Chemistry Commons^™

Carbide-Derived Carbon By Electrochemical Etching Of Vanadium Carbides, Luis G.B. Camargo, Benjamin G. Palazzo, Greg Taylor, Zach A. Norris, Yash K. Patel, Jeffrey D. Hettinger, Lei Yu

Jeffrey Hettinger

Carbide-derived Carbon (CDC) has been demonstrated to be an excellent electrode material for electrochemical devices including supercapacitors due to its chemical and electrochemical stability, large specific surface area and controllable pore size and morphology. Currently, CDC is prepared from metal carbides by chlorination in a chlorine gas atmosphere at temperatures of 350°C or higher. In this paper, conversion using electrochemical methods is reported, which can be achieved by oxidizing vanadium carbides (VC or V2C) in aqueous solutions at room temperature and a mild electrode potential to prepare CDC thin film as electrode materials for “on-chip” supercapacitiors. It was found that …

The Crystal Structure Of Nitrosomonas Europaea Sucrose Synthase Reveals Critical Conformational Changes And Insights Into The Sucrose Metabolism In Prokaryotes, Rui Wu, Matías D. Asención Diez, Carlos M. Figueroa, Matías Machtey, Alberto A. Iglesias, Miguel Ballicora, Dali Liu

Miguel A Ballicora

In this paper we report the first crystal structure of a prokaryotic sucrose synthase from the non-photosynthetic bacterium Nitrosomonas europaea. The obtained structure was in an open form, whereas the only other available structure from the plant Arabidopsis thaliana was in a closed conformation. Comparative structural analysis revealed a “hinge-latch” combination, which is critical to transition between the open and closed forms of the enzyme. The N. europaea sucrose synthase shares the same fold as the GT-B family of the retaining glycosyltransferases. In addition, a triad of conserved homologous catalytic residues in the family showed to be functionally critical in …

Chemistry 107 Chemistry For Health Professions Ii Online Fall 2015, David M. Wilson

David Wilson

No abstract provided.

Chemistry 107 Chemistry For Health Professions Ii Online Spring 2015, David M. Wilson

David Wilson

No abstract provided.

First-Principles And Model Simulation Of All-Optical Spin Reversal, Thomas F. George, G.P. Zhang, Z. Babyak, Y. Xue, Y. H. Bai

Thomas George

Proton Transfer And Esterification Reactions In Emimoac-Based Acidic Ionic Liquids, Anh T. Tran, Phuoc H. Lam, Alexandra M. Miller, Dustin J. Walczyk, Jay Tomlin, Timothy D. Vaden, Lei Yu

Lei Yu

Acetate-based ionic liquids (such as 1-ethyl-3-methylimidazolium acetate, EMIMOAc) have potential applications for CO2 absorption and electrochemical reduction, chemical separations and extractions, and Fischer esterification of alcohols, amines, and starch. Both strong and weak organic acids can be dissolved in EMIMOAc and yield interesting proton-rich acidic ionic liquid solutions. We have used GCMS vapor pressure measurements, spectroscopic methods, calorimetry, and viscosity/conductivity measurements to investigate the properties and reactions of various acids dissolved in EMIMOAc. Unique proton transfer and esterification reactions are observed in many of these acidic solutions with carboxylic acids or sulfonic acids as solutes. Some acids react with the …

Intramolecular Glycosylation, Alexei Demchenko, Xiao G. Jia

Alexei Demchenko

Oligomers Of Cyclopentadithiophene-Vinylene In Aromatic And Quinoidal Versions And Redox Species With Intermediate Forms, Paula Mayorga Burrezo, Rocío Domínguez, José L. Zafra, Ted M. Pappenfus, Pilar De La Cruz, Lorena Welte, Daron E. Janzen, Juan T. López Navarrete, Fernando Langa, Juan Casado

Daron E Janzen, Ph.D.

No abstract provided.

Cobalt-Doped Ceria/Reduced Graphene Oxide Nanocomposite As An Efficient Oxygen Reduction Reaction Catalyst And Supercapacitor Material, Shaikh Parwaiz, Kousik Bhunia, Ashok Kumar Das, Mohammad Mansoob Khan Dr, Debabrata Pradhan

Dr. Mohammad Mansoob Khan

Ionic Liquid Extraction Unveils Previously Occluded Humic-Bound Iron In Peat Soil Pore Water, Timothy J. Veverica, Evan S. Kane, Amy Marcarelli, Sarah A. Green

Amy Marcarelli

Globally, peatland ecosystems store tremendous amounts of C relative to their extent on the landscape, largely owing to saturated soils which limit decomposition. While there is still considerable uncertainty regarding CO2 production potential below the water table in peatland ecosystems, extracellular Fe reduction has been suggested as a dominant pathway for anaerobic metabolism. However, colorimetric methods commonly used to quantitate Fe and partition between redox species are known to be unreliable in the presence of complex humic substances, which are common in peatland pore water. We evaluated both the standard o-phenanthroline (o-P) Method and an ionic liquid extraction (ILE) Method …

Biophysical And Computational Studies Of The Vcci:Vmip-Ii Complex, Anna Nguyen, Nai-Wei Kuo, Laura Showalter, Ricardo Ramos, Cynthia Dupureur, Michael Colvin, Patricia Liwang

Cynthia Dupureur

Dengue Virus Ns2b/Ns3 Protease Inhibitors Exploiting The Prime Side, Kuan-Hung Lin, Akbar Ali, Linah Rusere, Djade I. Soumana, Nese Kurt Yilmaz, Celia A. Schiffer

Celia A. Schiffer

The mosquito-transmitted dengue virus (DENV) infects millions of people in tropical and subtropical regions. Maturation of DENV particles requires proper cleavage of the viral polyprotein, including processing of 8 of the 13 substrate cleavage sites by dengue virus NS2B/NS3 protease. With no available direct-acting antiviral targeting DENV, NS2/NS3 protease is a promising target for inhibitor design. Current design efforts focus on the nonprime side of the DENV protease active site, resulting in highly hydrophilic and nonspecific scaffolds. However, the prime side also significantly modulates DENV protease binding affinity, as revealed by engineering the binding loop of aprotinin, a small protein …

Interdependence Of Inhibitor Recognition In Hiv-1 Protease, Janet L. Paulsen, Florian Leidner, Debra A. Ragland, Nese Kurt Yilmaz, Celia A. Schiffer

Celia A. Schiffer

Molecular recognition is a highly interdependent process. Subsite couplings within the active site of proteases are most often revealed through conditional amino acid preferences in substrate recognition. However, the potential effect of these couplings on inhibition and thus inhibitor design is largely unexplored. The present study examines the interdependency of subsites in HIV-1 protease using a focused library of protease inhibitors, to aid in future inhibitor design. Previously a series of darunavir (DRV) analogs was designed to systematically probe the S1' and S2' subsites. Co-crystal structures of these analogs with HIV-1 protease provide the ideal opportunity to probe subsite interdependency. …

A Microreactor System For Measuring Size Selectivity In Porous Wo3 Sensor Materials, Meng Lu

Meng Lu

Our interest in studying reactions catalyzed by high surface area W03 powders is based on their potential application as the active material in sensors for low level (ppb) detection of flammable or toxic gases. A series of porous W03 powders with both meso- and micro-porosity have been synthesized by Waghe and Tripp. Preliminary results of the response of sensors fabricated from these materials indicated the possibility of size selectivity on the molecular scale. To provide support for the hypothesis of size selectivity and understand the reaction kinetics of alcohols over the new porous W03 powders for sensor applications, we have …

High Rate Detection Of Volatile Products Using Differential Electrochemical Mass Spectrometry: Combining An Electrode-Coated Membrane With Hydrodynamic Flow In A Wall-Tube Configuration, Subramanian Venkatachalam, Robert J. Angelici, L. Keith Woo, Andrew C. Hillier

Andrew C. Hillier

We present an experimental system that combines differential electrochemical mass spectrometry with hydrodynamic flow consisting of an impinging jet in a wall-tube configuration. This assembly allows simultaneous detection of electrochemical signals along with monitoring of dissolved gas species using differential electrochemical mass spectrometry under well-defined hydrodynamic conditions and over a wide range of mass transfer rates. The working electrode is deposited directly onto a thin, hydrophobic membrane, which also serves as the inlet to the mass spectrometer. This inlet provides extremely rapid mass detection as well as a high flux of products from the electrode surface into the mass spectrometer. …

Using Metastable-State Photoacid For Fluorescence And Ph Modulation, Renan S. Gongora, Juan Arias, Parth K. Patel, Karin Y. Chumbimuni-Torres

Juan Arias

7Β-Hydroxy­Artemisinin, Paulo B. Carvalho, Bo Liu, Yunshan Wu, John S. Williamson, Mitchell A. Avery

John S. Williamson

Crystals of the title compound [systematic name: (3R,6R,7S,8aR,9R,12aR)-7-hydr­oxy-3,6,9-trimethyl­octa­hydro-3,12-ep­oxy[1,2]dioxepino[4,3-i]isochromen-10(3H)-one], C15H22O6, were obtained from microbial transformation of artemisinin by a culture of Cunninghamella elegans. The stereochemistry of the compound is consistent with the spectroscopic findings in previously published works. A weak O—H⋯O hydrogen bond occurs in the crystal structure, together with intermolecular C—H⋯O hydrogen bonds.

Determination Of Optical Properties Of Secondary Organic Aerosols Using Uv-Vis Spectroscopy, Vanessa Selimovic, Matthew E. Wise, John Shilling

Matthew E. Wise

• Aerosols interact differently with the atmosphere depending on:
• Composition
• Size
• Phase
• Reactivity
• Optical Properties
• Reactivity with atmosphere determines impact on Earth’s radiative budget

[excerpt]

Digital Fabrication Of An Atmospheric Aerosol Impactor, Stefan J. Vincent, Shawn Daley, Matthew E. Wise

Matthew E. Wise

Atmospheric aerosol (AA) particles are defined as solid or liquid particles suspended in the air. AA particles smaller than 10 μm (1x10^-5 meters) in diameter are small enough to bypass the upper respiratory system which functions as a filter for harmful substances entering the lungs. AA particles can be collected using a device called an aerosol impactor. After collection, the particles can be analyzed offline for chemical composition using a variety of analytical techniques. The weight of a commercially manufactured AA particle impactor poses an issue if it is attached to a mobile AA particle sampling platform such as …

Discovery Of Thienoquinolone Derivatives As Selective And Atp Non-Competitive Cdk5/P25 Inhibitors By Structure-Based Virtual Screening, Arindam Chatterjee, Stephen J. Cutler, Robert J. Doerksen, Ikhlas A. Khan, John S. Williamson

John S. Williamson

Calpain mediated cleavage of CDK5 natural precursor p35 causes a stable complex formation of CDK5/p25, which leads to hyperphosphorylation of tau. Thus inhibition of this complex is a viable target for numerous acute and chronic neurodegenerative diseases involving tau protein, including Alzheimer’s disease. Since CDK5 has the highest sequence homology with its mitotic counterpart CDK2, our primary goal was to design selective CDK5/p25 inhibitors targeting neurodegeneration. A novel structure-based virtual screening protocol comprised of e-pharmacophore models and virtual screening workflow was used to identify nine compounds from a commercial database containing 2.84 million compounds. An ATP non-competitive and selective thieno[3,2- …

Chemistry 100-051w Online Introduction To Chemistry Fall 2015, Christina Beatty

Christina Beatty

No abstract provided.

Building Data And Information Literacy In The Undergraduate Chemistry Curriculum, Yasmeen Shorish, Barbara A. Reisner

Yasmeen Shorish

The Literature and Seminar sequence at James Madison University has been used to develop the chemistry information literacy skills of chemistry majors for over four decades. These courses have been continually updated to emphasize information literacy skills for the twenty-first century. This chapter describes the methods that have been developed to improve chemical, data and general information literacy at a large, public, primarily undergraduate institution. The focus of the first semester course, described in this chapter, is on skill building rather than teaching specific resources. It is a model of integration and collaboration between chemistry faculty and chemistry librarians. Changes …

Energy Efficient Process Heating: Insulation And Thermal Mass, Kevin Carpenter, J. Kelly Kissock

J. Kelly Kissock

Open tanks and exterior surfaces of process heating equipment lose heat to the surroundings via convection, radiation, and/or evaporation. A practical way of reducing heat loss is by insulating or covering the surfaces. This paper presents methods to quantify heat loss and energy savings from insulating hot surfaces and open tanks. The methods include radiation and evaporation losses, which are ignored by simplified methods. In addition, thermal mass, such as refractory, conveyor and racking equipment, acts as a heat sink and increases heating energy use in process heating applications. This paper presents lumped capacitance and finite-difference methods for estimating heat …

Novel Cell Penetrating Peptide-Adaptors Effect Intracellular Delivery And Endosomal Escape Of Protein Cargos, John C. Salerno, Verra M. Ngwa, Scott J. Nowak, Carol A. Chrestensen, Allison N. Healey, Jonathan L. Mcmurry

Jonathan McMurry

The use of cell penetrating peptides (CPPs) as biomolecular delivery vehicles holds great promise for therapeutic and other applications, but development has been stymied by poor delivery and lack of endosomal escape. We have developed a CPP-adaptor system capable of efficient intracellular delivery and endosomal escape of user-defined protein cargos. The cell penetrating sequence of HIV transactivator of transcription was fused to calmodulin, which binds with subnanomolar affinity to proteins containing a calmodulin binding site. Our strategy has tremendous advantage over prior CPP technologies because it utilizes high affinity noncovalent, but reversible coupling between CPP and cargo. Three different cargo …

Helicobacter Pylori Flha Binds The Sensor Kinase And Flagellar Gene Regulatory Protein Flgs With High Affinity, Jennifer Tsang, Takanori Hirano, Timothy R. Hoover, Jonathan L. Mcmurry

Jonathan McMurry

Flagellar biogenesis is a complex process that involves multiple checkpoints to coordinate transcription of flagellar genes with the assembly of the flagellum. In Helicobacter pylori, transcription of the genes needed in the middle stage of flagellar biogenesis is governed by RpoN and the two-component system consisting of the histidine kinase FlgS and response regulator FlgR. In response to an unknown signal, FlgS autophosphorylates and transfers the phosphate to FlgR, initiating transcription from RpoNdependent promoters. In the present study, export apparatus protein FlhA was examined as a potential signal protein. Deletion of its N-terminal cytoplasmic sequence dramatically decreased expression of two …

Convenient Synthesis Of 1,3-Dithiolane-2-Thiones: Cyclic Trithiocarbonates As Conformational Locks, Irina A. Dotsenko, Qinliang Zhao, Andreas H. Franz, Patrick Batoon, Nataliya M. Samoshina, Vyacheslav V. Samoshin

Andreas H. Franz

A series of novel 1,3-dithiolane-2-thiones, or cyclic trithiocarbonates, has been prepared by a new simple procedure: a treatment of the corresponding epoxides with the commercially available potassium ethyl xanthogenate, KSC(S)OEt. The stereochemistry of the products was determined by 1 H NMR and in some cases by single-crystal X-ray data. Cyclohexane-based 1,3- dithiolane-2-thiones revealed a trans-fusion of the carbo- and hetero-cycles. The products obtained from the mono-substituted cyclohexene oxides demonstrated an axial position of the substituents. Thus the epoxide transformation into trithiocarbonate can be used as a method for locking cyclic compounds in unstable conformations.

Synthesis And Nmr-Characterization Of Three Quinamide-Based Disaccharide Mimetics With Unusual Cyclohexane Twist-Conformation, Thuy Trang M. Nguyen, Paul H. Gross, Andreas H. Franz

Andreas H. Franz

The synthesis of amide-linked disaccharide mimetics has been explored starting with carbohydrate-based amines and a protected quinic acid lactone. Benzyl-2-amino-4,6-Obenzylidene-2-deoxy-α/β-D-glucopyranose (12) and D-glucamine (14) were successfully coupled to give the corresponding quinamides (13 and 15), while the quinoylation of Oacetylated L-fucopyranosyl methylamine (7) failed. The latter was prepared from per-O-acetylL-fucopyranose via the improved multigram scale synthesis of the corresponding per-O-acetylL-fucopyranosyl cyanide (3). Compound 3 was subsequently hydrogenated to yield a mixture of compound 7 and the per-O-acetylated bis-(fucopyranosylmethyl) amine (5). The vicinal coupling constants in the NMR spectra of all quinamide products revealed considerable flexibility of the cyclohexane ring in …

Structure Assignment And H/D-Exchange Behavior Of Several Glycosylated Polyphenols, Andreas H. Franz, Ilona Serebnitskaya, Gurbir Gudial, Christopher Wallis

Andreas H. Franz

The NMR-structures of six polyphenols, resveratrol (1), (-)-epicatechin (2), pelargonidin chloride (3), cyanidin chloride (4), cyanin chloride (5), and keracyanin chloride (6), were fully assigned. For the glycosylated polyphenols 5 and 6, the three-dimensional solution structure and long-range 1 H- 13C-coupling constants across the glycosidic bond were measured. Satisfactory fit to standard Karplus-equations was achieved for glycosides directly attached to the aromatic core in cyanin chloride. Molecular dynamics simulation data in vacuum at the AM1-level of theory were shown to approximate the NMR-solution data reasonably well. Selective HCl-catalyzed H/D-exchange was observed for aromatic protons H6 and H8 in flavonoid structures …

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

Andreas H. Franz

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.

Solution Conformations Of Three Small Cluster Oligosaccharide Mimetics (Scom) From D-Glucosamine, D-Altrosamine, And (-)-Quinic Acid, Q. L. Nguyen, L. Olmstead, S. Bains, Andreas H. Franz

Andreas H. Franz

Three small cluster oligosaccharide mimetics were synthesized, and their CDCl3 solution conformations were determined with NMR experiments. In this paper, we confirmed conformational similarities in rings A and B in all three compounds, and we provide the overall solution geometries. In all cases, an unusual cyclohexane twist-boat conformation with longrange 4 J-(W)-coupling was observed. The origin of the bias towards the twist-boat was attributed primarily to the fused ring system between the cyclohexane ring and the dioxacyclopentane (acetal) including hydrogen bonding. Temperature-annealed molecular dynamics simulations complemented the NMR experiments and supported the overall assignment.