Digital Commons Network^™

A Concise Synthesis Of Β-Sitosterol And Other Phytosterols, Jiliang Hang, Patrick Dussault

Patrick Dussault Publications

A convenient synthesis of sidechain-modified phytosterols is achieved via a temporary masking of the stigmasterol 5,6-alkene as an epoxide. Following performance of the desired modification, the alkene is regenerated through a mild deoxygenation. The approach is applied to the syntheses of β-sitosterol and campesterol acetate, and suggests a facile route to the (Z)-isomers of Δ^22–23 phytosterols.

Includes Supplementary Data.

The Synthesis, Characterization, And Electrochemical Study Of Tris(Pyrazolyl)-Type Iron(Ii) Complexes, Iron(Ii) Sulfur- And Selenium-Containing Complexes, And Tris(Pyrazolyl)-Type Ruthenium(Ii) Complexes, Christopher Underwood

All Theses

Highly reactive radical species such as hydroxyl radical cause oxidative stress, resulting in chronic or degenerative diseases. In the biological Fenton reaction, iron(II) generates hydroxyl radical, OH, but only within a specific electrochemical potential window (-324 mV to 640 mV). Selenium and sulfur compounds have been extensively studied for their antioxidant properties, and they may exert their effects by binding iron(II) and shifting its electrochemical potential out of this window. This work has investigated the synthesis and electrochemical characterization of iron(II) chalcogenate complexes and iron(II) chalcogenone complexes. Cyclic voltammetry (CV) of [Fe(EPh)4][(PPh4)2] (E = S, Se) complexes shows Fe2+/3+ redox …

Novel Neomycin Conjugates For Multi-Recognition Of Nucleic Acids, Albert Willis

All Dissertations

Neomycin is an aminoglycoside antibiotic known for its high affinity for RNA duplex structures. Recent developments from our labs have indicated that aminoglycoside binding is not limited to RNA, but to nucleic acids that, like RNA, adopt conformations similar to A-form. Our group sought to further expand the utility of aminoglycoside binding to B-DNA structures by conjugating neomycin, an aminoglycoside antibiotic, with the B-DNA minor groove binding ligand Hoechst 33258. Envisioning a dual groove-binding mode, we have extended the potential recognition process to include a third, intercalative moiety. Furthermore, we observe remarkable recognition of such conjugates with RNA duplex. Spectroscopic …

Synthesis And Optical Properties Of Silver Nanostructures, John Heckel

All Dissertations

Silver nanoparticles interact with light via the excitation of plasmon resonances that are the collective oscillations of the free electron density. This excitation represents the most efficient mechanism for the interaction of light with matter and therefore the nanoparticles are of great interest for both fundamental and practical points of view. In the following dissertation, silver nanoparticles, core-shell nanoparticles, and silver nanoparticle clusters were synthesized and there optical properties were investigated.
Chapter 1 contains general background information about the optical properties of bulk and silver nanoparticles. It also contains a concise description of two of my collaborative projects that did …

Preparation And Studies Of Fluorescent Carbon Nanomaterials, Xin Wang

All Dissertations

There have been rapid advances in the development and applications of semiconductor quantum dots (QDs) represented by CdSe/ZnS. However, a serious limitation of these QDs is the necessary use of toxic heavy metals. Fluorescent 'carbon dots' (surface passivated carbon nanoparticles) are developed as alternative to classical semiconductor QDs.
The carbon dots could be made to be highly fluorescence, with emission quantum yields close to 60%. Their optical properties resemble bandgap transitions found in nanoscale semiconductors, suggesting that carbon particles at the nanoscale acquire essentially semiconductor-like characteristics.
The fluorescence in carbon dots could be quenched efficiently by electron acceptor or donor …

Biochemical Characterization Of Theromin, A Novel Leech Inhibitor, And The Interaction Between The Fourth Metalbinding Domain Of Wilson Disease Protein And Its Copper(I) Chaperone Hah1, Brian A. Zeider

Dissertations

Theromin, a novel thrombin inhibitor from the leech Theromyzon tessulatum, has been shown to be the strongest inhibitor to date. There has been a lot of attention on direct thrombin inhibitors as a much more efficient drug for anticoagulation therapy. One main reason for the need of strong direct thrombin inhibitors is that the current therapy, heparin, causes alternative clotting events in some patients where antibodies are made to the heparin/thrombin complex and causes clots to occur by different methods. Recently there has been a strong inhibitor from a leech used, hirudin, that can inhibit with a K_{i …}

Nuclear Magnetic Resonance Affinity Screening Methods For Functional Annotation Of Proteins And Drug Discovery, Matthew D. Shortridge

Department of Chemistry: Dissertations, Theses, and Student Research

With nearly 1,350 complete genome sequences available our understanding of biology at the molecular level has never been more complete. A consequence of these sequencing projects was the discovery of large functionally unannotated segments of each genome. The genes (and proteins they encode) found in these unannotated regions are considered “hypothetical proteins”. Current estimates suggest between 12%-50% of the known gene sequences are functionally unannotated. Incomplete functional annotation of the various genomes significantly limits our understanding of biology. Pragmatically, identifying the functions of these proteins could lead to new therapeutics; making functional annotation of paramount importance.

This dissertation describes the …

Systematic Approach To Electrostatically Induced 2d Crystallization Of Nanoparticles At Liquid Interfaces, Sumit Kewalramani, Suntao Wang, Yuan Lin, Huong Giang Nguyen, Qian Wang, Masafumi Fukuto, Lin Yang

Faculty Publications

We report an experimental demonstration of a strategy for inducing two-dimensional (2D)crystallization of charged nanoparticles on oppositely charged fluid interfaces. This strategy aims to maximize the interfacial adsorption of nanoparticles, and hence their lateral packing density, by utilizing a combination of weakly charged particles and a high surface charge density on the planar interface. In order to test this approach, we investigated the assembly of cowpea mosaic virus (CPMV) on positively charged lipid monolayers at the aqueous solution surface, by means of in situX-ray scattering measurements at the liquid–vapor interface. Theassembly was studied as a function of the solution …

The Distribution Of Dna Translocation Times In Solid-State Nanopores, Jiali Li, David Talaga

Department of Chemistry and Biochemistry Faculty Scholarship and Creative Works

This paper systematically investigates the effects of solution viscosity, applied voltage and DNA chain length on the distribution of DNA translocation times through 8 ± 2 nm diameter silicon nitride nanopores. Linear dsDNA translocation events were selected based on the magnitude of current blockage and accumulated into scatter plots of current blockage and event duration (translocation time). The translocation time distribution was fitted to the solution of a Smoluchowski-type equation for 1D biased diffusion to a sink. The DNA drifting speed under bias and diffusion constant were extracted from the fits as functions of solution viscosity, applied voltage and DNA …

Work Towards The Isolation And Characterization Of The Muscle Isoform Of Glucose 1,6-Bisphosphatase, Caleb J. Hiller

Theses and Dissertations

Glucose 1,6-bisphosphate is an important small molecule involved in the regulation of glycolysis. Four enzymes synthesize this compound. One enzyme is known to degrade it, glucose 1,6-bisphosphatase. Other groups have produced work that indicates that there are two isoforms of this enzyme, one predominant in the brain and one in the muscle. This thesis contains the work performed in attempts to isolate and characterize the muscle isoform of glucose 1,6-bisphosphatase. While this enzyme was not isolated, much was learned about it and the results from this work may help in the future identification of this enzyme.

Design, Synthesis & Biological Activity Of Novel Protein Tyrosine Phosphatase (Ptp) Mimetics, Sridhar Reddy Kaulagari

USF Tampa Graduate Theses and Dissertations

Protein phosphorylation is a post translational modification of proteins in which a serine, a threonine or a tyrosine residue is phosphorylated by an enzyme, kinase. Phosphorylation of proteins is a reversible and very important regulatory mechanism that occurs in both prokaryotes and eukaryotes. Phosphorylation turns many protein enzymes on and off, preventing or causing many diseases such as diabetes, cancer and rheumatoid arthritis. The phosphorylation on tyrosine residues of proteins is essential for transmission of signals for cell growth, proliferation and differentiation. Protein tyrosine phosphatases (PTPs) in concert with protein tyrosine kinases (PTKs) regulate many signal transduction pathways by controlling …

A Highly Efficient Bismuth Salts-Catalyzed Route For The Synthesis Of Alpha-Aminophosphonates, Antara Banik, Sahil Batta, Debasish Bandyopadhyay, Bimal K. Banik

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

A convenient synthesis of different types of α-amino phosphonates via one-pot solvent-free three component reactions of aldehydes, amines and phosphites catalyzed by bismuth salts has been investigated. Bismuth triflate is found to be the most effective catalyst for this reaction.

Interaction-Dependent Pcr: Identification Of Ligand-Target Pairs From Libraries Of Ligands And Libraries Of Targets In A Single Solution-Phase Experiment, Lynn M. Mcgregor, David J. Gorin, Christoph E. Dumelin, David R. Liu

Chemistry: Faculty Publications

Interaction-dependent PCR (IDPCR) is a solution-phase method to identify binding partners from combined libraries of small-molecule ligands and targets in a single experiment. Binding between DNA-linked targets and DNA-linked ligands induces formation of an extendable duplex. Extension links codes that identify the ligand and target into one selectively amplifiable DNA molecule. In a model selection, IDPCR resulted in the enrichment of DNA encoding all five known protein-ligand pairs out of 67 599 possible sequences.

The Molecular Transport And Intercalation Of Guest Molecules Into Hydrogen–Bonded Metal-Organic Frameworks (Hmofs), Greg Anthony Hogan

Dissertations

The process of molecular transport and intercalation has been widely studied for many years, resulting in the discovery of molecular frameworks that are capable of hosting guest molecules or ions. Layered and porous metal-organic frameworks (MOFs) have been found to have applications in the field of catalysis, storage, separations, and ion-exchange. While MOFs are perhaps stronger materials, HMOFs have the advantage of being easily modifiable and more flexible. Because HMOFs have not been extensively studied for their ability to host molecules, and because their ability to withstand guest loss and guest exchange is essentially unknown, here we report the synthesis …

Dockomatic - Automated Ligand Creation And Docking, Casey W. Bullock, Reed B. Jacob, Owen M. Mcdougal, Greg Hampikian, Tim Andersen

Chemistry and Biochemistry Faculty Publications and Presentations

Background: The application of computational modeling to rationally design drugs and characterize macro biomolecular receptors has proven increasingly useful due to the accessibility of computing clusters and clouds. AutoDock is a well-known and powerful software program used to model ligand to receptor binding interactions. In its current version, AutoDock requires significant amounts of user time to setup and run jobs, and collect results. This paper presents DockoMatic, a user friendly Graphical User Interface (GUI) application that eases and automates the creation and management of AutoDock jobs for high throughput screening of ligand to receptor interactions.

Results: DockoMatic allows the user …

Importance Of Electronic Relaxation For Inter-Coulombic Decay In Aqueous Systems, Craig P. Schwartz, Shervin Fatehi, Richard J. Saykally, David Prendergast

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

Inspired by recent photoelectron spectroscopy experiments on hydroxide solutions, we have examined the conditions necessary for enhanced (and, in the case of solutions, detectable) inter-Coulombic decay (ICD)—Auger emission from an atomic site other than that originally excited. We present general guidelines, based on energetic and spatial overlap of molecular orbitals, for this enhancement of inter-Coulombic decay-based energy transfer in solutions. These guidelines indicate that this decay process should be exhibited by broad classes of biomolecules and suggest a design criterion for targeted radiooncology protocols. Our findings show that photoelectron spectroscopy cannot resolve the current hydroxide coordination controversy.

Dnmt1 Stability Is Regulated By Proteins Coordinating Deubiquitination And Acetylation-Driven Ubiquitination, Zhanwen Du, Jing Song, Yong Wang, Yiqing Zhao, Kishore Guda, Shuming Yang, Hung Ying Kao, Yan Xu, Joseph Willis, Sanford D. Markowitz, David Sedwick, Robert M. Ewing, Zhenghe Wang

Chemistry Faculty Publications

DNA methyltransferase 1 (DNMT1) is the primary enzyme that maintains DNA methylation. We describe a previously unknown mode of regulation of DNMT1 protein stability through the coordinated action of an array of DNMT1-associated proteins. DNMT1 was destabilized by acetylation by the acetyltransferase Tip60, which triggered ubiquitination by the E3 ligase UHRF1, thereby targeting DNMT1 for proteasomal degradation. In contrast, DNMT1 was stabilized by histone deacetylase 1 (HDAC1) and the deubiquitinase HAUSP (herpes virus–associated ubiquitin-specific protease). Analysis of the abundance of DNMT1 and Tip60, as well as the association between HAUSP and DNMT1, suggested that during the cell cycle the initiation …

Halo Ion Trap Mass Spectrometry: Design, Instrumentation, And Performance, Miao Wang

Theses and Dissertations

New ion trap mass spectrometry (ITMS) instrumentation, the toroidal IT and halo IT, were developed to meet the significant growth in on-site analysis applications. The miniature toroidal IT mass analyzer was operated with radio frequency (RF) trapping voltages of 3 kVp-p or less. Despite its reduced dimensions, it has roughly the same ion trapping capacity as conventional 3D quadrupole ITs. Unit-mass resolved spectra for n-butylbenzene, xenon, and naphthalene were obtained. The desired linear mass scale was obtained using conventional mass-selective instability scan combined with resonance ejection. The halo IT was also based on toroidal trapping geometry and microfabrication technology, consisting …

Electronic Properties Of N(5)-Ethyl Flavinium Ion, Vincent Sichula, Pavel Kucheryavy, Renat Khatmullin, Ying Hu, Ekaterina Mirzakulova, Shubham Vyas, Samuel F. Manzer, Christopher M. Hadad, Ksenija D. Glusac

Chemistry Faculty Publications

We investigated the electronic properties of N(5)-ethyl flavinium perchlorate (Et-Fl(+)) and compared them to those of its parent compound, 3-methyllumiflavin (Fl). Absorption and fluorescence spectra of Fl and Et-Fl(+) exhibit similar spectral features, but the absorption energy of Et-Fl(+) is substantially lower than that of Fl. We calculated the absorption signatures of Fl and Et-Fl(+) using time-dependent density functional theory (TD-DFT) methods and found that the main absorption bands of Fl and Et-Fl(+) are (pi,pi*) transitions for the S(1) and S(3) excited states. Furthermore, calculations predict that the S(2) state has (n,pi*) character. Using cyclic voltammetry and a simplistic consideration …

Photoinduced Charge Separation In Platinum Acetylide Oligomers, Chen Liao, James E. Yarnell, Ksenija D. Glusac, Kirk S. Schanze

Chemistry Faculty Publications

The series of three donor-spacer-acceptor complexes, DPAF-Ptn-NDI, has been synthesized and characterized using time-resolved absorption spectroscopy In these complexes, the donor is a (diphenylamino)-2,7-fluorenylene (DPAF) unit, the acceptor is a naphthalene diimide (NDI), and the spacers are a series of platinum acetylides of varying lengths, [-Pt(PBu(3))(2)C C-Ph-C C-](n) (where Bu = n-butyl Ph = 1,4-phenylene and n = 1 2, and 3) Electrochemistry indicates that the DPAF-Ptn-NDI system has a charge transfer state at ca 1 5 eV above the ground state that is based on one electron transfer from the DPAF donor to the NDI acceptor Transient absorption spectroscopy …

Activation Of The Innate Immune Response By The Alzheimer's Amyloid Beta Protein Via Toll-Like Receptors, Udan Lourdes Maria

Dissertations

Alzheimer’s Disease (AD) is the most common form of neurodegenerative disease characterized by the generation and deposition of amyloid beta plaques and the formation of neurofibrillary tangles. A wealth of data now demonstrate that inflammation is a prominent feature in AD pathology and a potential therapeutic target for the treatment and prevention of the disease. The emergence of evidence linking amyloid beta protein (Aβ), the primary component of senile plaques, to inflammation has led to new insights into understanding AD pathology. Aβ, a protein fragment resulting from cleavage of human amyloid precursor protein (APP), primarily exists in two forms: a …

Synthesis Of An Ortho-Triazacyclophane: N,N',N''-Trimethyltribenzo-1,4,7-Triazacyclononatriene, Andria M. Panagopoulos, Matthias Zeller, Daniel P. Becker

Chemistry: Faculty Publications and Other Works

N,N',N''-Trimethyltribenzo-1,4,7-triazacyclononatriene has been synthesized via sequential palladium-catalyzed Buchwald-Hartwig N-arylation reactions affording the 9-membered triaza o-cyclophane in 35% overall yield. An X-ray crystal structure shows the new cyclophane to have a C(2)-symmetric saddle conformation, as compared to the crown conformation exhibited by the related carbocyclic cyclotriveratrylene (CTV).

The Design And Synthesis Of Functionalized Porphyrins And Their Applications In Group Transfer Reactions, Medicine, And Materials, Kimberly Bliss Fields

USF Tampa Graduate Theses and Dissertations

Porphyrins and their analogs are a class of chemically and biologically important compounds that have found a variety of applications in different fields such as catalysis, medicine, and materials. The physical, chemical, and biological dependence of the peripheral substituents of porphyrins on their properties has prompted great effort towards the synthesis of new porphyrins with different electronic, steric, and conformational environments. To this end, porphyrins have been prepared using a modular approach from bromo- and triflate synthons. These synthons underwent palladium-catalyzed cross-coupling with chiral amines, amides, alcohols, and boronic esters to create products that were tested for biological activity.

Metalloporphyrins …

(1e,3e)-1,4-Bis(4-Methoxyphenyl)Buta1,3-Diene, Gopinathan Narayan, Nigam Rath, Suresh Das

Chemistry & Biochemistry Faculty Works

The title compound, C18H18O2, which exhibits blue emission in the solid state, is an inter­mediate in the preparation of liquid crystals and polymers. The mol­ecule is located on an inversion centre. In the crystal, mol­ecules are arranged in a herringbone motif.

Functionalization Of Diamond And Its Application In High Performance Liquid Chromatography And Solid Phase Extraction, Gaurav Saini

Theses and Dissertations

The primary focus of my work was to chemically functionalize diamond as normal and reversed phases for solid phase extraction (SPE) and high performance liquid chromatography (HPLC). Diamond was functionalized with -NH2 groups via self-limiting adsorption of an amine-containing polymer, polyallylamine (PAAm), onto oxidized diamond particles. The chemical stability of these particles was improved by thermal curing or chemical crosslinking with 1,2,5,6-diepoxycyclooctane. The reversed phase material for SPE was synthesized by reacting amine-functionalized diamond particles with long chain alkyl and a perfluorinated isocyanate. Unlike commercially available silica, functionalized diamond particles were stable under extreme pH conditions (pH 0-14). Functionalized diamond …

Scoring Function To Predict Solubility Mutagenesis, Ye Tian, Christopher Deutsch, Bala Krishnamoorthy

Chemistry Faculty Publications and Presentations

Background: Mutagenesis is commonly used to engineer proteins with desirable properties not present in the wild type (WT) protein, such as increased or decreased stability, reactivity, or solubility. Experimentalists often have to choose a small subset of mutations from a large number of candidates to obtain the desired change, and computational techniques are invaluable to make the choices. While several such methods have been proposed to predict stability and reactivity mutagenesis, solubility has not received much attention. Results: We use concepts from computational geometry to define a three body scoring function that predicts the change in protein solubility due to …

Electronic Structure Based Classification Of Neurotransmitters And Related Drugs, Amrita Jha

Theses and Dissertations

A fundamental understanding of the relationship between structure and activity of neurotransmitters in the human brain is of vital importance for the design targeted drugs. Using density functional theory and hybrid exchange correlation energy functionals we have studied the structure-activity-relationships of some important neurotransmitters and selected drugs by calculating their absolute hardness (η) and absolute electronegativity (χ). A plot of the η- χ diagram allowed us to assign them into three distinct groups, namely, (i) Acetylcholine analogs (positively charged structure), (ii) GABA analogs (zwitterionic structures) and (iii) monoamines. The results suggest that brain stem is chemically soft because of distribution …

Oga Inhibition By Glcnac-Selenazoline, E. J. Kim, D. C. Love, E. Darout, M. Abdo, B. Rempel, S. G. Withers, Paul R. Rablen, J. A. Hanover, S. Knapp

Chemistry & Biochemistry Faculty Works

The title compound, which differs from the powerful O-GlcNAcase (OGA) inhibitor GlcNAc-thiazoline only at the chalcogen atom (Se for S), is a much weaker inhibitor in a direct OGA assay. In human cells, however, the selenazoline shows comparable ability to induce hyper-O-GlcNAc-ylation, and the two show similar reduction of insulin-stimulated translocation of glucose transporter 4 in differentiated 3T3 adipocytes. (C) 2010 Elsevier Ltd. All rights reserved.

Chemistry & Biochemistry Newsletter, Department Of Chemistry & Biochemistry, South Dakota State University

Chemistry & Biochemistry Newsletter: 2002-2015

Inside:

Page 2 Career Award Will Help Build High-Tech Microscope

Page 4 Classroom Changes; Krsnak Wins Oz Memorial

Page 5 Chemistry Major John Lee is Academic All-American

Page 6 Program to Address Shortage of Medical Lab Scientists

Page 7 New Graduate Students

Page 8 Publications and Grants

Solving The Low Dimensional Smoluchowski Equation With A Singular Value Basis Set, Gregory E. Scott, Martin Gruebele

Chemistry and Biochemistry

Reaction kinetics on free energy surfaces with small activation barriers can be computed directly with the Smoluchowski equation. The procedure is computationally expensive even in a few dimensions. We present a propagation method that considerably reduces computational time for a particular class of problems: when the free energy surface suddenly switches by a small amount, and the probability distribution relaxes to a new equilibrium value. This case describes relaxation experiments. To achieve efficient solution, we expand the density matrix in a basis set obtained by singular value decomposition of equilibrium density matrices. Grid size during propagation is reduced from (100–1000) …