Physical Sciences and Mathematics Commons^™

Correlating Molecular Phylogeny With Venom Apparatus Occurrence In Panamic Auger Snails (Terebridae), Mandë Holford, Nicolas Puillandre, Maria Vittoria Modica, Maren Watkins, Rachel Collin, Eldredge Bermingham, Baldomero M. Olivera

Publications and Research

Central to the discovery of neuroactive compounds produced by predatory marine snails of the superfamily Conoidea (cone snails, terebrids, and turrids) is identifying those species with a venom apparatus. Previous analyses of western Pacific terebrid specimens has shown that some Terebridae groups have secondarily lost their venom apparatus. In order to efficiently characterize terebrid toxins, it is essential to devise a key for identifying which species have a venom apparatus. The findings presented here integrate molecular phylogeny and the evolution of character traits to infer the presence or absence of the venom apparatus in the Terebridae. Using a combined dataset …

Smooth Potential Energy Surface For Cavitation, Dispersion, And Repulsion Free Energies In Polarizable Continuum Model, Yali Wang, Hui Li

Hui Li Publications

The fixed points with variable areas [FIXPVA] tessellation scheme is used to obtain smooth potential energy surfaces for the cavitation G_cav, dispersion G_dis, and repulsion G_rep free energies in the polarizable continuum model (PCM). It is shown that FIXPVA can reproduce the standard GEPOL results to within 1 kcal/mol.

Investigation Of The Physical And Electronic Properties Of Indium Doped Zinc Oxide Nanofibers Synthesized By Electrospinning, A. F. Lotus, Y. C. Kang, R. D. Ramsier, George G. Chase

Chemical, Biomolecular, and Corrosion Engineering Faculty Research

Nanostructured metal oxides and particularly nanofiber based materials can provide significant advances for the miniaturization of electronic, optoelectronic, photonic, sensor, and energy conversion devices with enhanced performance based on their unique material properties. In this study, indium doped zinc oxide (IZO) nanofibers were synthesized by electrospinning. These nanofibers have diameters in the range 50-100 nm. The effects of indium addition on the structural, optical, and electrical properties of the zinc oxide nanofiber matrices were investigated. The IZO nanofibers undergo significant changes in their optical and electrical properties compared to undoped zinc oxide nanofibers.

Synthesis And Evaluation Of Some Steroidal Oximes As Cytotoxic Agents: Structure/Activity Studies (Ii), Jianguo Cui, Lei Fan, Yanmin Huang, Yi Xin, Aimin Zhou

Chemistry Faculty Publications

Hydroximinosteroids isolated from marine sponges display a variety of biological functions including cytotoxicity and anti-virus. In this study, we synthesized a series of hydroximinosteroid derivatives with a different functional group on the ring A or B and various side chains at position 17, and analyzed the cytotoxicity of these compounds against sk-Hep-1, H-292, PC-3 and Hey-1B cancer cells. Our results revealed that although a cholesterol-type side chain at position 17 is required for the biological activity of the compounds as we previously confirmed, elimination of the 4,5-double bond augmented the cytotoxic activity for the steroidal oximes. In addition, the presence …

How Does The Relocation Of Internal Water Affect Resonance Raman Spectra Of Rhodopsin? An Insight From Casscf/Amber Calculations, Tadeusz Andruniow, Massimo Olivucci

Chemistry Faculty Publications

The effect of relocation of the W2 crystallographic water in bovine rhodopsin has been investigated by comparing and analyzing simulated resonance Raman spectra of I HZX-and 1U19-based quantum mechanics/molecular mechanics (CASSCF/MM) models. The main target is to explore the sensitivity of the simulated resonance Raman spectra to protein cavity change. In particular, we focus on a quantitative investigation of the changes in the vibrational activity of rhodopsin induced by modifications in the protein cavity structure and in the water position. Comparison of the simulated FIR spectra of the Rh-1U19 and Rh-1HZX models with the measured spectrum of rhodopsin reveals that …

Improving Replica Exchange Using Driven Scaling, Steven W. Rick

Chemistry Faculty Publications

Replica exchange is a powerful simulation method in which simulations are run at a series of temperatures, with the highest temperature chosen so phase space can be sampled efficiently. In order for swaps to be accepted, the energy distributions of adjacent replicas must have some overlap. This can create the need for many replicas for large systems. In this paper, we present a new method in which the potential energy is scaled by a parameter, which has an explicit time dependence. Scaling the potential energy broadens the distribution of energy and reduces the number of replicas necessary to span a …

Polymer Nanocomposites Using Zinc Aluminum And Magnesium Aluminum Oleate Layered Double Hydroxides: Effects Of The Polymeric Compatibilizer And Of Composition On The Thermal And Fire Properties Of Pp/Ldh Nanocomposites, Charles Manzi-Nshuti, Ponusa Songtipya, Evangelos Manias, Maria Del Mar Jimenez-Gasco, Jeanne Hossenlopp, Charles A. Wilkie

Chemistry Faculty Research and Publications

A series of five oleate-containing layered double hydroxides with varied ratios of zinc to magnesium, i.e., with the general formula Zn_2−yMg_yAl(OH)₆ [CH₃(CH₂)₇CHCH(CH₂)₇COO]·nH₂O, were synthesized and used to prepare nanocomposites of polypropylene (PP). The nanomaterials were characterized by elemental analysis, attenuated total reflection-infrared spectroscopy (ATR-IR), X-ray diffraction (XRD) and thermogravimetric analysis (TGA), while the composites were characterized by XRD, TGA, transmission electron microscopy (TEM) and cone calorimetry. The zinc-containing LDH showed better dispersion in the polymer at the micrometer level …

The Effects Of Intralayer Metal Composition Of Layered Double Hydroxides On Glass Transition, Dispersion, Thermal And Fire Properties Of Their Pmma Nanocomposites, Charles Manzi-Nshuti, Dan Chen, Shengpei Su, Charles A. Wilkie

Chemistry Faculty Research and Publications

A series of aluminum-containing layered double hydroxides (LDHs), containing Mg, Ca, Co, Ni, Cu and Zn as the divalent metals, have been prepared by the co-precipitation method and used to prepare nanocomposites of PMMA by in situ bulk polymerization. The additives were characterized by Fourier transform infrared spectroscopy, X-ray diffraction spectroscopy (XRD) and thermogravimetric analysis while the polymer composites were characterized by XRD, transmission electron microscopy, differential scanning calorimetry and cone calorimetry. Polymerization of methyl methacrylate in the presence of these undecenoate LDHs results in composites with enhanced thermal stability. The glass transition temperatures of the composites and the pristine …

Fragmentation Properties Of Three-Membered Ring Heterocyclic Molecules By Partial Ion Yield Spectroscopy: C2h4o And C2h4s, Wayne C. Stolte, I. Dumitriu, S-W Yu, Gunnar Ohrwall, Maria Novella Piancastelli, Dennis W. Lindle

Chemistry and Biochemistry Faculty Research

We investigated the photofragmentation properties of two three-membered ring heterocyclic molecules, C₂H₄O and C₂H₄S, by total and partial ion yield spectroscopy. Positive and negative ions have been collected as a function of photon energy around the C 1s and O 1s ionization thresholds in C₂H₄O, and around the S 2p and C 1s thresholds in C₂H₄S. We underline similarities and differences between these two analogous systems. We present a new assignment of the spectral features around the C K-edge and the sulfur L_{2 …}

Absolute Configuration And Biosynthesis Of Pahayokolide A From Lyngbya Sp. Strain 15-2 Of The Florida Everglades, Li Liu

FIU Electronic Theses and Dissertations

Pahayokolides A-D are cytotoxic cyclic polypeptides produced by the freshwater cyanobacterium Lyngbya sp. strain 15-2 that possess an unusual β-amino acid, 3-amino-2,5,7,8-tetrahydroxy-10-methylundecanoic acid (Athmu). The absolute configuration of pahayokolides A-D was determined using advanced Marfey’s method. It was also confirmed that a pendant N-acetyl-N-methyl leucine moiety in pahayokolide A was absent in pahayokolides B and pahayokolides C-D were conformers of pahayokolide A. Feeding experiments indicated that the biosynthesis of the Athmu sidechain arises from leucine or α-ketoisovalerate, however could not be further extended by three rounds of condensation with malonate units. Putative four peptide and one unique polyketide synthetases in …

Analysis Of Globule Types In Malignant Melanoma, Jin Xu, Kapil Kumar Gupta, William V. Stoecker, Yamini Krishnamurthy, Harold S. Rabinovitz, Austin Bangert, David A. Calcara, Margaret C. Oliviero, Joseph M. Malters, Rhett J. Drugge, R. Joe Stanley, Randy Hays Moss, Mehmed Emre Celebi

Chemistry Faculty Research & Creative Works

Objective: To identify and analyze subtypes of globules based on size, shape, network connectedness, pigmentation, and distribution to determine which globule types and globule distributions are most frequently associated with a diagnosis of malignant melanoma. Design: Retrospective case series of dermoscopy images with globules. Setting: Private dermatology practices. Participants: Patients in dermatology practices. Intervention: Observation only. Main Outcome Measure: Association of globule types with malignant melanoma. Results: The presence of large globules (odds ratio [OR], 5.25) and globules varying in size (4.72) or shape (5.37) had the highest ORs for malignant melanoma among all globule types and combinations studied. Classical …

Scope And Mechanistic Investigations On The Solvent-Controlled Regio- And Stereoselective Formation Of Enol Esters From The Ruthenium-Catalyzed Coupling Reaction Of Terminal Alkynes And Carboxylic Acids, Chae S. Yi, Ruili Gao

Chemistry Faculty Research and Publications

The ruthenium-hydride complex (PCy₃)₂(CO)RuHCl was found to be a highly effective catalyst for the alkyne-to-carboxylic acid coupling reaction to give synthetically useful enol ester products. A strong solvent effect was observed for the ruthenium catalyst in modulating the activity and selectivity; the coupling reaction in CH₂Cl₂ led to the regioselective formation of gem-enol ester products, while the stereoselective formation of (Z)-enol esters was obtained in THF. The coupling reaction was found to be strongly inhibited by PCy₃. The coupling reaction of both PhCO₂H/PhC≡CD and PhCO_{2 …}

A General Asymmetric Aldol Reaction Of Silyl Ketene Acetals Derived From Simple Esters To Aryl Alpha-Ketoesters, Brian Pagenkopf, Julie Le Engers

Chemistry Publications

No abstract provided.

Wavepacket Approach To The Cumulative Reaction Probability Within The Flux Operator Formalism, Sophya Garashchuk, Tijo Vazhappilly

Faculty Publications

Expressions for the singular flux operator eigenfunctions and eigenvalues are given in terms of the Dirac δ-function representable as a localized Gaussian wavepacket. This functional form enables computation of the cumulative reaction probability N(E) from the wavepacket time-correlation functions. The Gaussian based form of the flux eigenfunctions, which is not tied to a finite basis of a quantum-mechanical calculation, is particularly useful for approximate calculation of N(E) with the trajectory based wavepacket propagation techniques. Numerical illustration is given for the Eckart barrier using the conventional quantum-mechanical propagation and the quantum trajectory dynamics with the approximate quantum potential. N(E) converges with …

Chemistry In Second Life, Andrew Lang, Jean-Claude Bradley

College of Science and Engineering Faculty Research and Scholarship

This review will focus on the current level on chemistry research, education, and visualization possible within the multi-user virtual environment of Second Life. We discuss how Second Life has been used as a platform for the interactive and collaborative visualization of data from molecules and proteins to spectra and experimental data. We then review how these visualizations can be scripted for immersive educational activities and real-life collaborative research. We also discuss the benefits of the social networking affordances of Second Life for both chemists and chemistry students.

Magnetoelastic Coupling Through The Antiferromagnet-To-Ferromagnet Transition Of Quasi-Two-Dimensional [Cu(Hf2)(Pyz)(2)]Bf4 Using Infrared Spectroscopy, J L. Musfeldt, L I. Vergara, T V. Brinzari, C Lee, L C. Tung, J Kang, Y J. Wang, J A. Schlueter, Jamie L. Manson, M H. Whangbo

Chemistry and Biochemistry Faculty Publications

We investigated magnetoelastic coupling through the field-driven transition to the fully polarized magnetic state in quasi-two-dimensional [Cu(HF2)(pyz)(2)]BF4 by magnetoinfrared spectroscopy. This transition modifies out-of-plane ring distortion and bending vibrational modes of the pyrazine ligand. The extent of these distortions increases with the field, systematically tracking the low-temperature magnetization. These distortions weaken the antiferromagnetic spin exchange, a finding that provides important insight into magnetic transitions in other copper halides.

Depositional Ice Nucleation On Solid Ammonium Sulfate And Glutaric Acid Particles, K. J. Baustian, M. E. Wise, M. A. Tolbert

CUP Faculty Research

Heterogeneous ice nucleation on solid ammonium sulfate and solid amorphous glutaric acid particles was studied using optical microscopy and Raman spectroscopy. Optical microscopy was used to detect selective nucleation events as water vapor was slowly introduced into an environmental sample cell. Particles that nucleated ice were dried via sublimation and examined in detail using Raman spectroscopy. Depositional ice nucleation occurred preferentially on just a few ammonium sulfate and glutaric acid particles in each sample. For freezing temperatures between 214 K and 235K average ice saturation ratios of S=1.10±0.07 for solid ammonium sulfate and S=1.39±0.16 for solid amorphous glutaric …

Reexamine Structures And Relative Stability Of Medium-Sized Silicon Clusters: Low-Lying Endohedral Fullerene-Like Clusters Si30-Si38, Soohaeng Yoo, Nan Shao, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

We report improved results of lowest-lying silicon clusters Si₃₁–Si₃₈. A large population of low-energy clusters are collected from previous searches by several research groups and the binding energies of these clusters are computed using density-functional theory (DFT) methods. Best candidates (isomers with high binding energies) are identified from the screening calculations. Additional constrained search is then performed for the best candidates using the basin-hopping method combined with DFT geometry optimization. The obtained low-lying clusters are classified according to binding energies computed using either the Perdew–Burke–Ernzerhof (PBE) functional or the Becke exchange and Lee–Yang–Parr correlation (BLYP) functional. …

Robust Quantization Of A Molecular Motor Motion In A Stochastic Environment, Vladimir Y. Chernyak, Nikolai A. Sinitsyn

Chemistry Faculty Research Publications

We explore quantization of the response of a molecular motor to periodic modulation of control parameters. We formulate the pumping-quantization theorem (PQT) that identifies the conditions for robust integer quantized behavior of a periodically driven molecular machine. Implication of PQT on experiments with catenane molecules are discussed. ACKNOWLEDGMENTS We are grateful to M. Chertkov, J. R. Klein, and J. Horowitz for useful discussions. This material is based upon work supported by NSF under Grant Nos. CHE-0808910 and ECCS-0925618.

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

Chemistry & Biochemistry Newsletter: 2002-2015

Inside:

Page 2 Research Finds New Uses for Light or Applied Photonics

Page 3 SDSU Grad Student Awarded EPA Sustainability Grant; Alumni Update

Page 4 New CLS Faculty

Page 5 Chemistry: It’s Elemental; Alumni Update

Page 6-7 New Graduate Students

Page 7 AHSC Construction Update

Page 8 Rice Named to National Science Foundation Committee

Unlv Magazine, Matthew K. Jacobsen, Holly Ivy De Vore, Lisa Arth, Cate Weeks, Greg Lacour, Tony Allen, Afsha Bawany, Barbara Cloud, Gian Galassi, Phil Hagen, Karyn S. Hollingsworth, Michelle Mouton, Erin O'Donnell

UNLV Magazine

No abstract provided.

Structure Of The Photochemical Reaction Path Populated Via Promotion Of Cf2i2 Into Its First Excited State, Patrick Z. El-Khoury, Alexander N. Tarnovsky, Igor Schapiro, Mikhail N. Ryazantsev, Massimo Olivucci

Chemistry Faculty Publications

The photochemical reaction path following the promotion of CF2I2 into its lowest-lying excited electronic singlet state has been modeled using ab initio multiconfigurational quantum chemical calculations. It is found that a conical intersection drives the electronically excited CF2I2* species either to the CF2I + I radical pair or back to the starting CF2I2 structure. The structures of the computed relaxation pathways explain the photoproduct selectivity previously observed in the gas phase. Furthermore, the results provide the basis for explaining the condensed-phase photochemistry of CF2I2.

Proteomic And Phospho-Proteomic Profile Of Human Platelets In Basal, Resting State: Insights Into Integrin Signaling, Amir H. Qureshi, Vineet Chaoji, Dony Maiguel, Mohd Hafeez Faridi, Constantinos J. Barth, Saeed M. Salem, Mudita Singhal, Darren Stoub, Bryan Krastins, Mitsunori Ogihara, Mohammed J. Zaki, Vineet Gupta

Faculty Work Comprehensive List

During atherogenesis and vascular inflammation quiescent platelets are activated to increase the surface expression and ligand affinity of the integrin αIIbβ3 via inside-out signaling. Diverse signals such as thrombin, ADP and epinephrine transduce signals through their respective GPCRs to activate protein kinases that ultimately lead to the phosphorylation of the cytoplasmic tail of the integrin αIIbβ3 and augment its function. The signaling pathways that transmit signals from the GPCR to the cytosolic domain of the integrin are not well defined. In an effort to better understand these pathways, we employed a combination of proteomic profiling and computational analyses of isolated …

An Expeditious Synthesis Of 3-Amino B-Lactams Derived From Polyaromatic Compounds, Gildardo Rivera, Debasish Bandyopadhyay, Sonam Jaggi, R. Christopher Gonzales, Bimal K. Banik

Chemistry Faculty Publications and Presentations

A simple an effective method for the synthesis of a few trans 3-amino B-lactams derived from polyaromatic compounds has been accomplished via the deprotection of phthalimido groups with ethylene diamine.

Lipid-Protein Interactions Probed By Electron Crystallography, Steve L. Reichow, Tamir Gonen

Chemistry Faculty Publications and Presentations

Electron crystallography is arguably the only electron cryomicroscopy (cryoEM) technique able to deliver an atomic-resolution structure of membrane proteins embedded in the lipid-bilayer. In the electron crystallographic structures of the light driven ion pump, bacteriorhodopsin, and the water channel, aquaporin-0, sufficiently high resolution was obtained and both lipid and protein were visualized, modeled and described in detail. An extensive network of lipid-protein interactions mimicking native membranes is established and maintained in two-dimensional (2D) crystalline vesicles used for structural analysis by electron crystallography. Lipids are tightly integrated into the protein's architecture where they can affect the function, structure, quaternary assembly and …

Hierarchical Subject Inter-Relations In Physical Chemistry, Carl W. David

Chemistry Education Materials

Students mystified by the progression of topics in Physical Chemistry may gain insight into their path through the material if acquainted with the diagrams presented and discussed herein.

The Α,Α-Difluorinated Phosphonate L-Pser-Analogue: An Accessible Chemical Tool For Studying Kinase-Dependent Signal Transduction In Vitro, And In Living Cells, Kaushik Panigrahi, Marijean Eggen, Jun-Ho Maeng, Quanrong Shen, David B. Berkowitz

David Berkowitz Publications

This overview focuses on the (α,α-difluoromethylene)phosphonate mimic of phosphoserine (pCF₂Ser) and its application to the study of kinase-mediated signal transduction – pathways of great interest to drug development. The most versatile modes of access to these chemical biological tools are discussed, organized by method of PCF₂-C bond. The pCF₂-Ser mimic may be site-specifically incorporated into peptides (SPPS) and proteins (expressed protein ligation). This isopolar, dianionic pSer mimic results in a “constitutive phosphorylation” phenotype, and is seen to support native protein-protein interactions that depend upon serine phosphorylation. Signal transduction pathways studied with this chemical biological …

Identification And Structural Analysis Of A Novel Carboxysome Shell Protein With Implications For Metabolite Transport, Michael G. Klein, Peter Zwart, Sarah C. Bag By, Fei Cai, Sallie W. Chisolm, Sabine Heinhorst, Gordon C. Cannon, Cheryl A. Kerfeld

Faculty Publications

Bacterial microcompartments (BMCs) are polyhedral bodies, composed entirely of proteins, that function as organelles in bacteria; they promote subcellular processes by encapsulating and co-localizing targeted enzymes with their substrates. The best-characterized BMC is the carboxysome, a central part of the carbon-concentrating mechanism that greatly enhances carbon fixation in cyanobacteria and some chemoautotrophs. Here we report the first structural insights into the carboxysome of Prochlorococcus, the numerically dominant cyanobacterium in the world's oligotrophic oceans. Bioinformatic methods, substantiated by analysis of gene expression data, were used to identify a new carboxysome shell component, CsoS1D, in the genome of Prochlorococcus strain MED4; …

Succination Of Thiol Groups In Adipose Tissue Proteins In Diabetes: Succination Inhibits Polymerization And Secretion Of Adiponectin, Norma Frizzell, Mathur Rajesh, Matthew J. Jepson, Ryoji Nagai, James A. Carson, Suzanne R. Thorpe, John W. Baynes

Faculty Publications

S-(2-Succinyl)cysteine (2SC) is formed by reaction of the Krebs cycle intermediate fumarate with cysteine residues in protein, a process termed succination of protein. Both fumarate and succination of proteins are increased in adipocytes cultured in high glucose medium (Nagai, R., Brock, J. W., Blatnik, M., Baatz, J. E., Bethard, J., Walla, M. D., Thorpe, S. R., Baynes, J. W., and Frizzell, N. (2007) J. Biol. Chem. 282, 34219-34228). We show here that succination of protein is also increased in epididymal, mesenteric, and subcutaneous adipose tissue of diabetic (db/db) mice and that adiponectin is a major target for succination in both …

A Spectral Time-Domain Method For Computational Electrodynamics, James V. Lambers

Faculty Publications

We present a new approach to the numerical solution of Maxwell’s equations in the case of spatially‐varying electric permittivity and/or magnetic permeability, based on Krylov subspace spectral (KSS) methods. KSS methods for scalar equations compute each Fourier coefficient of the solution using techniques developed by Gene Golub and Gérard Meurant for approximating elements of functions of matrices by Gaussian quadrature in the spectral, rather than physical, domain. We show how they can be generalized to coupled systems of equations, such as Maxwell’s equations, by choosing appropriate basis functions that, while induced by this coupling, still allow efficient and robust computation …