Digital Commons Network^™

Planar-To-Tubular Structural Transition In Boron Clusters: B20 As The Embryo Of Single-Walled Boron Nanotubes, Boggavarapu Kiran, Satya S. Bulusu, Hua-Jin Zhai, Soohaeng Yoo, Xiao Cheng Zeng, Lai-Sheng Wang

Xiao Cheng Zeng Publications

Experimental and computational simulations revealed that boron clusters, which favor planar (2D) structures up to 18 atoms, prefer 3D structures beginning at 20 atoms. Using global optimization methods, we found that the B₂₀ neutral cluster has a double-ring tubular structure with a diameter of 5.2 Å. For the B₂₀^- anion, the tubular structure is shown to be isoenergetic to 2D structures, which were observed and confirmed by photoelectron spectroscopy. The 2D-to-3D structural transition observed at B₂₀, reminiscent of the ring-to-fullerene transition at C₂₀ in carbon clusters, suggests it may be considered as the embryo …

Characterization Of Microbial Activity, Mark P. Buttner, Patricia Cruz, Klaus J. Stetzenbach, Abe Van Luik, Thomas Williams, Amy J. Smiecinski

Publications (YM)

The overall goal of this study is to investigate the phenomena that affect the fate and transport of radionuclides in the environment. The objective of this task, “Characterization of Microbial Activity”, is to develop a molecular biological method for the characterization of the microbial population indigenous to the Yucca Mountain Project site, with emphasis in detection and measurement of species or groups of microorganisms that could be involved in actinide and/or metal reduction, and subsurface transport. Subtasks consist of QA planning and preparation, and literature review. This task is part of a cooperative agreement between the UNLV Research Foundation and …

Thermodynamics Of Folding And Association Of Lattice-Model Proteins, Troy Cellmer, Dusan Bratko, John M. Prausnitz, Harvey Blanch

Chemistry Publications

Closely related to the “protein folding problem” is the issue of protein misfolding and aggregation. Proteinaggregation has been associated with the pathologies of nearly 20 human diseases and presents serious difficulties during the manufacture of pharmaceutical proteins. Computational studies of multiprotein systems have recently emerged as a powerful complement to experimental efforts aimed at understanding the mechanisms of proteinaggregation. We describe the thermodynamics of systems containing two lattice-model 64-mers. A parallel tempering algorithm abates problems associated with glassy systems and the weighted histogram analysis method improves statistical quality. The presence of a second chain has a substantial effect on single-chain …

Sulfoxides As An Intramolecular Sulfenylating Agent For Indoles And Diverse Applications Of The Sulfide-Sulfoxide Redox Cycle In Organic Chemistry, Parag V. Jog

Dissertations, Master's Theses and Master's Reports - Open

This dissertation involves study of various aspects of sulfoxide chemistry. Specifically designed t-butyl and propanenitrile sulfoxides tethered to indole-2-carboxamide were used as a source of intramolecular sulfenylating agents to synthesize novel indolo[3,2-b]-1-5-benzothiazepinones which are structurally analogous to the other biologically active benzothiazepinones. This study reveals that the intramolecular cyclization of sulfoxide follows an electrophilic sulfenylation (Sulfoxide Electrophilic Sulfenylation, SES) reaction pathway. Evidence of the absence of sulfenic acid as a transient reactive intermediate in such intramolecular cyclization is also provided.

In another study, sulfoxide was used as a “protecting group” of thioether to synthesize 8-membered, indole substituted, thiazocine-2-acetic acid derivative …

"Middle Georgia Waters:" Chemical Analysis By Gc&Su Undergraduates, Melanie Mobley, Lance Cramer, Daniel Brooks, Catrena Higginbotham Ph.D

The Corinthian

Every living organism on Earth depends on water, many of which must consume liters of fresh water daily. Unfortunately, a readily available source of clean, fresh water is diminishing. Over the years, the fresh water supply has been polluted by biological and chemical sources. The nutrient levels and pesticide chemical contamination of several water locations in the Middle Georgia area were analyzed and monitored by chemistry majors at GC&SU over the past two years.

Temperature And Ph Dependence Of The Cyclization Of Creatine: A Study Via Mass Spectrometry, Brian J. Diamond

Theses, Dissertations and Capstones

The creatine to creatinine cyclization is of significant biological importance, providing energy for muscle cells and indicating proper renal function. From a chemical perspective, the rate at which creatine cyclizes to form creatinine has interested researchers since the late 1920s, but the cyclization is poorly understood both energetically and mechanistically. Mass spectroscopy was used to determine the rate of creatine cyclization as a function of temperature and pH. Using these values, the energetic parameters, activation energy and Arrhenius factor, were determined as a function of pH to better understand this reaction and ultimately determine the mechanistic process for this reaction. …

Nature's Assembly Line Logic For Natural Products, Christopher T. Walsh, Ryan G. Kruger, David A. Vosburg

All HMC Faculty Publications and Research

Nature fashions a very large number of diverse products (molecular weights ranging from ca. 200 to 2000 daltons) from simple monomeric metabolites used in primary metabolism. These include polyketide scaffolds generated from the simple C₃ malonyl CoA and C₄ methylmalonyl CoA monomers and nonribosomal peptides made from both the 20 proteinogenic amino acids and dozens of nonpoteinogenic amino acids.¹ A large family of terpenoid skeletons are built from the Δ²- and Δ³-alkene isomers of the biological isoprene monomer, isoprenyl-pyrophosphate.²

Two Purified Domains Of Telomerase Reverse Transcriptase Reconstitute Sequence-Specific Interactions With Rna, C. M. O'Connor, Cary K. Lai, Kathleen Collins

Biology Faculty Publications

Telomerase reverse transcriptase (TERT) and telomerase RNA (TER) function together to create a uniquely specialized polymerase. Here we have described for the first time domains of bacterially expressed Tetrahymena TERT that interacted directly with TER in the absence of assembly chaperones. We used quantitative binding assays to define TER sequence requirements for recognition by the high affinity RNA binding domain and an independent N-terminal RNA interaction domain. The TERT RNA binding domain and N-terminal RNA interaction domain had distinct, nonoverlapping requirements for TER sequence and structure that together accounted for all of the sites of TER contact inferred for full-length …

Removal Of P-Cresol Sulfate By Hemodialysis, Andres W. Martinez, Natalie S. Recht, Thomas H. Hostetter, Timothy W. Meyer

Chemistry and Biochemistry

Protein-bound solutes are poorly cleared by dialysis. Among the most extensively studied of these solutes is p-cresol, which has been shown to be toxic in vitro. This study examined the form in which p-cresol circulates and quantified its removal by hemodialysis. HPLC analysis of plasma from hemodialysis patients contained a peak whose mobility corresponded to synthetic p-cresol sulfate (PCS) but no detectable unconjugated p-cresol. Treatment with sulfatase resulted in recovery of this peak as p-cresol, confirming its identity. Subsequent studies compared the removal of PCS and another protein-bound solute, indican, to the removal of urea during clinical hemodialysis treatments. …

Reduced Macrophage Apoptosis Is Associated With Accelerated Atherosclerosis In Low-Denstiy Lipoprotein Receptor-Null Mice, Michael Sinensky, J. Liu, D. P. Thweke, Y. R. Su, M. F. Linton, S. Fazio

Faculty Publications, Biological Sciences

Objective— The majority of apoptotic cells in atherosclerotic lesions are macrophages. However, the pathogenic role of macrophage apoptosis in the development of atherosclerosis remains unclear. Elevated expression of Bax, one of the pivotal proapoptotic proteins of the Bcl-2 family, has been found in human atherosclerotic plaques. Activation of Bax also occurs in free cholesterol-loaded and oxysterol-treated mouse macrophages. In this study, we examined the effect of Bax deficiency in bone marrow-derived leukocytes on the development of atherosclerosis in low-density lipoprotein receptor-null (LDLR−/−) mice. Methods and Results— Fourteen 8-week-old male LDLR−/− mice were lethally irradiated and reconstituted with either wild-type (WT) …

Characterization Of The Electronic Excited-State Energetics And Solution Structure Of Lanthanide(Iii) Complexes With The Polypyridine Ligand 6,6'-Bis[Bis(2-Pyridylmethyl)Aminomethyl]-2,2'-Bipyridine, Gilles Muller, P. Gawryszewska, J. Sokolnicki, A. Dossing, J. P. Riehl, J. Legendziewicz

Faculty Publications, Chemistry

Absorption, emission, and excitation spectra for solid-state and solution of Tb(III), Dy(III), and Gd(III) complexes with the polypyridine ligand 6,6‘-bis[bis(2-pyridylmethyl)-aminomethyl]-2,2‘-bipyridine (C36H34N8) are presented. Measurements of excited-state lifetimes and quantum yields in various solvents at room temperature and 77 K are also reported and used to characterize the excited-state energetics of this system. Special attention is given to the characterization of metal-to-ligand energy transfer efficiency and mechanisms. The measurement of circularly polarized luminescence (CPL) from the solution of the Dy(III) complex following circularly polarized excitation confirms the chiral structure of the complexes under study. No CPL is present in the luminescence …

Differential Tethering Of Log Phase Trypanosoma Brucei Onto Chemically Distinct Surfaces, Darrell R. Fry, Lydia Archuleta, Ashley Dunham, Justin Rains

Faculty Publications

Our long-term objective is to understand and model the motility of T. brucei. Obtaining high quality images of T. brucei that allow one to differentiate between cell body movement and flagallar movement is difficult with T. brucei because the flagellum is attached along the cell body. Currently, our approach his to tether T. brucei onto a microscope friendly surface. The contributions to the ISIS our progress to date. Specifically, we look at the adhesion density of T. brucei to numerous microscope friendly surfaces and at the optimum adhesion conditions for T. brucei.

Computational Study Of A Novel Dinuclear Metal Complex, Dragos Seghete

Inquiry: The University of Arkansas Undergraduate Research Journal

The first compound containing an M-H-M was recently reported by Vicic et al. With recent availability of large computational resources, molecular modeling has become a reliable tool for confirming experimental results. The novel dinuclear Ni complex [( dippm)2Ni2Br2]( 0 -H) was investigated in this work from a theoretical perspective. Full geometry optimization was carried on the dinuclear Ni complex at the DFT/B3LYP with the 6-31G* basis set. The result verifies the linear Ni-H-Ni bond. Two different starting structures that converged to the same geometry confirm that a global minimum was reached. The computed structure differs from the experimentally determined one …

Regional Scale Evidence For Improvements In Surface Water Chemistry 1990-2001, B. L. Skjelkvåle, J. L. Stoddard, D. S. Jeffries, K. Tørseth, T. Høgåsen, J. Bowman, J. Mannio, D. T. Monteith, R. Mosello, M. Rogora, D. Rzychon, J. Vesely, J. Wieting, A. Wilander, A. Worsztynowicz

United States Environmental Protection Agency: Publications

The main aim of the international UNECE monitoring program ICP Waters under the Convention of Long-range Transboundary Air Pollution (CLRTAP) is to assess, on a regional basis, the degree and geographical extent of the impact of atmospheric pollution, in particular acidification, on surface waters. Regional trends are calculated for 12 geographical regions in Europe and North America, comprising 189 surface waters sites. From 1990-2001 sulphate concentrations decreased in all but one of the investigated regions. Nitrate increased in only one region, and decreased in three North American regions. Improvements in alkalinity and pH are widely observed. Results from the ICP …

Recurrent Structural Rna Motifs, Isostericity Matrices And Sequence Alignments, Neocles B. Leontis, Aurélie Lescoute, Christian Massire, Eric Westhof

Chemistry Faculty Publications

The occurrences of two recurrent motifs in ribosomal RNA sequences, the Kink-turn and the C-loop, are examined in crystal structures and systematically compared with sequence alignments of rRNAs from the three kingdoms of life in order to identify the range of the structural and sequence variations. Isostericity Matrices are used to analyze structurally the sequence variations of the characteristic non-Watson-Crick base pairs for each motif. We show that Isostericity Matrices for non-Watson-Crick base pairs provide important tools for deriving the sequence signatures of recurrent motifs, for scoring and refining sequence alignments, and for determining whether motifs are conserved throughout evolution. …

Fluorescence Prediction Through Computational Chemistry, Daniel Craig Lathey

Theses, Dissertations and Capstones

With the growing demand for diverse fluorescent dyes, it is imperative to find a more efficient methodology by which to synthesize dyes. Our research group has found a computational method that can efficiently predict the optical properties of a molecule before it is synthesized. By evaluating different semi-empirical methods, we have found a way to predict the fluorescence maxima. With the new ability of Hyperchem 7.5 to geometrically optimize a molecule in an excited state, we can predict not only the absorption maxima, but we can also predict the fluorescence maxima within 25 nm of the actual fluorescence.

With this …

Terpenoids And Steroids From The Roots Of Salvia Blepharochlaena, Ufuk Kolak, Gülaçti Topçu, Seher Bi̇rteksöz, Gülten Ötük, Ayhan Ulubelen

Turkish Journal of Chemistry

From the roots of Salvia blepharochlaena Hedge and Hub. Mor. 4 triterpenoids, 4 steroids, 6 diterpenoids, and an aromatic ester were isolated. The structures of these compounds were established by spectroscopic methods. Formosanolide was isolated for the first time from the genus Salvia.

Electrochemical Detection Of Nanoscale Phase Separation In Binary Self-Assembled Monolayers, R. Carlisle Chambers, Christina E. Inman, James E. Hutchison

Faculty Publications - Department of Biological & Molecular Science

Developing methods to probe the nature and structure of nanoscale environments continues to be a challenge in nanoscience. We report a cyclic voltammetry investigation of internal, hydrogen-bond driven phase separation of amide-containing thiols and alkane thiols. Amide-containing thiols with a terminal ferrocene carboxylate functional group were investigated in two binary monolayers, one homogeneously mixed and the other phase separated. The electrochemical response of the ferrocene probe was used to monitor adsorbate coverage, environment and phase separation within each of these monolayers. The results demonstrate that the behavior of ferrocene containing monolayers can be used to probe nanoscale organization.

Preservation Of Eumelanin Hair Pigmentation In Proopiomelanocortin-Deficient Mice On A Nonagouti (A/A) Genetic Background, Andrzej Slominski, Przemyslaw M. Plonka, Alexander Pisarchik, James L. Smart, Virgine Tolle, Jacobo Wortsman, Malcolm J. Low

Faculty Publications - Department of Biological & Molecular Science

No abstract provided.

An Investigation Into The Ring-Enlargement Reactions Of Boron Subphthalocyanine And Boron Subnaphthalocyanine, Andrew Jeremiah Jones

Master's Theses and Doctoral Dissertations

Ring enlargement syntheses of axially substituted boron subphthalocyanine and boron subnaphthalocyanine were investigated. The trihexylsiloxy derivatives of subphthalocyanine and subnaphthalocyanine were synthesized. These derivatives were then used in the ring-enlargement trials. Symmetrical and asymmetrical ring-enlargement reactions were carried out in a mixture of toluene and dimethylsulfoxide at room temperature. This study represents the first synthesis of boron subphthalocyanine with trihexylsiloxy group in the axial position and the first investigation into the ring enlargement of boron subnaphthalocyanine in which the axial ligand is a trihexylsiloxy group. Precipitates were formed, and it is believed that the precipitates are the metalfree ring-enlarged products. …

In Situ Screening To Optimize Variables In Organic Reactions, David Berkowitz, Mohua Bose, Sungjo Choi

Department of Chemistry: Faculty Publications

A biphasic process for rapid screening of organic reactions comprising monitoring relative rates of parallel organic reactions. The screening process is suitable to determine the efficacy of different reactants, process conditions, and process enhancers such as catalysts or promoters. The biphasic process also allows multiple samples to be analyzed/monitored simultaneously. In addition because enzymes are used to monitor the reaction product in this invention, when that product is chiral and an enantio-discriminating enzyme is used to monitor the product, in addition to the relative rates, enantioselectivities of a set of parallel organic reactions can also be determined. The monitoring is …

Elucidation Of The Mass Spectral Fragmentation Pathways Of Cyclic Hepatopeptides Microcystins, Paloma Muniz Ortea

Theses

The most frequently found cyanobacterial toxins in blooms from fresh and brackish waters are the cyclic peptide microcystins (MCs) and nodularin family. These toxins cause fatal poisonings of agricultural livestock, wild animals, birds and fish on a worldwide basis. The involvement of these toxins in human health problems has also been inferred in several countries and their presence in drinking water sources is of interest to the drinking water industry.

One of the biggest problems in the analysis of MCs is the lack of commercially available standards to be used for the identification and characterisation of these cyanobacterial toxins. One …

Analytical And Synthetic Methods For Anatoxins., Janet Crowley

Theses

This thesis is focused on the potent cyanobacterial neurotoxins anatoxin-a (AN), its methyl analogue homoanatoxin-a (HMAN) and their non-toxic dihydro- and epoxydegradation products. In commencing the investigation into this area a literature review was performed in order to identify areas where more research and method development was required (Chapter 1). The review highlighted the fact that although a number of analytical methods had been developed for the analysis of AN, there were few methods for the determination of its potent homologue HMAN and their non-toxic degradation products. As these neurotoxins degrade quickly it is important to monitor their degradation products, …

An Hmm-Based Framework For Video Semantic Analysis, Gu Xu, Yu-Fei Ma, Hong-Jiang Zhang, Shiqiang Yang

Chemistry Faculty Research & Creative Works

Video semantic analysis is essential in video indexing and structuring. However, due to the lack of robust and generic algorithms, most of the existing works on semantic analysis are limited to specific domains. In this paper, we present a novel hidden Markove model (HMM)-based framework as a general solution to video semantic analysis. In the proposed framework, semantics in different granularities are mapped to a hierarchical model space, which is composed of detectors and connectors. In this manner, our model decomposes a complex analysis problem into simpler subproblems during the training process and automatically integrates those subproblems for recognition. The …

Potential Energy Surface Of The Reaction Of Imidazole With Peroxynitrite: Density Functional Theory Study, Valentin Gogonea

Chemistry Faculty Publications

This article presents a theoretical investigation of the reaction mechanism of imidazole nitration by peroxynitrite using density functional theory calculations. Understanding this reaction mechanism will help in elucidating the mechanism of guanine nitration by peroxynitrite, which is one of the assumed chemical pathways for damaging DNA in cells. This work focuses on the analysis of the potential energy surface (PES) for this reaction in the gas phase. Calculations were carried out using Hartree–Fock (HF) and density functional theory (DFT) Hamiltonians with double-zeta basis sets ranging from 6-31G(d) to 6-31++G(d,p), and the triple-zeta basis set 6-311G(d). The computational results reveal that …

Synthesis, Characterization And Application Of Polymeric Surfactants In Micellar Electrokinetic Chromatography: Use Of Ionic Liquids As Modifiers, Simon M. Mwongela

LSU Doctoral Dissertations

The goal of the research presented in this dissertation is to synthesize, characterize, and apply a novel chiral amino acid-based surfactant and achiral sulfate-based surfactants for the effective separations of chiral and achiral compounds in micellar electrokinetic chromatography (MEKC). The first part of this research involves novel synthesis, characterization, and application of polysodium oleyl-L-leucyl-valinate (poly-L-SOLV) for the separation of chiral compounds in MEKC. Surface tensiometry, proton nuclear magnetic resonance, infrared spectroscopy, densitometry and analytical ultracentrifugation were used as the characterization techniques. Optimal MEKC separating conditions were established by varying surfactant concentration, buffer concentration and pH, applied voltage, and capillary temperature. …

Simulations Of Nanopore Formation And Phosphatidylserine Externalization In Lipid Membranes Subjected To A High-Intensity, Ultrashort Electric Pulse, Q. Hu, R. P. Joshi, K. H. Schoenbach

Bioelectrics Publications

A combined MD simulator and time dependent Laplace solver are used to analyze the electrically driven phosphatidylserine externalization process in cells. Time dependent details of nanopore formation at cell membranes in response to a high-intensity (100kV∕cm), ultrashort (10ns) electric pulse are also probed. Our results show that nanosized pores could typically be formed within about 5ns. These predictions are in very good agreement with recent experimental data. It is also demonstrated that defect formation and PS externalization in membranes should begin on the anode side. Finally, the simulations confirm that PS externalization is a nanopore facilitated event, rather than the …

Molecular Recognition And Its Underlying Mechanisms In Molecularly Imprinted Polymers, Ryan Simon

LSU Doctoral Dissertations

Molecular recognition in molecularly imprinting polymers (MIPs) is governed by two mechanisms: pre-organization of functional groups and shape specificity of the binding site. While pre-organization of functional groups has been studied extensively, shape specificity of the binding site has not been rigorously explored. The goal of this research is to determine the influence of shape specificity on molecular recognition in MIPs (Chapter 2). Once shape selectivity was proven to play a vital role in molecular recognition, it was important to determine if pre-organization of functional groups or shape specificity was the dominating factor in determining molecular recognition in the binding …

The Synthesis And Characterization Of Bicyclooxacalixarenes, Kevin J. Selby

Honors Theses

Bicyclooxacalixarenes were synthesized in high yield via a selective, room temperature Sn Ar reaction of phluoroglucinol with 2,6-dichloropyridines. Functionality on the 2,6-dichloropyridioe was varied by changing the electron-withdrawing groups in the 3 and 5 positions (using chlorine, nitro groups, and cyano groups) and the side-chains in the 4-position (using ethyl, butyl, phenyl and ρ-tolyl groups). The resulting cage-like molecules were studied by X-ray crystallography and tested for metal complexation.

Synthesis And Spectral Investigations Of Some Platinum Metals Ions Coordination Compounds Of 4[N-(Furan-2'-Carboxalidene)Amino]Antipyrine Thiosemicarbazone And 4[N-(3',4',5'-Trimethoxybenzalidene)Amino]Antipyrine Thiosemicarbazone, Ram K. Agarwal, Surendra Prasad

Turkish Journal of Chemistry

The present work describes the synthesis and spectral properties of some platinum metals chlorides coordination compounds of 4[N-(-(furan-2'-carboxalidene)amino]antipyrine thiosemicarbazone (FFAAPTS) and 4[N-(3',4',5'-trimethoxybenzalidene)amino]antipyrine thiosemicarbazone (TMBAAPTS). All the compounds have the general composition MCl_2(L) (M = Pd^{2+} or Pt^{2+} ; L = FFAAPTS or TMBAAPTS) or MCl_3(L) (M = Ru^{3+} , Rh^{3+} or Ir^{3+} ; L = FFAAPTS or TMBAAPTS). All the complexes were characterized by elemental analyses, molar conductance, molecular weight, magnetic measurements, and infrared and electronic spectra. The infrared spectra suggest that both the thiosemicarbazones behave as neutral tridentate (N,N,S) ligands. The magnetic and electronic spectra suggest that Pd^{2+} and …