations. Mechanisms that allowed these nascent populations to overcome this problem must have been advantageous.

Results: Using continuous in vitro evolution experimentation with an increased mutation rate imposed by MnCl2, it was found that clonal 100-molecule populations of ribozymes clearly exhibit certain characteristics of a quasispecies. This is the first time this has been seen …

Nuclear Quantum Effects In The Structure And Lineshapes Of The N2 Near-Edge X-Ray Absorption Fine Structure Spectrum, Shervin Fatehi, Craig P. Schwartz, Richard J. Saykally, David Prendergast

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

We study the relative ability of several models of x-ray absorption spectra to capture the Franck–Condon structure apparent from an experiment on gaseous nitrogen. In doing so, we adopt the Born–Oppenheimer approximation and a constrained density functional theory method for computing the energies of the x-ray-excited molecule. Starting from an otherwise classical model for the spectrum, we systematically introduce more realistic physics, first by substituting the quantum mechanical nuclear radial density in the bond separation R for the classical radial density, then by adding the effect of zero-point energy and other level shifts, and finally by including explicit rovibrational quantization …