Chemistry Commons^™

Studies Toward The Total Synthesis Of Antascomicin B, David Ross Clay

Graduate Theses and Dissertations

The following dissertation describes synthetic efforts toward the synthesis of the C21-C34 fragment of antascomicin B. Our initial enzymatic approach is detailed as well as an asymmetric transfer hydrogenation (ATH) strategy that will be used in the eventual total synthesis of the molecule. Several investigations into anomalies observed during (ATH) reactions are also discussed.

Designed Guanidinium-Rich Amphipathic Oligocarbonate Molecular Transporters Complex, Deliver And Release Sirna In Cells, E. I. Geihe, Christina B. Cooley, J. R. Simon, M. K. Kiesewetter, J. A. Edward, R. P. Hickerson, R. L. Kaspar, J. L. Hedrick, R. M. Waymouth, P. A. Wender

Chemistry Faculty Research

The polyanionic nature of oligonucleotides and their enzymatic degradation present challenges for the use of siRNA in research and therapy; among the most notable of these is clinically relevant delivery into cells. To address this problem, we designed and synthesized the first members of a new class of guanidinium-rich amphipathic oligocarbonates that noncovalently complex, deliver, and release siRNA in cells, resulting in robust knockdown of target protein synthesis in vitro as determined using a dual-reporter system. The organocatalytic oligomerization used to synthesize these co-oligomers is step-economical and broadly tunable, affording an exceptionally quick strategy to explore chemical space for optimal …

Wet Oxidation Of Maleic Acid By A Pumice Supported Copper (Ii) Shiff Base Catalyst, Jeg Mdoe, Raj Minja, L Daniel

Tanzania Journal of Science

Pumice supported Cu (II) Schiff base catalysts were prepared by surface chemical modification followed by complexation with Cu (II) acetate. The resulting materials were characterised by Diffuse Reflectance Fourier Transform Spectroscopy (DRIFTS) to confirm the modification. The materials were tested in a wet oxidation of maleic acid using air or hydrogen peroxide as an oxidant. Results indicate that up to 80% degradation of maleic acid could  be achieved in the presence of the catalyst using hydrogen peroxide as an oxidant. The degradation was found to depend on the type of oxidant, temperature and whether the parent pumice was acid pre-treated …

Ni Mineralization And Pge Characterization In The Kabanga And Luhuma Ni-Cu Sulfide Deposits, North West Tanzania, As Macheyeki

Tanzania Journal of Science

Nickel mineralization in the Kabanga sulfide ores is found associated with (1) peripheral veins in the country-rock metapelites, (2) contact type massive sulfide mineralization, and (3) disseminated and vein mineralization. This work, apart from giving general highlight of the Ni mineralization (and other associated elements) in the Kabanga and Luhuma, intends to assess the PGE content in both areas. Cores (mafic-ultramafic and metasedimentary rocks as well as ore sections) from both Kabanga and Luhuma areas were sampled, cut, crushed, pulverized and analyzed for both major and trace elements. Results show that all the Iridium Platimum Group Elements (IPGEs) have very …

Data Mining Of Protein Databases, Christopher Assi

School of Computing: Dissertations, Theses, and Student Research

Data mining of protein databases poses special challenges because many protein databases are non-relational whereas most data mining and machine learning algorithms assume the input data to be a relational database. Protein databases are non-relational mainly because they often contain set data types. We developed new data mining algorithms that can restructure non-relational protein databases so that they become relational and amenable for various data mining and machine learning tools. We applied the new restructuring algorithms to a pancreatic protein database. After the restructuring, we also applied two classification methods, such as decision tree and SVM classifiers and compared their …

Synthesis Of Half-Loaded Nitroimidazole Indocyanine Green Dyes Attached To Carbon Nanotubes, Courtney L. Stanford

Master's Theses

Indocyanine green dye is the only FDA approved NIR fluorescent dye that can be used in humans. 2-Nitroimidazoles are very effective radiosensitizers, have low cytotoxicity, and target hypoxic tissue. By coupling the two together, hypoxic tumors can be targeted and imaged. Previous work has been done to couple 2-nitroimidazole to both sides of the indocyanine green dye. This work focuses on expanding that concept to couple 2-nitroimidazole to only one side of the dye, thus allowing for the other end to be available to couple to another compound, generating a half loaded 2-nitroimidazole indocyanine green dye. In theory, this half-loaded …

Accurate Methodology For Monitoring Biomembrane Events, Christine A. Winschel

Theses and Dissertations

Abstract ACCURATE METHODOLOGY FOR MONITORING BIOMEMBRANE EVENTS By Christine A. Winschel, Ph.D. A Dissertation submitted in partial fulfillment of the requirements for the degree of Doctorate of Philosophy in Chemistry at Virginia Commonwealth University. Virginia Commonwealth University, 2012 Major Director: Dr. Vladimir A. Sidorov ASSOCIATE PROFESSOR, DEPARTMENT OF CHEMISTRY This study describes the synthesis and characterization of a new receptor (cyclen 1) capable of strong selective binding of pyrene-based anionic dyes under near-physiological conditions. This receptor comprises four naphthylthiourea groups tethered to a cyclen core via an ester linkage. The most important finding was the ability of cyclen 1 to …

Development Of Nano-Scale Featured Materials For Electrode Modification And Solid Supports., Amy Rue

Theses and Dissertations

This work utilized the sol-gel process in two ways. First, macroporous silica thin films were developed using a combination of casting techniques and templating. Macroporsity was introduced to the silica thin films by either doping the silica sol before casting or by ordering the template on a substrate and then casting a sol over it. These techniques were first used to create silica thin films with long microchannel pores (200 nm x 60 µm) from a doped sol with the bacteria, B. Megaterium, as the template for nanomaterial formation. To enable the formation long microchannels, the flexible bacteria chains were …

Discrimination Of Colon Cancer Stem Cells Using Noncanonical Amino Acid, Xinrui Duan, Honglin Li, Hexin Chen, Qian Wang

Faculty Publications

Cancer stem cells (CSCs) may be responsible for tumor recurrence. Metabolic labelling of newly synthesized proteins with non-canonical amino acids allows us to discriminate CSCs in mixed populations due to the quiescent nature of these cells.

Fluorescence Tagging Of Marine Low Molecular Weight Carboxylic Acids, Brian C. Gismervik

Master's Theses

This thesis aims at the evaluation of the best amide bonding strategy that places a fluorescence aminomethyl coumarin tag onto a LMW organic acid in aqueous solution. A three-stage study was conducted. First, a suitable aminomethyl coumarin fluorophore was synthesized. Second, a library of acid-derivatized standards was synthesized for use in optimizing the anticipated HPLC separation of a mixture of LMW acids expected to be found in marine samples. Third, the aforementioned amide coupling strategies were screened to identify the most applicable method for our reaction conditions to the tagging of LMW organic acids in a large number of field …

Novel Acceptor Materials For Solar Cells, Diana M. Brus, Marta Izquierdo, Luis Echegoyen

COURI Symposium Abstracts, Summer 2012

In recent years organic photovoltaics, OPVs, have gained an increasing amount of attention for their potential use as low-cost solar energy conversion devices. The interest in solar cells using fullerenes as an acceptor component has been rapidly growing in the last years.

The research on the origin of the open circuit voltage of bulk heterojunction solar cells containing a polymer and a mono-substituted fullerene are attracting extensive academic interest. To date, a vast majority of the efficient devices reported use the regioregular poly(3-hexylthiophene) (P3HT) polymer and PCBM-C₆₀ (Phenyl-C₆₁-Butyric Acid Methyl Ester) respectively as electron-donor and electron acceptor …

54th Rocky Mountain Conference On Analytical Chemistry

Rocky Mountain Conference on Magnetic Resonance

Final program, abstracts, and information about the 54th annual meeting of the Rocky Mountain Conference on Analytical Chemistry, co-endorsed by the Colorado Section of the American Chemical Society and the Society for Applied Spectroscopy. Held in Copper Mountain, Colorado, July 15-19, 2012.

Development And Validation Of An Lc–Ms/Ms Method For Pharmacokinetic Study Of Methoxyamine In Phase I Clinical Trial, Shuming Yang, Panayiotis Savvides, Lili Liu, Stanton L. Gerson, Yan Xu

Chemistry Faculty Publications

Methoxyamine (MX) is the first DNA base-excision-repair (BER) inhibitor evaluated in humans. This work described the development and validation of an LC–MS/MS method for quantitative determination of MX in human plasma. In this method, MX and its stable isotope methoxyl-d3-amine (MX-d3 as internal standard) were directly derivatized in human plasma with 4-(N,N-diethylamino)benzaldehyde. The derivatized MX and IS were extracted by methyl-tert-butyl ether, and separated isocratically on a Xterra C18 column (2.1 mm × 100 mm) using an aqueous mobile phase containing 45% acetonitrile and 0.4% formic acid at a flow rate of 0.200 ml/min. Quantitation of MX was carried out …

Spectroelectrochemical Elucidation Of The Kinetics Of Two Closely Spaced Electron Transfers, Robert L. Keesey, Michael D. Ryan

Chemistry Faculty Research and Publications

The use of spectroelectrochemistry to facilitate the analysis of an EE mechanism was reported in this work. Using a set of spectra as a function of potential, the spectra of all three oxidation states were determined using evolving window factor analysis. From these spectra, the concentration of each species in solution was determined for each potential. Using these data, the current was calculated. Unlike the direct measurement of current, the current due to each redox process was determined, allowing one to analyze each redox process separate from the other. With the use of the Butler–Volmer equation, the redox potential and …

Transition States Of Dbt Molecule At The Mos2/Co9s8 Interface: First Principles, Svetlana Gelpi, Alvaro S. Laham, Gilles Berhault, Brenda Torres, Russel R. Chianelli, Manuel Ramos *

COURI Symposium Abstracts, Summer 2012

Sulfur removal in crude oil, is one of most important application when designing catalytic material to target hydrodesulphurization reactions. This particular study comprehends the quantum computational calculations for the transitional states during the HDS reaction in the molecular model of MoS₂/Co₉S₈, which is a theoretical molecular model to describe the synergic contact between both crystallographic structures. Results produced using the exchange correlation Perdew-Burke-Ernzerhof(PBE) functional indicate the existence of endothermic and exothermic transitions during the attachment of DBT molecules. In addition, it proves that promotion (addition of Co, Ni) provokes the electronic configuration of electron …

Mitigating Ros Induced Neurodegenerative Pathogenesis Through Polyphenolic Phytochemicals, Brittany N. Talamantes, Parijat Kabiraj, Mahesh Naryan

COURI Symposium Abstracts, Summer 2012

The United States accounts for 16% of all Alzheimer’s disease (AD) cases. The margin of elderly population increasing, due to the baby boomer generation, also contributes greatly to the increase in neurodegenerative diseases. This rise in neurodegenerative disease highlights the importance of research and its potential ability to alleviate financial health burdens as well creating protection for younger generations. Cell lines, PC12 and SHSY-5Y chosen as Parkinsonian and Alzheimer’s models because of their ability to release dopamine were treated with the phytochemical ellagic acid, and analyzed to view its protective capabilities against reactive oxidative stress (ROS). ROS was induced by …

Chaperonin Mediated Refolding Of The Green Fluorescent Protein, Danielle Y. Martinez, Ricardo A. Bernal, Timothy P. Brown

COURI Symposium Abstracts, Summer 2012

In order to prevent misfolded proteins from aggregating and becoming insoluble, we are developing a chaperonin-mediated protein refolding assay that makes use of an easily traceable protein. Chaperonins function by providing a protective enclosed chamber for a protein to fold without interference from cellular component with the cytoplasm. To our knowledge, the inner workings of the chaperonin and its facilitation of protein folding are complicated but can be traced by monitoring ATP. Tracing this reaction, however, requires that the product of hydrolysis (inorganic phosphate) react with a second substrate to produce a product that can be observed by absorption of …

Highly Sensitive, Multiplexed, Point Of Care Diagnosis Of Meningitis Through Microfluidics, Isaac Torres, Xiujun J. Li, Gabriel Scott

COURI Symposium Abstracts, Summer 2012

Bacterial meningitis is a severe bacterial infection that can become fatal within 24 hours of symptom onset. The most common detection methods include gram stain and cell culture, which are either not reliable, time-consuming or require expensive equipment and trained personnel. In a third world setting, having a reliable and low-cost diagnostic tool for detection of meningitis is therefore crucial. Our project then, is to allow for integrated DNA amplification, and easy to read colorimetric indicators in one PDMS/paper hybrid microfluidic device. The amplification will be done through loop-mediated isothermal amplification (LAMP), which is a novel approach to DNA amplification …

Fluorescence Correlation Spectroscopy Study Of Protein Transport And Dynamic Interactions With Clustered-Charge Peptide Adsorbents, Lydia Kisley

Faculty Scholarship

Ion-exchange chromatography relies on electrostatic interactions between the adsorbent and the adsorbate and is used extensively in protein purification. Conventional ion-exchange chromatography uses ligands that are singly charged and randomly dispersed over the adsorbent, creating a heterogeneous distribution of potential adsorption sites. Clustered-charge ion exchangers exhibit higher affinity, capacity, and selectivity than their dispersed-charge counterparts of the same total charge density. In the present work, we monitored the transport behavior of an anionic protein near clustered-charge adsorbent surfaces using fluorescence correlation spectroscopy. We can resolve protein-free diffusion, hindered diffusion, and association with bare glass, agarose-coated, and agarose-clustered peptide surfaces, demonstrating …

Synthesis Of Methylene Γ-Lactones Using Carbon Dioxide, Bryan P. Ferrell, Shizue Mito, Giber Martinez, Intesar El-Feitouri

COURI Symposium Abstracts, Summer 2012

Many industrial processes generate the greenhouse gas, carbon dioxide, as a byproduct. Carbon dioxide can be captured and recycled by using it in organic synthesis to prepare beneficial compounds. The goal of this project is to develop a new method of synthesizing methylene γ-lactones using CO₂-metal complexes. Many gamma lactones are biologically active, and their synthesis is of importance to pharmaceutical and other industries. Allenes can react with a transition metal-CO₂ complex. It is proposed that a titanium metal complex prepared with an aldehyde will bind to an allene, and a seven-membered ring forms as CO_{2 …}

Evolutionary History And Phylodynamics Of Influenza A And B Neuraminidase (Na) Genes Inferred From Large-Scale Sequence Analyses, Haizhen Zhong

Chemistry Faculty Publications

Background: Influenza neuraminidase (NA) is an important surface glycoprotein and plays a vital role in viral replication and drug development. The NA is found in influenza A and B viruses, with nine subtypes classified in influenza A. The complete knowledge of influenza NA evolutionary history and phylodynamics, although critical for the prevention and control of influenza epidemics and pandemics, remains lacking.

Methodology/Principal findings: Evolutionary and phylogenetic analyses of influenza NA sequences using Maximum Likelihood and Bayesian MCMC methods demonstrated that the divergence of influenza viruses into types A and B occurred earlier than the divergence of influenza A …

Angular And Dynamical Properties In Resonant Inelastic X-Ray Scattering: Case Study Of Chlorine-Containing Molecules, Renaud Guillemin, Wayne C. Stolte, Loic Journel, Stephane Carniato, Maria Novella Piancastelli, Dennis W. Lindle, Marc Simon

Chemistry and Biochemistry Faculty Research

Polarization-dependent resonant inelastic x-ray scattering (RIXS) has been shown to be a probe of molecular-field effects on the electronic structure of isolated molecules. In this experimental analysis we explain the linear dichroism observed in Cl 2p polarized RIXS following Cl 1s excitation of a series of chlorofluoromethanes (CF3Cl, CF2Cl2, CFCl3, and CCl4) as due to molecular-field effects, including singlet-triplet exchange. We present an approach to extract directly the 2p inner-shell electronic state populations from the experimental measurements. Using the angular properties of the measured KV emission we also are able to determine the value of the polarization anisotropy parameter βp …

Derivative Couplings With Built-In Electron-Translation Factors: Application To Benzene, Shervin Fatehi, Joseph E. Subotnik

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

Derivative couplings are the essential quantities at the interface between electronic-structure calculations and nonadiabatic dynamics. Unfortunately, standard approaches for calculating these couplings usually neglect electronic motion, which can lead to spurious electronic transitions. Here we provide a general framework for correcting these anomalies by incorporating perturbative electron-translation factors (ETFs) into the atomic-orbital basis. For a range of representative organic molecules, we find that our ETF correction is often small but can be qualitatively important, especially for few-atom systems or highly symmetric molecules. Our method entails no additional computational cost, such that ETFs are “built-in,” and it is equivalent to a …

Laser Ablation-Inductively Coupled Plasma-Mass Spectrometry Analysis Of Lower Pecos Rock Paints And Possible Pigment Sources, Jon Russ, Kaixuan Bu, Jeff Hamrick, James V. Cizdziel

Master of Science in Analytics (MSAN) Faculty Research

Chemical analyses of prehistoric rock paints from the Lower Pecos Region of southwestern Texas were undertaken using laser ablation-inductively coupled plasma-mass spectrometry. This technique allowed us to measure the chemical composition of the paint pigments with minimal interference from a natural rock coating that completely covers the ancient paints. We also analyzed samples representing potential sources of paint pigments, including iron-rich sandstones and quartzite from the study area and ten ochre samples from Arizona. Cluster analysis, principle component analysis and bivariate plots were used to compare the chemical compositions of the paint and pigment sources. The results indicate that limonite …

Synthesis Of Peptide Thioesters Without Loss Of Chiral Integrity, Renato A. Sousa, Andrew Pardo, Katja Michael

COURI Symposium Abstracts, Summer 2012

The chemical synthesis of polypeptides can be accomplished with a technique called Native Chemical Ligation (NCL), which requires two peptides, one with a C-terminal thioester and another one with an N-terminal cysteine. Conventional peptide thioester syntheses require coupling in the presence of organic bases, which can cause a serious epimerization problem, and consequently purification difficulties, as well as low reaction yields of the desired stereoisomer. There is a great need for alternative methods that avoid or minimize epimerization and preserve the chiral integrity of the C-terminal amino acid. The goal of this research is to demonstrate that a photochemical base-free …

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 …

Praseodymium Nitride Endohedral Metallofullerene As Donor In Photovoltaic Cells, Luis F. Gardea, Manuel N. Chaur, Luis Echegoyen

COURI Symposium Abstracts, Summer 2012

Trimetallic nitride template endohedral metallofullerenes (TNT EMFs) have been found to have structures and electronic properties that make them suitable for fields like molecular electronics. The particular compounds synthesized were the family of TNT EMFs Pr₃N@C_2n due to the relatively high yield of Pr₃N@C­₈₈ and even more due to its low first oxidation potential (0.06 V) and therefore this compound has the ability to act as a capable electron donor in a multilayer organic photovoltaic cell. The compound was synthesized through the use of a Kratschmer-Huffman arc reactor. A mixture of Praseodymium Oxide and …

Preparation Of Novel Endohedral Metallofullerenes By The Krätschmer-Hoffman Arc Reactor Method, Markus J. Meyer, Manuel N. Chaur, Luis A. Echegoyen

COURI Symposium Abstracts, Summer 2012

Since the discovery of C₆₀ fullerene 25 years ago, the pursuit of encapsulating different metals, metallic clusters, and small molecules have attracted the attention of the scientific community due to the possibility of tuning the electronic and chemical properties of these compounds. As of today various metal-non-metal combinations have been obtained such as metallic nitrides, sulfides, metal carbides and metal oxides, however, none of them (except for Sc₃N@C₈₀) has been prepared in high yields. In this work we study the preparation process of different metallofullerenes and the dependence of the fullerene yield on various parameters …

Bimetallic Systems As Platforms For Supramolecular Chemistry And Metal Organic Frameworks, Jose M. Veleta, Dino Villagrán

COURI Symposium Abstracts, Summer 2012

Homonuclear M₂ units (M = Ru, Mo) with tetraacetate ligands are used as starting materials to react with a wide variety of electron rich molecules; HDAniF (N,N’-di-p-anisylformamidine) has been used as a bridging ligand for the M-M units, and bisbidentate carboxylate and carboxamidate ligands have been used as linkers between M₂ units. Special interest is focused in the study of compounds with multiple bonds between bimetallic units, as well as paramagnetic and electrochemical active complexes. The reactivity of these bimetallic complexes leads to the synthesis of monomeric and dimeric species, which are building blocks for the design of …

One-Pot Γ-Amino Acids Synthesis From Co2 Via Zirconacycle, Teresita J. Maldonado, Diego A. Pedroza, Shizue Mito

COURI Symposium Abstracts, Summer 2012

One-pot γ-amino acids synthesis from CO₂ via zirconacycle was studied. It has been reported that ketone and isocyanides are viable substrates for insertion into Zr‒C bonds of zirconocene‒1-aza-1,3-diene complexes. The purpose of this project is to explore the viability of CO₂ insertion to develop a new method for γ-amino acids synthesis in which all the reactions are executed in a single pot. In this method, first zirconocene‒1-aza-1,3-diene complex is prepared by using Cp₂Zr₂Cl₂ and an α, β-unsaturated imine. Second, CO₂ was introduced into the zirconocene complex solution to form the seven-membered ring …