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A Control Switch For Prothrombinase: Characterization Of A Hirudin-Like Pentapeptide From The Cooh Terminus Of Factor Va Heavy Chain That Regulates The Rate And Pathway For Prothrombin Activation, Michael A. Bukys, Paul Y. Kim, Michael E. Nesheim, Michael Kalafatis

Chemistry Faculty Publications

Membrane-bound factor Xa alone catalyzes prothrombin activation following initial cleavage at Arg(271) and prethrombin 2 formation (pre2 pathway). Factor Va directs prothrombin activation by factor Xa through the meizothrombin pathway, characterized by initial cleavage at Arg(320) (meizo pathway). We have shown previously that a pentapeptide encompassing amino acid sequence 695-699 from the COOH terminus of the heavy chain of factor Va (Asp-Tyr-Asp-Tyr-Gln, DYDYQ) inhibits prothrombin activation by prothrombinase in a competitive manner with respect to substrate. To understand the mechanism of inhibition of thrombin formation by DYDYQ, we have studied prothrombin activation by gel electrophoresis. Titration of plasma-derived prothrombin activation …

Phosphorus-31 Nmr Of The Intact Crystalline Lens: I. The Living Lens Spectrum. Ii. The Spectroscopic Effects Of Deuterium Oxide Incubation, Thomas Glonek, Stephen J. Kopp, Jack V. Greiner

President's Research

Spectra of intact bovine and canine crystalline lenses in vitro at 37°C were generated using phosphorus-31 nuclear magnetic resonance (NMR). Lens incubation in a pure D2O buffer results in a progressive narrowing of the tissue P-31 NMR signals.

Attachment Of Motile Bacterial Cells To Prealigned Holed Microarrays, Sergey Rozhok, Zhifang Fan, Dorjderem Nyamjav, Chang Liu, Chad A. Mirkin, Richard C. Holz

Chemistry Faculty Research and Publications

Construction of biomotors is an exciting area of scientific research that holds great promise for the development of new technologies with broad potential applications in areas such as the energy industry and medicine. Herein, we demonstrate the fabrication of prealigned microarrays of motile Escherichia coli bacterial cells on SiOx substrates. To prepare these arrays, holed surfaces with a gold layer on the bottom of the holes were utilized. The attachment of bacteria to the holes was achieved via nonspecific interactions using poly-l-lysine hydrobromide (PLL). Our data suggest that a single motile bacterial cell can be selectively attached to an individual …

Biomass Burning And Anthropogenic Sources Of Co Over New England In The Summer 2004, Carsten Warneke, J. A. De Gouw, A. Stohl, O. R. Cooper, P. D. Goldan, W. C. Kuster, J. S. Holloway, E. J. Williams, B. M. Lerner, S. A. Mckeen, M. Trainer, F. C. Fehsenfeld, E. L. Atlas, Stephen G. Donnelly Ph.D., Verity Stroud, Amy Lueb, S. Kato

Chemistry Faculty Publications

During the summer of 2004 large wildfires were burning in Alaska and Canada, and part of the emissions were transported toward the northeast United States, where they were measured during the NEAQS-ITCT 2k4 (New England Air Quality Study-Intercontinental Transport and Chemical Transformation) study on board the NOAA WP-3 aircraft and the NOAA research vessel Ronald H. Brown. Using acetonitrile and chloroform as tracers the biomass burning and the anthropogenic fraction of the carbon monoxide (CO) enhancement are determined. As much as 30% of the measured enhancement is attributed to the forest fires in Alaska and Canada transported into the region, …

Generating New Specific Rna Interaction Interfaces Using C-Loops, Kirill A. Afonin, Neocles B. Leontis

Chemistry Faculty Publications

New RNA interaction interfaces are reported for designing RNA modules for directional supramolecular self-assembly. The new interfaces are generated from existing ones by inserting C-loops between the interaction motifs that mediate supramolecular assembly. C-Loops are new modular motifs recently identified in crystal structures that increase the helical twist of RNA helices in which they are inserted and thus reduce the distance between pairs of loop or loop-receptor motifs from 11 to 9 base-stacking layers while maintaining correct orientation for binding to cognate interaction interfaces. Binding specificities of C-loop-containing molecules for cognate molecules that also have inserted C-loops were found to …

Incorporating Electron-Transfer Functionality Into Synthetic Metalloproteins From The Bottom-Up, Jing Hong, Olesya A. Kharenko, Michael Y. Ogawa

Chemistry Faculty Publications

The alpha-helical coiled-coil motif serves as a robust scaffold for incorporating electron-transfer (ET) functionality into synthetic metalloproteins. These structures consist of a supercoiling of two or more R helices that are formed by the self-assembly of individual polypeptide chains whose sequences contain a repeating pattern of hydrophobic and hydrophilic residues. Early work from our group attached abiotic Ru-based redox sites to the most surface-exposed positions of two stranded coiled-coils and used electron-pulse radiolysis to study both intra- and intermolecular ET reactions in these systems. Later work used smaller metallopeptides to investigate the effects of conformational gating within electrostatic peptide-protein complexes. …

The Proteomics Of N-Terminal Methionine Cleavage, Frédéric Frottin, Aude Martinez, Philippe Peynot, Sanghamitra Mitra, Richard C. Holz, Carmela Giglione, Thierry Meinnel

Chemistry Faculty Research and Publications

Methionine aminopeptidase (MAP) is a ubiquitous, essential enzyme involved in protein N-terminal methionine excision. According to the generally accepted cleavage rules for MAP, this enzyme cleaves all proteins with small side chains on the residue in the second position (P1′), but many exceptions are known. The substrate specificity of Escherichia coli MAP1 was studied in vitro with a large (>120) coherent array of peptides mimicking the natural substrates and kinetically analyzed in detail. Peptides with Val or Thr at P1′ were much less efficiently cleaved than those with Ala, Cys, Gly, Pro, or Ser in this position. Certain residues …

Observation Of Fano Asymmetry In Raman Spectra Of Srtio3 And Cax Sr1-Xtio3 Perovskite Nanocubes, Sarbajit Banerjee, Dae In Kim, Richard D. Robinson, Irving P. Herman, Yuanbing Mao, Stanislaus S. Wong

Chemistry Faculty Publications and Presentations

Bulk SrTi O3 is cubic and not expected to exhibit any first-order Raman scattering. However, nanocubes of SrTi O3 with an edge length of 80±10 nm show strong first-order Raman scattering originating from the breaking of symmetry caused by frozen surface dipoles (local tetragonality) and the presence of nanoscopic polar domains (arising from incorporated impurities). Rapid polarization fluctuations within these nanoscopic ferroelectric regions interfere with a polar phonon, resulting in a Fano-like asymmetric line shape in these SrTi O3 nanocubes, as well as in Ca0.3 Sr0.7 Ti O3 nanocubes.

Statistical Thermodynamics And Kinetics Of Dna Multiplex Hybridization Reactions, Albert S. Benight, M. T. Horne, D. J. Fish

Chemistry Faculty Publications and Presentations

A general analytical description of the equilibrium and reaction kinetics of DNA multiplex hybridization has been developed. In this approach, multiplex hybridization is considered to be a competitive multichannel reaction process: a system wherein many species can react both specifically and nonspecifically with one another. General equations are presented that can consider equilibrium and kinetic models of multiplex hybridization systems comprised, in principle, of any number of targets and probes. Numerical solutions to these systems for both equilibrium and kinetic behaviors are provided. Practical examples demonstrate clear differences between results obtained from more common simplex methods, in which individual hybridization …

Synthesis Of Indolizines And Benzoindolizines By Annulation Of Donor-Acceptor Cyclopropanes With Electron-Deficient Pyridines And Quinolines, Nicholas A. Morra, Christian L. Morales, Barbora Bajtos, Xin Wang, Hyosook Jang, Jian Wang, Brian Pagenkopf

Chemistry Publications

The formal [3+2] dipolar cycloaddition (or annulation) of donor-acceptor cyclopropanoate esters with pyridines and 5-nitroquinoline is reported. Electron-deficient pyridine dipolarophiles (R=CN, CO₂Et, COMe) participate in the annulation whereas electron rich species do not. The product 2,3-dihydroindolizines undergo rapid autooxidation, and the X-ray structures for two of the aromatic products are reported.

Multiwalled Ice Helixes And Ice Nanotubes, Jaeil Bai, Jun Wang, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

We report six phases of high-density nano-ice predicted to form within carbon nanotubes (CNTs) at high pressure. High-density nano-ice self-assembled within smaller-diameter CNT (17,0) exhibits a double-walled helical structure where the outer wall consists of four double- stranded helixes, which resemble a DNA double helix, and the inner wall is a quadruple-stranded helix. Four other double-walled nano-ices, self-assembled respectively in two larger-diameter CNTs (20,0 and 22,0), display tubular structure. Within CNT (24,0), the confined water can freeze spontaneously into a triple-walled helical nanoice where the outer wall is an 18-stranded helix and the middle and inner walls are hextuple-stranded helixes.

Rovibrational Resonance Effects In Collision-Induced Electronic Energy Transfer: I2(E,V=0-2)+Cf4, J. M. Hutchison, Benjamin Robert Booth Carlisle , '05, Thomas Alex Stephenson

Chemistry & Biochemistry Faculty Works

Collisions of I-2 in the E(0(g)(+)) electronic state with CF4 molecules induce electronic energy transfer to the nearby D, beta, and D-' ion-pair states. Simulations of dispersed fluorescence spectra reveal collision-induced electronic energy transfer rate constants and final vibrational state distributions within each final electronic state. In comparison with earlier reports on I-2(upsilon(E)=0-2) collisions with He or Ar atoms, we find markedly different dynamics when I-2, excited to the same rovibronic states, collides with CF4. Final vibrational state distributions agree with the associated Franck-Condon factors with the initially prepared state to a greater degree than those found with He or …

U.S.-Japan-Hong Kong Planning Visit: Long Term Collaborative Research Studying Fe Effects On Ecosystem Structure In The Subarctic Pacific, Mark L. Wells

University of Maine Office of Research Administration: Grant Reports

This award supports a short-term U.S-Japan-Hong Kong Planning Visit in preparation for a long-term collaborative research project studying Fe effects on ecosystem structure in the Sub arctic Pacific. The collaborators are Professor Mark Wells at the University of Maine and Professor Shigenobu Takeda at the University of Tokyo in Japan and Professor Paul Harrison at the Hong Kong University of Science and Technology. Virtually the entire Sub arctic Pacific to the Aleutian Islands is a High Nitrate Low Chlorophyll (HNLC) region, characterized by persistently elevated concentrations of macronutrients throughout the year. Independent studies have demonstrated that a shortage of the …

Synthesis Of Multisubstituted Halo-Olefins Via Pd-Catalyzed Cross-Coupling Reactions : Applications In Nucleoside Chemistry, Daniela Andrei

FIU Electronic Theses and Dissertations

The enzyme S-adenosyl-L-homocysteine (AdoHey) hydrolase effects hydrolytic cleavage of AdoHcy to adenosine (Ado) and L-homocysteine (Hcy). The cellular levels of AdoHcy and Hcy are critical because AdoHcy is a potent feedback inhibitor of crucial transmethylation enzymes. Also, elevated plasma levels of Hcy in humans have been shown to be a risk factor in coronary artery disease.

On the basis of the previous finding that AdoHcy hydrolase is able to add the enzyme-sequestered water molecule across the 5',6'-double bond of (halo or dihalohomovinyl)-adenosines causing covalent binding inhibition, we designed and synthesized AdoHcy analogues with the 5',6'-olefin motif incorporated in place of …

Tetrakis(N-Ethyl-9-Oxo-4-Azonia-5-Aza-9h-Fluorene) Tetra-Μ3-Iodo-Hexa-Μ2-Iodo-Dodecaiodohexabismuthate, Meredith A. Tershany, Andrea M. Goforth, Mark D. Smith, Leroy Peterson Jr., Hans-Conrad Zur Loye

Faculty Publications

The new iodobismuthate compound (C₁₃H₁₁N₂O)₄[Bi₆I₂₂] has been synthesized solvothermally by reacting BiI₃, Zn(NO₃)₂·6H₂O and 4,5-diazafluoren-9-one in a water/ethanol solvent mixture. The asymmetric unit of the compound contains two independent [N-ethyl-4,5-dafo]⁺ cations and one-half of a centrosymmetric [Bi₆I₂₂]^4- anion. The average terminal Bi-I, Bi-₂-I and Bi-₃-I bond lengths in the anion are 2.8923 (2), 3.1403 (2) and 3.3022 (2) Å, respectively.

Α,Ω-Dithiol Oligo(Phenylene Vinylene)S For The Preparation Of High-Quality Π-Conjugated Self-Assembled Monolayers And Nanoparticle-Functionalized Electrodes, Dwight S. Seferos, Rebecca Lai, Kevin W. Plaxco, Guillermo C. Bazan

Rebecca Lai Publications

While thioacetate-terminated oligo(phenylene vinylene)s (OPVs) have been synthesized and employed in applications involving the formation of metal–molecule–metal junctions, the synthesis and application of potentially more versatile α,ω-dithiol OPVs have not previously been described. Here, a thiomethyl-precursor route to the synthesis of α,ω-dithiol OPVs is reported and their ability to form well-ordered self-assembled monolayers (SAMs) without the addition of exogenous deprotection reagents is described. α,ω-Dithiol OPV monolayers exhibit thicknesses consistent with molecular length and are nearly defect-free, as assayed by electrochemical measurements. To demonstrate the ease with which SAMs containing these bifunctional OPVs can, in contrast to thioacetate functionalized OPVs, be …

True Blue: Blue-Emitting Aluminum(Iii) Quinolinolate Complexes, Cesar Perez-Bolivar, Victor A. Montes, Pavel Anzenbacher Jr.

Chemistry Faculty Publications

Blue-emitting heteroleptic aluminum(III) bis(2-methyl-8-quinolinolate) phenolate complexes were synthesized. A tunable, blue-to-green emission is achieved by attaching electron-withdrawing modulators to the emisssive quinaldinate ligand. The electronic nature of modulator substituents attached to the position of the highest HOMO (highest occupied molecular orbital) density is used to modulate ligand HOMO levels to achieve effective emission tuning to obtain blue-emitting materials. Optical and electrochemical properties of the resulting complexes were investigated and compared to the results of density functional theory (DFT/B3LYP/6-31G*) studies. The resulting materials may find application as organic light-emitting device materials.

Oxidized Derivatives Of Ω-3 Fatty Acids: Identification Of Ipf 3Α-Vi In Human Urine, John A. Lawson, Seongjin Kim, William S. Powell, Garret Gerald A. Fitzgerald, Joshua Rokach

Chemistry and Chemical Engineering Faculty Publications

Isoprostanes (iPs) are prostaglandin-like molecules derived from autoxidation of polyunsaturated fatty acids (PUFAs). Urinary iP levels have been used as indices of in vivo lipid peroxidation. Thus far, it has only been possible to measure iPs derived from arachidonic acid in urine, because levels of iPs/neuroprostanes (nPs) derived from ω3-PUFAs have been found to be below detection limits of available assays. Because of the interest in ω3-PUFA dietary supplementation, we developed specific methods to measure nPF4α-VI and iPF3α-VI [derived from 4,7,10,13,16,19-docosahexaenoic acid (DHA) and 5,8,11,14,17-eicosapentaenoic acid (EPA)] using a combination of chemical synthesis, gas chromatography/mass spectrometry (GC/MS), andliquid chromatography tandem …

Styrenic Polymer Nanocomposites Based On An Oligomerically-Modified Clay With High Inorganic Content, Jinguo Zhang, David D. Jiang, Dongyan Wang, Charles A. Wilkie

Chemistry Faculty Research and Publications

Clay was modified with an oligomeric surfactant containing styrene and lauryl acrylate units along with a small amount of vinylbenzyl chloride to permit the formation of an ammonium salt so that this can be attached to a clay. The oligomerically-modified clay contains 50% inorganic clay, and styrenic polymer nanocomposites, including those of polystyrene (PS), high-impact polystyrene (HIPS), styrene–acrylonitrile copolymer (SAN) and acrylonitrile–butadiene–styrene (ABS), were prepared by melt blending. The morphologies of the nanocomposites were evaluated by X-ray diffraction and transmission electron microscopy. Mixed intercalated/delaminated nanocomposites were formed for SAN and ABS while largely immiscible nanocomposites were formed for PS and …

Bis(1,2-Dihydroxy­Benzene) Hexa­Methyl­Ene­Tetra­Mine, Philias Daka, Kraig A. Wheeler

Faculty Research and Creative Activity

The title binary complex, 2C6H6O2·C6H12N4, is constructed from hexa­methyl­ene­tetra­mine, positioned about a twofold symmetry operator, and 1,2-dihydroxy­benzene. Each of the four tertiary amine N atoms participates in O—H⋯N contacts that produce mol­ecular strands that propagate along the c axis.

(Acetonitrile-Κn){2-[Bis­(2-Pyridylethyl)­Amino]Ethanol-Κ4n,N′,N′′,O}Zinc(Ii) Bis­(Perchlorate) Monohydrate, Hong-Chang Liang, Marcel M. Hetu, Kraig A. Wheeler, Lev N. Zakharov, Arnold L. Rheingold

Faculty Research and Creative Activity

In the title compound, [Zn(C2H3N)(C16H21N3O)](ClO4)2·H2O, the ZnII ion is coordinated by two pyridyl N atoms, one amine N atom, and an ethanol O atom from the N,N′,N′′,O-tetra­dentate 2-[bis­(2-pyridylethyl)amino]­ethanol donor ligand. The fifth coordination site is filled by an acetonitrile N atom, and there is one solvent water mol­ecule in the asymmetric unit. The 2+ charge of the cationic portion of the complex is balanced by two perchlorate counter-anions.

Central Dysregulation Of The Hypothalamic-Pituitary-Adrenal Axis In Neuron-Specific Proopiomelanocortin-Deficient Mice, James L. Smart, Virgine Tolle, Veronica Otero-Corchon, Malcolm J. Low

Faculty Publications - Department of Biological & Molecular Science

No abstract provided.

Nickel(Ii) And Cobalt(Ii) Nitrate And Chloride Networks With 2-Aminopyrimidine, Robert D. Pike, Mi Jung Lim, Ellen A. L. Wilcox, Tristan A. Tronic

Arts & Sciences Articles

The coordination chemistry of 2-aminopyrimidine (PymNH2) with nickel(II) and cobalt(II) nitrate and chloride is reported, including seven new X-ray crystal structures. Two [Ni(NO3)2(PymNH2)2(OH2)] isomers were found (A: C2/c, a=13.3006(5), b=7.9727(3), c=28.5453(11), β=101.758(2), V=2963.48(19), Z=8 and B·1/2 acetone: P21/c, a=7.66060(10), b=10.6792(2), c=20.6790(3), β=100.2970(10), 1664.48(5), Z=4). In both cases one nitrate is monodentate and the other is chelating and the PymNH2 ligands coordinate through ring nitrogen atoms. Hydrogen bonding results in double sheet structure for isomer A, and a three dimensional channeled network for isomer B. [Co(NO3)2(PymNH2)2(OH2)] ( …

Fourier Series, Examples And The Fourier Integral, Carl W. David

Chemistry Education Materials

The derivation of the Fourier Integral from the Fourier series in complex form is carried out and illustrations of the Fourier Integral are done.

Periodic Boundary Condition Induced Breakdown Of The Equipartition Principle And Other Kinetic Effects Of Finite Sample Size In Classical Hard-Sphere Molecular Dynamics Simulation, Randall B. Shirts, Scott R. Burt, Aaron M. Johnson

Faculty Publications

We examine consequences of the non-Boltzmann nature of probability distributions for one-particle kinetic energy, momentum, and velocity for finite systems of classical hard spheres with constant total energy and nonidentical masses. By comparing two cases, reflecting walls (NVE or microcanonical ensemble) and periodic boundaries (NVEPG or molecular dynamics ensemble), we describe three consequences of the center-of-mass constraint in periodic boundary conditions: the equipartition theorem no longer holds for unequal masses, the ratio of the average relative velocity to the average velocity is increased by a factor of [N/(N–1)]^1/2, and the ratio of average collision energy to average kinetic energy is …

Nano-Chemistry, Erwin P. Enriquez

Chemistry Faculty Publications

Nanotechnology is a highly interdisciplinary field, with contributions from all fields: physics, chemistry, biology, materials science, engineering, and others. The explosive number of publications in this field makes it nearly impossible to give an extensive review even in chemistry alone. Nonetheless, one may track its emergence and rapid advancement from the point of view of a chemist's. This paper aims to provide a conceptual overview of chemistry for nanotechnology, a brief classification of different approaches and applications, together with some sample cases.

Acrosome Reaction Is Subfamily Specific In Sea Star Fertilization, Mia Nakachi, Hideaki Moriyama, Motonori Hoshi, Midori Matsumoto

Hideaki Moriyama Publications

In the fertilization process of sea stars, sperm is activated to go through the acrosome reaction before cell fusion. We focused on induction of the acrosome reaction as a key process in fertilization. Six species of sea stars were used in this study: Asterias amurensis, Asterias rubens, Asterias forbesi, Aphelasterias japonica, Distolasterias nipon, and Asterina pectinifera. Acrosome reaction assays indicate that the acrosome reaction can be induced across species within Asteriinae subfamily. However, cross-fertilization assays indicate that sea stars have species specificity in fertilization. Therefore, steps after the acrosome reaction are responsible for the …

Homogeneous Nucleation At High Supersaturation And Heterogeneous Nucleation On Microscopic Wettable Particles: A Hybrid Thermodynamic/Density-Functional Theory, T. V. Bykov, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

Homogeneous nucleation at high supersaturation of vapor and heterogeneous nucleation on microscopic wettable particles are studied on the basis of Lennard-Jones model system. A hybrid classical thermodynamics and density-functional theory (DFT) approach is undertaken to treat the nucleation problems. Local-density approximation and weighted-density approximation are employed within the framework of DFT. Special attention is given to the disjoining pressure of small liquid droplets, which is dependent on the thickness of wetting film and radius of the wettable particle. Different contributions to the disjoining pressure are examined using both analytical estimations and numerical DFT calculation. It is shown that van der …

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

Chemistry & Biochemistry Newsletter: 2002-2015

Inside:

Page 2-3 Grad students attend International Summer School in Green Chemistry

Page 3 Alumni News

Page 4 Alum receives brigadier general stars

Page 5 New Grad Students

Page 6 Tanaka endows undergraduate scholarship; Midwest Seeds becomes internship partner

Page 7 The 2006/2007 Burris Lecturer leader in drug discovery

Page 8 New Faculty; Perfecting the formula for the future of SDSU chemistry

Structures And Relative Stability Of Neutral Gold Clusters: AuN (N=15–19), Satya S. Bulusu, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

We performed a global-minimum search for low-lying neutral clusters (Au_n) in the size range of n=15–19 by means of basin-hopping method coupled with density functional theory calculation. Leading candidates for the lowest-energy clusters are identified, including four for Au₁₅, two for Au₁₆, three for Au₁₇, five for Au₁₈, and one for Au₁₉. For Au₁₅ and Au₁₆ we find that the shell-like flat-cage structures dominate the population of low-lying clusters, while for Au₁₇ and Au₁₈ spherical-like hollow-cage structures dominate the low-lying population. The transition …