Chemistry Commons^™

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 …

Microfabrication And Evaluation Of Planar Thin-Film Microfluidic Devices, Bridget Ann Peeni

Theses and Dissertations

Over the past 15 years, research in the field of microfluidics has rapidly gained popularity. By seeking to miniaturize and automate separation-based analysis, microfluidic research seeks to improve current methods through decreased cost, analysis time, and sources of contamination. My work has focused on developing a novel fabrication method, based on standard microfabrication techniques, to create thin-film microfluidic devices. This microfabrication format makes it possible to generate devices that provide high efficiencies, enable mass fabrication, and provide a platform capable of integrating the microfluidic and electronic components necessary for a micro-total analysis system (μ-TAS). Device fabrication combines the processes of …

The Free Energy Of Dissociation Of Oligomeric Structure In Phycocyanin Is Not Linear With Denaturant, Katie L. Thoren, Katelyn B. Connell, Taylor E. Robinson, David D. Shellhamer, Margaret S. Tammaro, Yvonne Gindt

Department of Chemistry and Biochemistry Faculty Scholarship and Creative Works

Using SEC HPLC and fluorescence anisotropy, absorption spectra were assigned to the specific oligomeric structures found with phycocyanin. The absorption spectra were used to quantify the population of each oligomeric form of the protein as a function of both urea concentration and temperature. Phycocyanin hexamers dissociate to trimers with equilibrium constants of 10 -6 to 10-5. Phycocyanin trimers dissociate to monomers with equilibrium constants of 10-15 to 10-12. Both dissociation constants increase linearly with increasing urea concentration, and ΔG° values calculated from the equilibrium constants fit best with an exponential function. Our findings appear in contrast with the commonly used …

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

A New Colorimetric Assay For Methionyl Aminopeptidases: Examination Of The Binding Of A New Class Of Pseudopeptide Analog Inhibitors, Sanghamitra Mitra, Anna M. Dygas-Holz, Jiri Jiracek, Miroslava Zertova, Lenka Zakova, Richard C. Holz

Chemistry Faculty Research and Publications

A direct and convenient spectrophotometric assay has been developed for methionine aminopeptidases (MetAPs). The method employs the hydrolysis of a substrate that is a methionyl analogue of p-nitroaniline (l-Met-p-NA), which releases the chromogenic product p-nitroaniline. This chromogenic product can be monitored continuously using a UV–Vis spectrophotometer set at 405 nm. The assay was tested with the type I MetAP from Escherichia coli (EcMetAP-I) and the type II MetAP from Pyrococcus furiosus (PfMetAP-II). Using l-Met-p-NA, the kinetic constants k_cat and K_m were determined for EcMetAP-I and PfMetAP-II …

Additional Evidence For The Migration Of Clay Upon Heating Of Clay–Polypropylene Nanocomposites From X-Ray Photoelectron Spectroscopy (Xps), Jianwei Hao, Menachem Lewin, Charles A. Wilkie, Jiangqi Wang

Chemistry Faculty Research and Publications

The explanation for reduction in the peak heat release rate of polymer–clay nanocomposites which is normally accepted is that clay accumulates at the surface, forming a thermal shield which is also a barrier to mass transport. The process by which this clay arrives at the surface has never been described in print but the common assumption is that pyrolysis is required for clay accumulation to occur. In this work, X-ray photoelectron spectroscopy, a tool much more sensitive in surface analysis than conventional techniques, is used to probe the surface of polypropylene–clay nanocomposites that have been annealed at relatively low temperatures, …

2004 Jeffress Research Grant Awards

Virginia Journal of Science

List of winners of the 2004 Jeffress Research Grant Awards.

Minutes: Council Meeting

Virginia Journal of Science

Minutes of the VAS Council meeting Friday May 26, 2006, 8 - 9:40 AM, at Skelton Conference Center Inn, Virginia Tech, Blacksburg VA. Minutes were edited for publication.

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 …

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 …

Afci Quarterly Input – Unlv July 1 Through September 30, 2006, Harry Reid Center For Environmental Studies. Nuclear Science And Technology Division

Transmutation Research Program Reports (TRP)

Quarterly report highlighting research projects, activities and objectives of the Transmutation Research Program at the Nuclear Science & Technology Division, Harry Reid Research Center.

The University of Nevada, Las Vegas supports the AFCI through research and development of technologies for economic and environmentally sound refinement of spent nuclear fuel. The UNLV program has four components: infrastructure, international collaboration, student-based research, and management and program support.

Sequence-Specific Recognition And Cooperative Dimerization Of N-Terminal Aromatic Peptides In Aqueous Solution By A Synthetic Host, Lisa M. Heitmann, Alexander B. Taylor, P John Hart, Adam R. Urbach

Chemistry Faculty Research

This article describes the selective recognition and noncovalent dimerization of N-terminal aromatic peptides in aqueous solution by the synthetic host compound, cucurbit[8]uril (Q8). Q8 is known to bind two aromatic guests simultaneously and, in the presence of methyl viologen, to recognize N-terminal tryptophan over internal and C-terminal sequence isomers. Here, the binding of Q8 to aromatic peptides in the absence of methyl viologen was studied by isothermal titration calorimetry (ITC), ¹H NMR spectroscopy, and X-ray crystallography. The peptides studied were of sequence X-Gly-Gly, Gly-X-Gly, and Gly-Gly-X (X = Trp, Phe, Tyr, and His). Q8 selectively binds and dimerizes Trp-Gly-Gly …

Studies On Cyclooxygenase-1, Its Structure And Splice Variants, And Modulation Of Cyclooxygenase-2 By Inducible Nitric Oxide Synthase And Novel Phytochemicals., Yibing Xu

Theses and Dissertations

Cyclooxygenases (COXs) are of important therapeutic value as they are the target site of aspirin-like drugs. Here I report nine new COX-1 splice variants in chapter 1, which I characterized with regard to heme-binding and other properties. Inducible NO synthase (iNOS) and cyclooxygenase-2 (COX-2) are co-inducible in many tissues following mitogenic and proinflammatory stimulation. In chapter 2, I investigate the physical and enzymatic properties of human COX-2 and iNOS and demonstrate that, despite reports to the contrary by another laboratory, they do not interact. The only reported COX-1 splice variant to exhibit cyclooxygenase activity has been isolated from …

(E,E)-1,3-Bis[9,10-Dihydro-9-Nitro-10-(Trinitro­Meth­Yl)-9-Anthr­Yl]Propane, Mustafa Arslan, Erol Asker, John Masnovi, Ronald J. Baker

Chemistry Faculty Publications

The title compound, C₃₃H₂₄N₈O₁₆, was obtained as a product of the photoreaction between 1,3-di-9-anthrylpropane and tetra­nitro­methane. The mol­ecule occupies a special position on a twofold axis. The trinitro­methyl and nitro substituents on the 9,10-dihydro­acridine system are E oriented.

A 2:1 Complex Of 1,3-Bis­(9h-Carbazol-9-Yl)Propane And Tetra­Chloro-P-Benzoquinone (P-Chloranil), Mustafa Arslan, Randolph B. Krafcik, John Masnovi, Ronald J. Baker

Chemistry Faculty Publications

In the title electron donor–acceptor complex, C₂₇H₂₂N₂·0.5C₆Cl₄O₂, the p-chloranil mol­ecule lies on a crystallographic inversion center, which is located at the center of the benzene ring. In the crystal structure, one p-chloranil mol­ecule lies above and below the central rings of each donor group of two neighboring 1,3-bis­(9H-carbazol-9-yl)propane mol­ecules, with a ring-centroid separation of 3.444 (1) Å. The angle between the planes of the stacking rings of the carbazole and p-chloranil mol­ecules is 3.4 (2)°.

Cleavage Of Phosphate Ester Bonds By Use Of Novel Group 13 Chelate Compounds, David A. Atwood

Chemistry Faculty Patents

A novel chemical compound has a general formula (LX)_nY wherein X is selected from a group consisting of a group 13 element other than boron, Y is selected from a group consisting of a halide, a chlorate, a sulfate and a nitrate and L is a chelating ligand containing two nitrogen and two oxygen donor groups where n=1 or 2.

Absorption Properties Of A Porous Organic Crystalline Apohost Formed By A Self-Assembled Bis-Urea Macrocycle, Mahender B. Dewal, Michael W. Lufaso, Andrew D. Hughes, Stevan A. Samuel, Perry J. Pellechia, Linda S. Shimizu

Faculty Publications

We report herein the characterization and binding properties of a microporous crystalline host formed by the self assembly of a bis-urea macrocycle 1. Bis-urea macrocycle 1 has been designed to crystallize into stacked hollow columns. The self-assembly process is guided primarily by hydrogen bonding and aromatic stacking interactions that yield crystals of filled host 1âacetic acid (AcOH). The AcOH guests are bound in the cylindrical cavities of the crystal. The guest AcOH can be removed by heating to form a stable crystalline apohost 1. Apohost 1 displays a type I gas adsorption isotherm with CO₂ that is consistent with …

Novel Mesoscale Defect Structure On Nio(1 0 0) Surfaces By Atomic Force Microscopy, S. C. Petitto, Cindy L. Berrie, Marjorie Langell

Marjorie A. Langell Publications

Cleaved NiO(1 0 0) surfaces were imaged with atomic force microscopy (AFM) to determine defect concentrations and morphology. Random (0 1 0) and (0 0 1) oriented steps, which have been previously characterized, were the most common defect observed on the cleaved surface and formed with step heights in multiples of 2.1 Å, the Ni–O nearest-neighbor distance, and terrace widths in the range of 25–100 nm. In addition, the surface showed novel mesoscale (~0.5–2 μm) square pyramidal defects with the pyramid base oriented along (1 0 0) symmetry related directions. Upon etching, the pyramidal defects converted to more stable cubic …

Tau-Tubulin Kinase 1 (Ttbk1), A Neuron-Specific Tau Kinase Candidate, Is Involved In Tau Phosphorylation And Aggregation, Shinji Sato, Ronald Cerny, James L. Buescher, Tsuneya Ikezu

Ronald Cerny Publications

Neurofibrillary tangles, which are major pathological hallmarks of Alzheimer’s disease (AD), are composed of paired helical filaments (PHFs) containing hyperphosphorylated tau. Specific kinases regulate tau phosphorylation and are closely linked to the pathogenesis of AD. We have characterized a human tau-tubulin kinase 1 (TTBK1) gene located on chromosome 6p21.1. TTBK1 is a serine/threonine/tyrosine kinase that is conserved among species and belongs to the casein kinase 1 superfamily. It is specifically expressed in the brain, especially in the cytoplasm of cortical and hippocampal neurons. TTBK1 phosphorylates tau proteins in both a Mg²⁺- and a Mn²⁺-dependent manner. Phosphopeptide …

N-(2-Aminobenzyl)-N,N-Bis(Quinolin- 2-Ylmethyl)Amine, Abhijit Mitra, Pamela J. Seaton, Kraig A. Wheeler

Faculty Research and Creative Activity

The title new diquinaldine derivative, C27H24N4, forms mol­ecular assemblies organized by inter­molecular quinoline π–π stacking [3.356 (3) and 3.440 (3) Å] and both inter- and intra­molecular N—H⋯N hydrogen bonds [3.039 (3)–3.104 (3) Å and 129 (2)–172 (2)°]. The combination of such inter­actions provides readily definable contacts that propagate along each crystallographic axis.

Molecular-Wire Behavior Of Oled Materials: Exciton Dynamics In Multichromophoric Alq3-Oligofluorene-Pt(Ii)Porphyrin Triads, Victor A. Montes, Cesar Perez-Bolıvar, Neeraj Agarwal, Joseph Shinar, Pavel Anzenbacher Jr.

Chemistry Faculty Publications

Donor-bridge-acceptor triads consisting of the Alq₃ complex, oligofluorene bridge, and Pt^II tetraphenylporphyrin (PtTPP) were synthesized. The triads were designed to study the energy level/distance-dependence in energy transfer both in a solution and in solid state. The materials show effective singlet transfer from the Alq3-fluorene fluorophore to the porphyrin, while the triplet energy transfer, owing to the shorter delocalization of triplet excitons, appears to take place via a triplet energy cascade. Using femtosecond transient spectroscopy, the rate of the singlet−singlet energy transfer was determined. The exponential dependence of the donor−acceptor distance and the respective energy transfer rates of 7.1 …

Single-Crystal, Polarized, Raman Scattering Study Of The Molecular And Lattice Vibrations For The Energetic Material Cyclotrimethylene Trinitramine, James C. Haycraft, Lewis L. Stevens, Craig J. Eckhardt

Craig J. Eckhardt Publications

The single-crystal, polarized, Raman spectra for cyclotrimethylene trinitramine (RDX) have been studied at room temperature and pressure over the region of 5–3400 cm^-1. While the observed Raman bands agree well with a previous Raman study, this work provides a consistent interpretation of the Raman spectra by assignment of fundamental modes, overtones, and combination bands. A total of 56 internal vibrations were observed, 36 of which were labeled as fundamental molecular vibrations. In addition, all 24 lattice optical phonons are identified. All six possible polarizations were probed to obtain the A_g, B_1g, B_{2 …}

Synthesis, Structure, Anion Binding, And Sensing By Calix[4]Pyrrole Isomers, Ryuhei Nishiyabu, Manuel A. Palacios, Wim Dehaen, Pavel Anzenbacher Jr.

Chemistry Faculty Publications

The synthesis, structure, and anion binding properties of chromogenic octamethylcalix[4] pyrroles (OMCPs) and their N-confused octamethylcalix[4] pyrrole isomers (NC-OMCPs) containing an inverted pyrrole ring connected via alpha'- and beta-positions are described. X-ray diffraction analyses proved the structures of two synthesized isomeric pairs of OMCPs and NC-OMCPs. The addition of anions to solutions of chromogenic OMCPs and NC-OMCPs resulted in different colors suggesting different anion-binding behaviors. The chromogenic NC-OMCPs showed significantly stronger anion-induced color changes compared to the corresponding chromogenic OMCP, and the absorption spectroscopy titrations indicated that chromogenic OMCPs and NC-OMCPs also possess different anion binding selectivity. Detailed NMR studies …

Tris(1,9-Diethyladeninium) Triiodide Diiodide, Elizabeth F. Day, Norman S. Dean, Andreas H. Franz

College of the Pacific Faculty Articles

X-ray analysis of the title compound reveals three crystallographically distinct cations of 1,9-diethyl­adeninium, two iodide anions and one triiodide anion in the asymmetric unit, giving six residues and the formula 3C9H14N5+·I3-·2I-. Standard purine nomenclature is used to identify the atoms of each adenine moiety. Hydrogen bonding is observed between atoms N6 and N7 of a pair of cations [N...N = 2.885 (4)/2.902 (3) and 2.854 (3)/2.854 (3) Å], with additional hydrogen bonding to I- anions via the other N6 H atom [N...I = 3.708 (3), 3.738 (3) and 3.638 (3) Å]. The triiodide anion is not involved in hydrogen bonding. …

Rnase L: Its Biological Roles And Regulation, Shu Ling Liang, David Quirk, Aimin Zhou

Chemistry Faculty Publications

2'-5'oligoadenylate-dependent ribonuclease L (RNase L) is one of the key enzymes involved in the function of interferons (IFNs), a family of cytokines participating in innate immunity against viruses and other microbial pathogens. Upon binding with its activator, 5'-phosphorylated, 2'-5' linked oligoadenylates (2-5A), RNase L degrades single-stranded viral and cellular RNAs and thus plays an important role in the antiviral and antiproliferative functions of IFNs. In recent years, evidence has revealed that RNase L displays a broad range of biological roles which are summarized in this review.

Low-Energy Nondipole Effects In Molecular Nitrogen Valence-Shell Photoionization, Oliver Hemmers, Renaud Guillemin, D. Rolles, A. Wolska, Dennis W. Lindle, E. P. Kanter, B. Krassig, S. H. Southworth, R. Wehlitz, B. Zimmermann, V. Mckoy, P. W. Langhoff

Environmental Studies Faculty Publications

Observations are reported for the first time of significant nondipole effects in the photoionization of the outer-valence orbitals of diatomic molecules. Measured nondipole angular-distribution parameters for the 3σ_g, 1π_u, and 2σ_u shells of N₂ exhibit spectral variations with incident photon energies from thresholds to ∼200  eV which are attributed via concomitant calculations to particular final-state symmetry waves arising from (E1)⊗(M1,E2) radiation-matter interactions first-order in photon momentum. Comparisons with previously reported K-edge studies in N₂ verify linear scaling with photon momentum, accounting in part for the significantly enhanced nondipole behavior observed in inner-shell ionization …

Tertiary Structural And Functional Analyses Of A Viroid Rna Motif By Isostericity Matrix And Mutagenesis Reveal Its Essential Role In Replication, Neocles B. Leontis, Xuehua Zhong, Shuiming Qian, Asuka Itaya, Yijun Qi, Kathleen Boris-Lawrie, Biao Ding

Chemistry Faculty Publications

RNA-templated RNA replication is essential for viral or viroid infection, as well as for regulation of cellular gene expression. Specific RNA motifs likely regulate various aspects of this replication. Viroids of the Pospiviroidae family, as represented by the Potato spindle tuber viroid (PSTVd), replicate in the nucleus by utilizing DNA-dependent RNA polymerase II. We investigated the role of the loop E (sarcin/ricin) motif of the PSTVd genomic RNA in replication. A tertiary-structural model of this motif, inferred by comparative sequence analysis and comparison with nuclear magnetic resonance and X-ray crystal structures of loop E motifs in other RNAs, is presented …

Introduction: Self-Organization In Nonequilibrium Chemical Systems, Irving R. Epstein, John A. Pojman, Oliver Steinbock

Faculty Publications

The field of self-organization in nonequilibrium chemical systems comprises the study of dynamical phenomena in chemically reacting systems far from equilibrium. Systematic exploration of this area began with investigations of the temporal behavior of the Belousov-Zhabotinsky oscillating reaction, discovered accidentally in the former Soviet Union in the 1950s. The field soon advanced into chemical waves in excitable media and propagating fronts. With the systematic design of oscillating reactions in the 1980s and the discovery of Turing patterns in the 1990s, the scope of these studies expanded dramatically. The articles in this Focus Issue provide an overview of the development and …