Chemistry Commons^™

Mutagenesis Of Α-Conotoxins For Enhancing Activity And Selectivity For Nicotinic Acetylcholine Receptors, Matthew W. Turner, Leanna A. Marquart, Paul D. Phillips, Owen M. Mcdougal

Chemistry and Biochemistry Faculty Publications and Presentations

Nicotinic acetylcholine receptors (nAChRs) are found throughout the mammalian body and have been studied extensively because of their implication in a myriad of diseases. α-Conotoxins (α-CTxs) are peptide neurotoxins found in the venom of marine snails of genus Conus. α-CTxs are potent and selective antagonists for a variety of nAChR isoforms. Over the past 40 years, α-CTxs have proven to be valuable molecular probes capable of differentiating between closely related nAChR subtypes and have contributed greatly to understanding the physiological role of nAChRs in the mammalian nervous system. Here, we review the amino acid composition and structure of several …

Synthesis, Biological Evaluation And Molecular Modeling Studies Of Novel Chromone/Aza-Chromone Fused Α-Aminophosphonates As Src Kinase Inhibitors, S. Bapat, N. Viswanadh, M. Mujahid, Amir Nasrolahi Shirazi, Rakesh Tiwari, Keykavous Parang, M. Karthikeyan, M. Muthukrishnan, Renu Vyas

Pharmacy Faculty Articles and Research

A series of novel chromone/aza-chromone fused α-aminophosphonate derivatives were synthesized in good yields using silica chloride as the catalyst. All the synthesized compounds were tested for their c-Src kinase inhibitory activity. Aza-chromone compound showed Src kinase inhibition with an IC50 value of 15.8 µM. The compounds were subjected to molecular docking and dynamics simulations to study the atomic level interactions with an unphosphorylated proto-oncogenic tyrosine protein kinase Src (PDB code 1Y57) as well as phosphorylated tyrosine protein kinase Src (PDB code 2H8H). Docking and molecular dynamic results revealed phosphorylated Src tyrosine kinase protein better results than unphosphorylated tyrosine Src kinase …

Surface Coupling Of Octaethylporphyrin With Silicon Tetrachloride, Jayne C. Garno, Phillip C. Chambers, Neepa M. K. Kuruppu Arachchige, Ashley M. Taylor

Faculty Publications

The surface assembly of 2,3,7,8,12,13,17,18-octaethylporphyrin (OEP) using silicon tetrachloride as a coupling agent was investigated using atomic force microscopy (AFM). Nanopatterned films of Si-OEP were prepared by protocols of colloidal lithography to evaluate the morphology, thickness, and molecular orientation for samples prepared on Si(111). The natural self-stacking of porphyrins can pose a challenge for molecular patterning. When making films on surfaces, porphyrins will self-associate to form co-planar configurations of random stacks of molecules. There is a tendency for the flat molecules to orient spontaneously in a side-on arrangement that is mediated by physisorption to the substrate as well as by …

Functional Polymers Through Mechanochemistry, Stephen Schrettl, Diedrik W.R. Balkenende, Céline Calvino, Marc Karman, Ana Lavrenova, Laura N. Neumann, Yoshimitsu Sagara, Ester Verde-Sesto, Michela Di Giannantonio, Yoan C. Simon, Katharina M. Fromm, Marco Lattuada, Christoph Weder

Faculty Publications

While coupling mechanical and chemical processes is widespread in living organisms, the idea to harness the mechanically induced dissociation of weak covalent and non-covalent bonds to create artificial materials that respond to mechanical stimulation has only recently gained attention. Here we summarize our activities that mainly revolve around the exploitation of non-covalent interactions in (supramolecular) polymeric materials with the goal to translate mechanical stresses into useful, pre-defined events. Focusing on mechano- chromic polymers that alter their optical absorption or fluorescence properties, several new operating principles, mechanosensitive entities, and materials systems were developed. Such materials are expected to be useful for …

Extra-Mitochondrial Cu/Zn Superoxide Dismutase (Sod1) Is Dispensable For Protection Against Oxidative Stress But Mediates Peroxide Signaling In Saccharomyces Cerevisiae, Claudia Montllor-Albalate, Alyson E. Colin, Bindu Chandrasekharan, Naimah Bolaji, Joshua L. Andersen, Franklin W. Outten, Amit R. Reddi

Faculty Publications

Cu/Zn Superoxide Dismutase (Sod1) is a highly conserved and abundant metalloenzyme that catalyzes thedisproportionation of superoxide radicals into hydrogen peroxide and molecular oxygen. As a consequence, Sod1serves dual roles in oxidative stress protection and redox signaling by both scavenging cytotoxic superoxideradicals and producing hydrogen peroxide that can be used to oxidize and regulate the activity of downstreamtargets. However, the relative contributions of Sod1 to protection against oxidative stress and redox signaling arepoorly understood. Using the model unicellular eukaryote, Baker's yeast, we found that only a small fraction ofthe total Sod1 pool is required for protection against superoxide toxicity and that …

Synthesis And Evaluation Of Novel Iodine-124 Labeled Nucleoside Analogs As Pet Imaging Agents To Predict Response To Gemcitabine Therapy, Kishore Kumar Gangangari

Dissertations, Theses, and Capstone Projects

Gemcitabine (gem) is a nucleoside analog that is used to treat pancreatic cancers (PaCa), which have dismal prognosis and low survival rate. Though gem is used as first line of treatment for PaCa, the response rate is quite low (~30%). Currently, there is no a priori way to determine a responder from a non-responder to gem therapy either invasively or non-invasively. Any biomarker that can act as a prognostic indicator of gem response will greatly aid in selecting responsive patients to gem therapy and provide alternative options such as Folfirinox or other treatments to resistant patient population. Amongst various known …

Pretargeted Radioimmunotherapy Utilizing The Inverse Electron Demand Diels-Alder Reaction, Rosemery Membreno

Dissertations, Theses, and Capstone Projects

Radioimmunotherapy capitalizes on the specificity and affinity of antibodies for their antigens to localize radioactivity at the tumor site. One limitation in using antibodies is their long circulation time, which can take days to weeks to fully clear from blood circulation. When a radioisotope is directly conjugated to this immunoglobulin vector, the red marrow and other healthy organs are receiving a constant radiation dose while it is in blood circulation. This not only harms healthy organs, but limits the dose of radioactivity that can be administered thus prolonging treatment. A promising alternative to limit the radiation dose to non-tumor tissue …

Analysis Of Oxygen-18 Labeled Phosphate To Study Positional Isotope Experiments Using Lc-Qtof-Ms, Sujatha Chilakala, Iteen Cheng, Ireen Lee, Yan Xu

Chemistry Faculty Publications

A method is proposed in this paper for the determination of oxygen-18 labeled phosphate so that positional isotope experiments using sensitive and rapid liquid chromatography–QTOF–mass spectrometry (LC-QTOF-MS) experiments can be carried out. The positional isotope exchange technique is a useful tool in understanding the mechanisms and kinetics of many enzyme-catalyzed reactions. Detection of the positions and concentration of these exchanged isotopes is the key. Gas chromatography–mass spectrometry (GC-MS) and nuclear magnetic resonance imaging are commonly used analytical techniques for measurement of ¹⁸O/¹⁶O, ³¹P and ¹⁵N isotope enrichment. Since these techniques either require a time-consuming derivatization …

Carbohydrate Polymers As Controlled Release Devices For Pesticides, Soma Chakraborty, Maria Cleofe Neri-Badang

Chemistry Faculty Publications

Controlled release technology addresses problems associated with excessive use of toxic agricultural chemicals. This paper reviews the studies on the use of carbohydrate polymers as controlled release matrices for pesticides. Alginates, starch and its derivatives, chitosan, carboxymethylcellulose and ethylcellulose are some of the natural polymers discussed in this review. The advantages and disadvantages of these polymeric systems as well as the factors that affect pesticide release are presented. A discussion on the polymers’ encapsulation efficiency and release profile is also included, which will aid future researchers in identifying the suitable formulation for controlled release of pesticides. Combination of two polymers, …

Thermotropic Liquid-Crystalline Properties Of Viologens Containing 4-N-Alkylbenzenesulfonates, Pradip K. Bhowmik, Anthony Chang, Jongin Kim, Erenz J. Dizon, Ronald Carlo G. Principe, Haesook Han

Chemistry and Biochemistry Faculty Research

A series of viologens containing 4-n-alkylbenzenesulfonates were synthesized by the metathesis reaction of 4-n-alkylbenzenesulfonic acids or sodium 4-n-alkylbezenesulfonates with the respective viologen dibromide in alcohols. Their chemical structures were characterized by Fourier Transform Infrared, ¹H and ¹³C Nuclear Magnetic Resonance spectra and elemental analysis. Their thermotropic liquid-crystalline (LC) properties were examined by differential scanning calorimetry and polarizing optical microscopy. They formed LC phases above their melting transitions and showed isotropic transitions. As expected, all the viologen salts had excellent stabilities in the temperature range of 278–295 °C as determined by thermogravimetric analysis.

Solvation Thermodynamic Mapping In Computer Aided Drug Design, Steven Ramsey

Dissertations, Theses, and Capstone Projects

The displacement of water from surfaces upon biomolecular recognition and association makes a significant contribution to the free energy changes of these processes. We therefore posit that accurate characterization of local structural and thermodynamic molecular water properties can improve computational model accuracy and predictivity of recognition and association processes. In this thesis, we discuss Solvation Thermodynamic Mapping (STM) methods that we have developed using inhomogeneous fluid solvation theory (IST) to better characterize active site water structural and thermodynamic properties on protein surfaces and the open source tools that we have developed, GIST-CPPTRAJ and SSTMap, which implement these methods which we …

Potential Degradation Of Hexabromocyclododecane (Hbcdd) In Sediments: Stereoisomer Specific Reaction Of Hbcdd With Reduced Sulfur Species Or Fe(Ii) Bound To Iron Oxides, Xianmiao Zhang

Dissertations, Theses, and Capstone Projects

The individual degradation rates of the three dominant stereoisomers (alpha, beta, gamma) of hexabromocyclododecane (HBCDD) with bisulfide and polysulfides were investigated at pH 9-10 in methanol/water solutions at two different temperatures (25 °C and 40 °C). alpha-HBCDD reacts significantly slower than beta-HBCDD and gamma-HBCDD. It was also observed that the reaction of HBCDD with polysulfides is faster than with bisulfide. For the reaction of HBCDD with bisulfide, the experiments were performed in 20% water/80% methanol, 50% water/50% methanol and 80% water/20% methanol at 40 °C. It was determined that the solvent polarity affects the reaction and the second-order rate constants …

Bisthioether Stapled Peptides Targeting Polycomb Repressive Complex 2 Gene Repression, Gan Zhang

Dissertations, Theses, and Capstone Projects

Interactions between proteins play a key role in nearly all cellular process, and therefore, disruption of such interactions may lead to many different types of cellular dysfunctions. Hence, pathologic protein-protein interactions (PPIs) constitute highly attractive drug targets and hold great potential for developing novel therapeutic agents for the treatment of incurable human diseases. Unfortunately, the identification of PPI inhibitors is an extremely challenging task, since traditionally used small molecule ligands are mostly unable to cover and anchor on the extensive flat surfaces that define those binary protein complexes. In contrast, large biomolecules such as proteins or peptides are ideal fits …

Development Of Palladium(0)-Catalyzed Suzuki Cross-Coupling Polymerizations, Wei Peng

Dissertations, Theses, and Capstone Projects

The synthesis of well-defined and high molecular weight π-conjugated polymers under mild condition within short reaction time is a challenging and important task in both organic chemistry and polymer chemistry. As one of the most efficient and high tolerance to solvents and reaction conditions, palladium(0)-catalyzed cross-coupling reactions would give us a good chance to achieve the goal. Thus, my Ph. D dissertation research projects focused on developing Pd(0)-catalyzed Suzuki cross-coupling polymerization reactions including controlled ones.

My research first studied t-Bu₃P-coordinated 2-phenylaniline-based palladacycle complex catalyzed Suzuki cross-coupling polymerization of aryl dibromides with aryldiboronic acids at room temperature. Based …

Radical Scavenging Of Poly(Methyl Methacrylate) Bone Cement By Rifampin And Clinically Relevant Properties Of The Rifampin-Loaded Cement, G. A. Funk, E. M. Menuey, K. A. Cole, Thomas P. Schuman, K. V. Kilway, T. E. Mciff

Chemistry Faculty Research & Creative Works

Objectives: The objective of this study was to characterize the effect of rifampin incorporation into poly(methyl methacrylate) (pMMA) bone cement. While incompatibilities between the two materials have been previously noted, we sought to identify and quantify the cause of rifampin's effects, including alterations in curing properties, mechanical strength, and residual monomer content.

Methods: Four cement groups were prepared using commercial pMMA bone cement: a control; one with 1 g of rifampin; and one each with equimolar amounts of ascorbic acid or hydroquinone relative to the amount of rifampin added. The handling properties, setting time, exothermic output, and monomer loss were …

Functionalized Carbon Nanotube Adsorption Interfaces For Electron Transfer Studies Of Galactose Oxidase, Mulugeta B. Wayu, Michael J. Pannell, Najwa Labban, William S. Case, Julie A. Pollack, Michael C. Leopold

Chemistry Faculty Publications

Modified electrodes featuring specific adsorption platforms able to access the electrochemistry of the copper containing enzyme galactose oxidase (GaOx) were explored, including interfaces featuring nanomaterials such as nanoparticles and carbon nanotubes (CNTs). Electrodes modified with various self-assembled monolayers (SAMs) including those with attached nanoparticles or amide-coupled functionalized CNTs were examined for their ability to effectively immobilize GaOx and study the redox activity related to its copper core. While stable GaOx electrochemistry has been notoriously difficult to achieve at modified electrodes, strategically designed functionalized CNT-based interfaces, cysteamine SAM-modified electrode subsequently amide-coupled to carboxylic acid functionalized single wall CNTs, were significantly more …

Proton-Coupled Reduction Of An Iron Nitrosyl Porphyrin In The Protic Ionic Liquid Nanodomain, Abderrahman Atifi, Piotr J. Mak, Michael D. Ryan

Chemistry Faculty Research and Publications

The one-electron reduction of many molecules becomes much more favorable if combined with proton transfers or strong hydrogen bonding. Protic room temperature ionic liquids (RTILs), which can form nanodomains in solutions with molecular solvents (MS), can provide an efficient avenue for this process. In this work, we report on the voltammetry, UV/visible and resonance Raman spectroelectrochemistryof Fe(TPP)(NO) in the presence of aprotic/protic ammonium-based ionic liquids. While aprotic RTILs did shift the reduction to more positive potentials, similar shifts could be observed at much lower concentrations of diethylmethylammonium triflate (HAmOTf, a protic ionic liquid). Deconvolution of the rotating ring-disk electrode (RRDE) …

Viscosities, Diffusion Coefficients, And Mixing Times Of Intrinsic Fluorescent Organic Molecules In Brown Limonene Secondary Organic Aerosol And Tests Of The Stokes–Einstein Equation, Dagny A. Ullmann, Mallory L. Hinks, Adrian M. Maclean, Christopher Butenhoff, James W. Grayson, Kelley Barsanti, Jose L. Jimenez, Sergey A. Nizkorodov, Saeid Kamal, Allan K. Bertram

Physics Faculty Publications and Presentations

Viscosities and diffusion rates of organics within secondary organic aerosol (SOA) remain uncertain. Using the bead-mobility technique, we measured viscosities as a function of water activity (a_w) of SOA generated by the ozonolysis of limonene followed by browning by exposure to NH₃ (referred to as brown limonene SOA or brown LSOA). These measurements together with viscosity measurements reported in the literature show that the viscosity of brown LSOA increases by 3–5 orders of magnitude as the aw decreases from 0.9 to approximately 0.05. In addition, we measured diffusion coefficients of intrinsic fluorescent organic molecules within brown …

Sensitivity Analysis Of Computations Of The Vapor-Liquid Equilibria Of Methane + Methanol Or Glycols At Gas Hydrate Formation Conditions, Christopher E. Ozigagu, Anthony J. Duben

Faculty Publications

The Soave-Redlich-Kwong (SRK-EOS) and Peng-Robinson (PR-EOS) equations of state are used often to describe the behavior of pure substances and mixtures despite difficulties in handling substances, like water, with high polarity and hydrogen bonding. They were employed in studying the binary vapor-liquid equilibria (VLE) of methane + methanol, monoethylene glycol (MEG), and triethylene glycol (TEG). These liquids are used to inhibit the formation of gas hydrates. The investigation focused on the conditions at which methane-water clathrates can form 283.89 K to 323.56 K and 5.01 MPa to 18.48 MPa. The pressure of methane in methanol is overestimated by a factor …

Immobilization Adjusted Clock Reaction In The Urea-Urease-H+ Reaction System, John A. Pojman

Faculty Publications

The bell-shaped reactivity-pH curve is the fundamental reason that the temporal programmable kinetic switch in clock reactions can be obtained in bio-competitive enzymatic reactions. In this work, urease was loaded on small resin particles through ionic binding. Experimental results reveal that the immobilization not only increased the stability of the enzyme and the reproducibility of the clock reaction, but also shifted the bell-shaped activity curve to lower pHs. The latter change enables the clock reaction to occur from an initial pH of 2.3, where the free enzyme had already lost its activity. Two mechanisms explain the influence of the immobilization …

Manori Perera And Problems For Automobiles During Sub-Zero Temperatures, Eric Stock

Interviews for WGLT

Eric Stock,WGLT Radio, spoke to Professor of Chemistry Manori Perera about the hazards that sub-zero temperatures create for automobiles.

Catalytic Mechanism For The Conversion Of Salicylate Into Catechol By The Flavin-Dependent Monooxygenase Salicylate Hydroxylase, Débora M. A. Costa, Stefanya V. Gómez, Simara S. De Araújo, Mozart S. Pereira, Rosemeire B. Alves, Denize C. Favaro, Alvan C. Hengge, Ronaldo A. P. Nagem, Tiago A. S. Brandão

Chemistry and Biochemistry Faculty Publications

Salicylate hydroxylase (NahG) is a flavin-dependent monooxygenase that catalyzes the decarboxylative hydroxylation of salicylate into catechol in the naphthalene degradation pathway in Pseudomonas putida G7. We explored the mechanism of action of this enzyme in detail using a combination of structural and biophysical methods. NahG shares many structural and mechanistic features with other versatile flavin-dependent monooxygenases, with potential biocatalytic applications. The crystal structure at 2.0 Å resolution for the apo form of NahG adds a new snapshot preceding the FAD binding in flavin-dependent monooxygenases. The k_cat/K_m for the salicylate reaction catalyzed by the holo form is …

An Experimental And Numerical Investigation Of Flow Accelerated Flibe Corrosion, David B. Weitzel

Nuclear Engineering ETDs

Renewed interest in molten salt reactor technology has brought to light the need for a better understanding of FLiBe corrosion. To this end a flowing FLiBe corrosion test loop was designed to test the flow effects of FLiBe corrosion. The loop consists of a pump, melt tank, and stainless-steel tubing assembly that heats the molten salt to high temperatures and circulates it over test specimens. The experiment has been constructed and has completed initial shakedown testing.

To support the flowing FLiBe experiment, a numerical corrosion model that couples FLiBe electrochemistry, solid metal diffusion, and mass transport was implemented. The model …

Speciated And Total Emission Factors Of Particulate Organics From Burning Western Us Wildland Fuels And Their Dependence On Combustion Efficiency, Coty N. Jen, Lindsay E. Hatch, Vanessa Selimovic, Robert J. Yokelson, Robert Weber, Arantza E. Fernandez, Nathan M. Kreisberg, Kelley C. Barsanti, Allen H. Goldstein

Chemistry and Biochemistry Faculty Publications

Western US wildlands experience frequent and large-scale wildfires which are predicted to increase in the future. As a result, wildfire smoke emissions are expected to play an increasing role in atmospheric chemistry while negatively impacting regional air quality and human health. Understanding the impacts of smoke on the environment is informed by identifying and quantifying the chemical compounds that are emitted during wildfires and by providing empirical relationships that describe how the amount and composition of the emissions change based upon different fire conditions and fuels. This study examined particulate organic compounds emitted from burning common western US wildland fuels …

Amino Alkynylisoquinoline And Alkynylnaphthyridine Compounds Potently Inhibit Acute Myeloid Leukemia Proliferation In Mice, N Naganna, Clement Opuku-Temeng, Eun Yong Choi, Elizabeth Larocque, Elizabeth T. Chang, Brandon A. Carter-Cooper, Modi Wang, Sandra E. Torregrossa-Allen, Bennett D. Elzey, Rena G. Lapidus, Herman Sintim

Department of Chemistry Faculty Publications

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ackground: Acute myeloid leukemia (AML) remains one of the most lethal, rarely cured cancers, despite decades of active development of AML therapeutics. Currently, the 5-year survival of AML patients is about 30% and for elderly patients, the rate drops to b10%. About 30% of AML patients harbor an activating mutation in the tyrosine kinase domain (TKD) of Fms-Like Tyrosine kinase 3 (FLT3) or a FLT3 internal tandem duplication (FLT3-ITD). In- hibitors of FLT3, such as Rydapt that was recently approved by the FDA, have shown good initial response but pa- tients often relapse due to secondary mutations in the …

Chemistry & Biochemistry Guest Lecture Series, Desmond Murray

Andrews Agenda: Campus News

No abstract provided.

The Van Der Waals Fluid’S Liquid Vapor Coexistence Locus, Using Maxima/Gnuplot, Carl W. David

Chemistry Education Materials

The Maxima/Gnuplot code for plotting the van der Waals locus of liquid and vapor molar volumes as a function of pressure and temperature (all reduced) is presented.

Dual Geometry Schemes In Tetrel Bonds: Complexes Between Tf4(T = Si, Ge, Sn) And Pyridine Derivatives, Wiktor Zierkiewicz, Mariusz Michalczyk, Rafał Wysokiński, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

When an N-base approaches the tetrel atom of TF4(T = Si, Ge, Sn) the latter moleculedeforms from a tetrahedral structure in the monomer to a trigonal bipyramid. The base can situateitself at either an axial or equatorial position, leading to two different equilibrium geometries.The interaction energies are considerably larger for the equatorial structures, up around 50 kcal/mol,which also have a shorter R(T··N) separation. On the other hand, the energy needed to deform thetetrahedral monomer into the equatorial structure is much higher than the equivalent deformationenergy in the axial dimer. When these two opposite trends are combined, it is the axial …

Synthetic Ionophores As Non-Resistant Antibiotic Adjuvants, George Gokel, Mohit Patel, Evan Garrad, Joseph Meisel, Saeedeh Negin, Michael Gokel

Chemistry & Biochemistry Faculty Works

Antimicrobial resistance is a world-wide health care crisis. New antimicrobials must both exhibit potency and thwart the ability of bacteria to develop resistance to them. We report the use of synthetic ionophores as a new approach to developing non-resistant antimicrobials and adjuvants. Most studies involving amphiphilic antimicrobials have focused on either developing synthetic amphiphiles that show ion transport, or developing non-cytotoxic analogs of such peptidic amphiphiles as colistin. We have rationally designed, prepared, and evaluated crown ether-based synthetic ionophores (‘hydraphiles’) that show selective ion transport through bilayer membranes and are toxic to bacteria. We report here that hydraphiles exhibit a …

Development Of Ultrafast Broadband Electronic Sum Frequency Generation For Charge Dynamics At Surfaces And Interfaces, Gang-Hua Deng, Yuqin Qian, Yi Rao

Chemistry and Biochemistry Faculty Publications

Understandings of population and relaxation of charges at surfaces and interfaces are essential to improve charge collection efficiency for energy conversion, catalysis, and photosynthesis. Existing time-resolved surface and interface tools are limited to either under ultrahigh vacuum or in a narrow wavelength region with the loss of spectral information. There lacks an efficient time-resolved surface/interface-specific electronic spectroscopy under ambient conditions for the ultra fast surface/interface dynamics. Here we developed a novel technique for surface/interface-specific broadband electronic sum frequency generation (ESFG). The broadband ESFG was based on a stable two-stage BiB₃O₆ crystal-based optical parametric amplifier, which generates a …