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Mass Spectrometry Of Dendrimer Metal Complexes, Jason David Batchelor

Theses, Dissertations and Capstones

Dendrimers are hyper-branched macromolecules with unique properties. They form using a “cascade-like” synthesis involving repetitive reaction steps. These steps are controlled, resulting in monodisperse dendrimers. Synthesis is divergent, core to exterior, or convergent, exterior to core. Dendrimers are created from various molecules with numerous functional properties. They are used as catalysts, diagnostic agents, and others.

This thesis studies 1st generation poly(propylene) imine, consisting of a diaminobutane core with 4 propyl amine branches. Fragmentation of protonated and metal (Co, Ni, Cu and Zn) complexed dendrimers was analyzed by ion-trap mass spectrometry. Two isotopically labeled dendrimers were synthesized for neutral loss identification …

Synthesis Towards Novel 1,3-Azaborine Heterocycles As Potential Dual-Mode Hiv-1 Protease Inhibitors, Amanda Blackmore

Undergraduate Honors Theses

Drug discovery has resulted in many life-saving therapies, making a great impact on modem medicine and the human condition. Even though new therapies are available many drugs are highly susceptible to resistance development, have poor bioavailability, and some of them are toxic. HIV-I protease inhibitors presently on the market show high specificity but have low bioavailability and high toxicity. Furthermore, the available drugs have a very low affinity for mutant forms of HIV -1 protease. Recent studies have shown that boronated HIV-I protease inhibitors, which demonstrate both competitive and associative inhibition, have a higher affinity for HIV-I protease at lower …

Synthesis Of 5,6 Dihydropyran-2-Ones As Potential Inhibitors Of Hiv-1 Protease, Jesse Lee Nye

Undergraduate Honors Theses

HIV/ AIDS has affected about 40 million people. One type of drug that is used to treat HIV/AIDS is a protease inhibitor. HIV-I protease is an enzyme responsible for the release of mature HIV viral particles in the body. HIV-I protease eventually becomes resistant to the inhibitors that are used as drugs and new inhibitors are needed. This research builds on a previous research effort, in which structures for HIV -1 protease inhibitors were designed using molecular modeling methods, including neural networks. These inhibitors were designed to possess better inhibitory properties, and possibly have increased bioavailability and less toxicity than …

A Streamlined Molecular Biology Module For Undergraduate Biochemistry Labs, Gregory W. Muth, Joseph W. Chihade

Chemistry Faculty Work

Site-directed mutagenesis and other molecular biology techniques, including plasmid manipulation and restriction analysis, are commonly used tools in the biochemistry research laboratory. In redesigning our biochemistry lab curricula, we sought to integrate these techniques into a term-long, project-based course. In the module presented here, students use structural data to design a site-directed mutant and make the mutation using the Ku¨ nkel method. A second, silent mutant, that creates or removes a restriction site, is simultaneously introduced. Restriction digestion and agarose gel electrophoresis are used to assess the success of mutagenesis. Placing these procedures in the context of continuous, studentdriven project …

Open Circuit Potential Shifts Of Activated Carbon In Aqueous Solutions During Chemical And Adsorption Interactions, Mikhail M. Goldin, Vladimir A. Kolesnikov, Mogely Sh. Khubutiya, Alexander G. Volkov, Gary J. Blanchard, Anatoly K. Evseev, Mark M. Goldin

Faculty Publications and Presentations

Interaction of certain inorganic and organic compounds with activated carbon and the effect of such interaction on open circuit potential of activated carbon were studied. Open circuit potential shifts were observed for an overwhelming majority of the substances and brands of activated carbons investigated. Both negative and positive potential shifts were observed. It was shown that open circuit potential shifts for organic substances depend on degree of coverage of the activated carbon surface. Whereas adsorption of investigated organic compound on activated carbon led to positive potential shifts, desorption of adsorbates from the activated carbon surface led to potential shifts in …

A General And Rapid Cell-Free Approach For The Interrogation Of Protein–Protein, Protein–Dna, And Protein–Rna Interactions And Their Antagonists Utilizing Split-Protein Reporters, Jason R. Porter, Cliff I. Stains, Benjamin W. Jester, Indraneel Ghosh

Cliff Stains Publications

Split-protein reporters have emerged as a powerful methodology for imaging biomolecular interactions which are of much interest as targets for chemical intervention. Herein we describe a systematic evaluation of split-proteins, specifically the green fluorescent protein, β-lactamase, and several luciferases, for their ability to function as reporters in completely cell-free systems to allow for the extremely rapid and sensitive determination of a wide range of biomolecular interactions without the requirement for laborious transfection, cell culture, or protein purification (12–48 h). We demonstrate that the cell-free split-luciferase system in particular is amenable for directly interrogating protein–protein, protein–DNA, and protein–RNA interactions in homogeneous …

Conserved Sequences Of Sperm-Activating Peptide And Its Receptor Throughout Evolution, Despite Speciation In The Sea Star Asterias Amurensis And Closely Related Species, Mia Nakachi, Motonori Hoshi, Midori Matsumoto, Hideaki Moriyama

Hideaki Moriyama Publications

The asteroidal sperm-activating peptides (asterosaps) from the egg jelly bind to their sperm receptor, a membrane-bound guanylate cyclase, on the tail to activate sperm in sea stars. Asterosaps are produced as single peptides and then cleaved into shorter peptides. Sperm activation is followed by the acrosome reaction, which is subfamily specific. In order to investigate the molecular details of the asterosap-receptor interaction, corresponding cDNAs have been cloned, sequenced and analysed from the Asteriinae subfamily including Asterias amurensis, A. rubens, A. jorbesi and Aphelasterias japonica, as well as Distolasterias nipon from the Coscinasteriinae subfamily. Averages of 29% and 86% identity …

Brainstem Raphe Pallidus And The Adjacent Area Contain A Novel Action Site In The Melanocortin Circuitry Regulating Energy Balance, Liugen Lei, Yan Gu, Jonathan G. Murphy, Pinxuan Yu, James L. Smart, Malcolm J. Low, Wei Fan

Faculty Publications - Department of Biological & Molecular Science

The central melanocortin system plays a critical role in the regulation of energy balance in rodents and humans. The melanocortin signals in both the hypothalamus and brainstem contribute to this regulation. However, how the melanocortin signals of the hypothalamus interact with those intrinsic to the brainstem in the regulation of energy balance is poorly understood. The brainstem raphe pallidus (RPa) and adjacent areas contain melanocortin 4 receptor (MC4-R)-bearing neurons and sympathetic premotor neurons regulating thermogenesis. Here we report that α-melanocyte-stimulating hormone (α-MSH)-immunoreactive (IR) fibers are in close apposition to MC4-R neurons in the RPa. Retrograde tracing studies revealed a unique …

Mutational Analysis Of The Stability Of The H2a And H2b Histone Monomers, Matthew R. Stump, Lisa M. Gloss

Faculty Publications - Department of Biological & Molecular Science

The eukaryotic histone heterodimer H2A–H2B folds through an obligatory dimeric intermediate that forms in a nearly diffusion-limited association reaction in the stopped-flow dead time. It is unclear whether there is partial folding of the isolated monomers before association. To address the possible contributions of structure in the monomers to the rapid association, we characterized H2A and H2B monomers in the absence of their heterodimeric partner. By far-UV circular dichroism, the H2A and H2B monomers are 15% and 31% helical, respectively—significantly less than observed in X-ray crystal structures. Acrylamide quenching of the intrinsic Tyr fluorescence was indicative of tertiary structure. The …

Plasma Surface Modifications For Biomedical And Electrical Applications, Dhiman Bhattacharyya

Chemistry & Biochemistry Dissertations - Archive

The focus of this work centers on molecular structuring of surfaces. The surface modifications were achieved using plasma polymerization technology, specifically variable duty cycle pulsed plasmas. The results obtained demonstrate that both exacting film chemistry and film thickness control were achieved during deposition of thin polymeric films on selected substrates. The following achievements are detailed in this thesis:* Identification of a new class of volatile monomers which can be successfully used to synthesize thermoresponsive hydrogel films. A unique aspect of this work is that the lower critical solution temperatures of these gels can be controllably varied by simple adjustment of …

Cytotoxicity Studies On Metallo-Salens And Their Applications In Gene Delivery, Getachew Abebe Woldemariam

Chemistry & Biochemistry Dissertations - Archive

Most of biological catalysts including nucleases are made of active metal centers. Metal complexes that are able to interact with DNA and RNA mimicking these natural nucleases will be valuable as therapeutic agents that target nucleic acids. Metal complexes have been used for very long time to treat different kinds of illnesses including cancer. Platinum based compounds are among the most widely used anticancer agents in clinical use. The first chapter of this dissertation highlights the roles of metal ions and their complexes with regard to biochemical activities, as enzyme inhibitors, anticancer agents and metallo-nucleases. Moreover, we will discuss the …

Development And Application Of New Mass Spectrometry-Based Proteomics Technologies To Post-Translational Modifications, Yue Chen

Chemistry & Biochemistry Dissertations - Archive

Post-translational modifications (PTMs) represent one of the major cellular mechanisms to diversify the limited number of proteins coded by genome. They provide dynamic regulation of protein functions and the means to fine-tune protein functions in response to the changing cellular environment and physiological conditions. Despite their crucial roles in cellular functions, efficient and sensitive analysis of PTMs remains a daunting analytical challenge. Traditional chemical approaches to characterize PTMs are labor-intensive and time-consuming, often with low sensitivity and specificity. Over the past ten years, biological mass spectrometry has emerged as an indispensable tool to identify and characterize PTMs. Mass spectrometry-based proteomic …

Synthesis And Characterization Of Biotin Derivatives As Multifunctional Oligosaccharide Tags, Nandkishor S. Chindarkar, Andreas H. Franz

College of the Pacific Faculty Articles

The synthesis of novel multifunctional oligosaccharide tags with amino, azido, and alkyne termini is described. Tags with an amino terminus can be introduced into the carbohydrate at the reducing end through reductive amination, while 1,3-dipolar cycloaddition (“click chemistry”) can be used to label azido sugars with oligosaccharide tags having an alkyne terminus and vice versa.

Syntheses Of Small Cluster Oligosaccharide Mimetics, Andreas H. Franz, Paul H. Gross, Vyacheslav V. Samoshin

College of the Pacific Faculty Articles

We designed multiple Small Cluster Oligosaccharide Mimetics (SCOMs) - potential glycosidase inhibitors - to be metabolically stable and small enough to enter cells or bacteria. Therefore, minimal scaffolds (urea, amide, ammonia) or simply non-glycosidic linkages of carbohydrate structures were central to our synthetic strategy, including: (a) coupling of several natural carbohydrate precursors; (b) total syntheses of aminomethyl tetrahydropyrans and their chiral amides with quinic acid; (c) glycopyranosyl cyanide reduction to prepare crowded clusters on a urea scaffold; (d) total syntheses via cycloadditions leading to amide-linked C-glycosides; (e) reduction of nitromethyl C-glycosides; and (f) a synthesis of hydroxylated 1,2- cyclohexanedicarboxylic acids.

Benzene-1,3-Diamidoethanethiol (Bdeth2) And Its Metal Compounds, Kamruz Md Zaman

University of Kentucky Doctoral Dissertations

There is a global need to find a permanent and readily implemented solution to the problem of heavy metal pollution in aqueous environments. A dithiol compound, benzene-1,3-diamidoethanethiol (BDETH₂), also known as N,N'-bis(2-mercaptoethyl) isophthalamide or N,N'-bis(2-mercaptoethyl)-1,3-benzenedicarboxamide, capable of binding divalent metal ions, has been synthesized and characterized. A broad range of BDET-metal compounds, spanning the periodic chart, has been prepared and characterized by IR, MS, EA, Raman, XAFS and TGA. The characteristics of the BDET-M compounds were determined through secondary reactions. In an effort to derivatize BDET-M compounds through alkylalumination a new cyclic compound, 1,3- bis(4,5-dihydrothiazolo)benzene, has …

Metabolite Analysis Of Clostridium Thermocellum Using Capillary Electrophoresis Based Techniques, Anup P. Thakur

University of Kentucky Doctoral Dissertations

Clostridium thermocellum is a thermophilic bacterium that converts biomass to ethanol directly; however, high sensitivity of this bacterium toward ethanol limits its commercial utility. To elucidate the effect of ethanol on the growth of this bacterium a metabolite analysis of C. thermocellum was performed. The hypothesis of the project was that exogenous ethanol alters the metabolite profile of C. thermocellum. For metabolite analysis, capillary electrophoresis-electrospray ionization-mass spectrometry method (CE-ESI-MS) was developed due to highly polar and charged nature of metabolites. To increase the sensitivity of CE-ESI-MS, several parameters at the ESI interface were optimized. The application of 50% isopropanol …

Synthesis And Dye Leakage Assay Of Human And Rat Islet Amyloid Polypeptide 10-19 And Insulin 14-18, Andrew William Gray

Master's Theses and Doctoral Dissertations

Islet amylin polypeptide (IAPP) is co-secreted along with insulin in the pancreatic islets of Langerhans. During type 2 diabetes mellitus, human IAPP (hIAPP) fibrilizes to form amyloid deposits that are found post-mortem in more than 95% of people with the disease. Rodents do not suffer from type 2 diabetes mellitus as their IAPP (rIAPP) does not undergo self-aggregation. Although the amyloid deposit is found in those with the disease, the actual cause of the disease is the cytotoxicity of the mechanism that forms those amyloid deposits. The self-aggregation of IAPP to form amyloid deposits is inhibited by insulin due to …

Staphylococcus Aureus Primase Has Higher Initiation Specificity, Interacts With Single-Stranded Dna Stronger, But Is Less Stimulated By Its Helicase Than Escherichia Coli Primase, Scott A. Koepsell, Marilynn A. Larson, Christopher Frey, Steven H. Hinrichs, Mark A. Griep

Mark A. Griep Publications

The study of primases from model organisms such as Escherichia coli, phage T7 and phage T4 has demonstrated the essential nature of primase function, which is to generate de novo RNA polymers to prime DNA polymerase. However, little is known about the function of primases from other eubacteria. Their overall low primary sequence homology may result in functional differences. To help understand which primase functions were conserved, primase and its replication partner helicase from the pathogenic Gram-positive bacteria Staphylococcus aureus were compared in detail with that of E. coli primase and helicase. The conserved properties were to primer initiation …

Polyaniline Nanofiber-Based Gas Sensors, Zhe-Fei Li, Frank D. Blum, Massimo F. Bertino, Chang-Soo Kim

Chemistry Faculty Research & Creative Works

There has been recent interest in conducting polymers that have very promising chemical and electrical applications. Some of these polymers have shown great potential for use in sensors.1 Polyaniline is one particular example of a prospective material. In our laboratory, we have studied the synthesis of polyaniline nanofibers. We have carried out one-pot syntheses to obtain polyaniline nanofibers in aqueous solutions where the polymerization was influenced by γ-radiation2 or UV-radiation.3 This polymer can also be patterned with an appropriate photo mask. In our present report, polyaniline nanofiber thin film sensors have been fabricated in one step by employing UV-irradiation and …

Pressure Perturbation Calorimetry And Guest-Host Chemistry Of Ndmg And N-Map With P-Sulfonatocalix[6]Arene, Cassandra Newell

Honors Theses

The aim of this project is to provide an explanation for recently obtained binding constants for two similar guest molecules, NDMG and N-MAP, with a p-sulfonatocalix[6]arene host in ammonium acetate buffer. This work was done primarily using pressure perturbation calorimetry, which is a technique that determines the coefficient of thermal expansion, α, which is in turn related to the solute molecule's effect on the order of the surrounding water molecules. A series of experiments were designed to test the effects of suspected confounding variables on the validity of PPC data. PPC was then used to study NDMG and N-MAP in …

The Selective Synthesis Of Oxacalix[6]Arenes And The Exploration Of Azacalix[N]Arenes, W. Christian Crannell

Honors Theses

Calix[n]arenes, cyclIc molecules composed of "n" benzene rings meta-linked by a methylene to form a macrocycle, are very prevalent jn the literature and enjoy a wide range of applications. However, the oxygen bridged and nitrogen bridged systems, oxacalllx[n)arenes and azacalix[n]arenes, respectively, are far less common because they are synthetically challenging. Furthermore, the selective synthesis of oxacalix[6]arene systems has not previously been well documented, but the systems can now be accessed in a facile approach disclosed here. The insight and knowledge gained from the synthesis of oxacalix{6]arenes has provided a foray into the synthesis of azacalix[nlarenes.

Effects Of The Anticancer Agent Cloretazine On Human Apurinic Endonuclease-1 Activity, Jennifer L. Bushee

Honors Theses

The carbamolyating activity of Cloretazine, a novel anticancer prodrug, modifies protein function and acts synergistically with the choroethyalting species, which a1kylales DNA. The reactive subspecies responsible for carbamolylating activity is methyl isocyanate, which reacts with sulfhydryl groups and amines. DNA repair enzymes have been identified as potential targets for the modification by methyl isocyanate; in particular, base excision repair enzymes. Enzymes in DNA base excision repair include DNA polymerase beta (Pol ?) and apurinic/apyrimidic endonucease-l (APE/Ref-1). APE/Ref-1 hydrolyzes the 5' -phosphodiester DNA backbone from an abasic DNA template, where the base was excised by a DNA glycosylase. The entire nucleotide …

A Tribute To Peter George Brewer In Celebration Of His 65th Birthday, George T. F. Wong, Robert F. Anderson, Michael P. Bacon, Hein J. W. De Baar, James W. Murray, Mary I. Scranton

OES Faculty Publications

Peter George Brewer is an ocean chemist of the rare breed that can cross back and forth over the divide between being a front-line research scientist and being a research executive. As if that is not remarkable enough, in the process, he has also demonstrated sustained growth in the depth, breadth, and diversity of his scientific endeavors. Some of his formidable contributions to ocean chemistry have already been highlighted in a profile of him as a major mover and shaker in the field (Irion, 2001). Here, we provide additional glimpses of him from the perspective of a group of individuals …

Naturally Present Fatty Acids As Internal Calibrants For Fourier Transform Mass Spectra Of Dissolved Organic Matter, Rachel L. Sleighter, Georgina A. Mckee, Zhanfei Liu, Patrick G. Hatcher

Chemistry & Biochemistry Faculty Publications

The analysis of dissolved organic matter ( DOM) by Fourier transform ion cyclotron resonance mass spectrometry ( FTICR- MS) has gained wide interest recently, driven primarily by its ultrahigh resolving power and mass accuracy. Accurate calibration of mass spectra is a key step to successfully decipher the DOM components. We propose a simple and accurate method to internally calibrate the peaks in the complex spectra without the need to add a calibrant. Mass spectra of DOM samples from the Dismal Swamp, Virginia, and the lower Chesapeake Bay display the presence of naturally occurring fatty acids which can be readily recognized …

Determination Of Photochemically Produced Carbon Dioxide In Seawater, Emily M. White, David J. Kieber, Kenneth Mopper

Chemistry & Biochemistry Faculty Publications

An analytical system was developed to determine photochemically produced carbon dioxide in marine waters. Our system was designed to measure low levels of carbon dioxide by maintaining a closed system to prevent atmospheric contamination during sample preparation, irradiation, and analysis. To detect low levels of photoproduced carbon dioxide in seawater, background dissolved inorganic carbon (DIC) was removed before irradiation. To strip out DIC, samples were acidified to pH 3.0 (converting DIC to carbon dioxide) and bubbled with low carbon dioxide air. The pH was then readjusted back to the original value, and the resulting low-DIC seawater samples were transferred pneumatically …

Efficient Synthesis Of Imidazole Derivatives: An Important Synthon For The Preparation Of Biologically Active Compounds, Asghar Davood, Eskandar Alipour, Abbas Shafiee

Turkish Journal of Chemistry

4(5)-Chloro-imidazole-5(4)-carboxaldehyde derivatives are important precursors for the preparation of biologically active compounds. We developed a simple, novel, and efficient method for the synthesis of these compounds. The chemistry described is amenable to large-scale use and is flexible enough to allow the preparation of analogs.

Solid Phase Extraction Of Cadmium In Edible Oils Using Zinc Piperazinedithiocarbamate And Its Determination By Flame Atomic Absorption Spectrometry, Mehtap Yağan Aşci, Ayşegül Efendi̇oğlu, Beki̇r Bati

Turkish Journal of Chemistry

A method was developed for preconcentration of cadmium with zinc-piperazinedithiocarbamate (ZnPDC) in edible oils and its determination by flame atomic absorption spectrometer (FAAS). The preconcentration method is based on the adsorption of the Cd(II) on to ZnPDC and the elution of them with mercury(II) nitrate. The accuracy of the method was tested with standard reference material (CONOSTAN S-21) and Cd added samples. Under optimum conditions, the recovery and the detection limit for cadmium were 99.67% (\pm 0.67) and 0.028 mg/L, respectively. The calibration curve was linear over the concentration range 0.1-3.0 mg/L (r^2 = 0.9979). The proposed method was applied …

Synthesis And Antimicrobial Activity Of Some 3(2h)-Pyridazinone And 1(2h)-Phthalazinone Derivatives, Deni̇z S. Doğruer, Ti̇jen Önkol, Semi̇ha Özkan, Selda Özgen, M. Fethi̇ Şahi̇n

Turkish Journal of Chemistry

Some 3(2H)-pyridazinone and 1(2H)-phthalazinone derivatives were synthesized. The structures of these new compounds were confirmed by IR, ^1H-NMR, mass spectrum, and elemental analysis. The synthesized compounds were evaluated for their antibacterial activity against various gram-positive and gram-negative strains of bacteria and their clinical isolates and for their antimycobacterial activity against M. tuberculosis H37Rv. The results showed that the synthesized compounds were generally active against B. subtilis and its clinical isolate. Among the target compounds, compound 14c exhibited the best antibacterial activity, with a MIC value of 15.62 \mu g/mL against B. subtilis. Compound 15e had the highest antimycobacterial activity.

The Crystal Structure Of 2-Nitro-N-(4-Nitrophenyl)Benzamide, Aamer Saeed, Shahid Hussain, Ulrich Flörke

Turkish Journal of Chemistry

2-Nitro-N-(4-nitrophenyl)benzamide was synthesized and characterized by spectroscopy and elemental analysis. The crystal structure was determined from single-crystal X-ray diffraction data. It crystallizes in the orthorhombic space group, P 2_12_12_1, with unit cell dimensions a = 8.9443(10) Å, b = 9.7147(11) Å, and c = 13.8016(16) Å. The dihedral angle between the 2 aromatic rings is 82.32(4)^{\circ}. The N2 and N3 nitro groups are oriented with respect to their attached phenyl rings at dihedral angles of 1.97(3)^{\circ} and 15.73(3)^{\circ}, respectively. The intramolecular C-H{\ldots}O hydrogen bond results in the formation of a non-planar 6-membered ring. In the crystal structure, intermolecular N-H...O hydrogen …

Potentiometric Utility Of The New Solid-State Sensor Based On Crowned Ionophore For The Determination Of K^+, Bariş Kemer, Mustafa Özdemi̇r

Turkish Journal of Chemistry

All solid-state contact poly vinyl chloride (PVC) membrane potassium-selective electrode has been developed. The construction of the ion selective electrode membrane was organized using ionophore 4,4'-bis[4''-phenoxy(15-crown-5) methyl]benzyl in PVC cocktail. The potentiometric performance characteristics of the electrode were investigated by a computerized system. The electrode was found highly selective to K^+ ions over a wide variety of other cations. The electrode almost exhibited a Nernstian response (\ge 55 (\pm15) mV/decade of K activity) to K^+ within the concentration range 1.5 x 10^{-1} - 1.0 \times 10^{-5} M. The operational pH range of the electrode was 5--7. The response time of …