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

Chemistry & Biochemistry Newsletter: 2002-2015

Inside:

Page 2-3 A Semester Break in Antarctica

Page 4 Chemistry Student Receives Goldwater Scholarship; Recent Publications by the Department’s Faculty

Page 5 Hach Scientific Foundation provides two new scholarships; Recent Publications by the Department’s Faculty

Page 6 Chemistry Alum elected to National Academy of Sciences; Recent Funding by the Department Faculty

Page 7 2007 Lardy Lecture; Scholarships and Awards

Page 8 2007 Chemistry and Biochemistry Graduates

Classification Of Chemical Substances Using Particulate Representations Of Matter: An Analysis Of Student Thinking, Marilyne Stains, Vicente Talanquer

Department of Chemistry: Faculty Publications

We applied a mixed-method research design to investigate the patterns of reasoning used by novice undergraduate chemistry students to classify chemical substances as elements, compounds, or mixtures based on their particulate representations. We were interested in the identification of the representational features that students use to build a classification system, and in the characterization of the thinking processes that they follow to group substances in different classes. Students in our study used structural and chemical composition features to classify chemical substances into elements, compounds, and mixtures. Many of the students’ classification errors resulted from strong mental associations between concepts (e.g., …

Structural Studies Examining The Substrate Specificity Profiles Of Pc-Plcbc Protein Variants, Aaron P. Benfield, Nina Goodey, Lauren T. Phillips, Stephen F. Martin

Department of Chemistry and Biochemistry Faculty Scholarship and Creative Works

The phosphatidylcholine preferring phospholipase C from Bacillus cereus (PC-PLCBc) catalyzes the hydrolysis of phospholipids in the following order of preference: phosphatidylcholine (PC) > phosphatidylethanolamine (PE) > phosphatidylserine (PS). In previous work, mutagenic, kinetic, and crystallographic experiments suggested that varying the amino acids at the 4th, 56th, and 66th positions had a significant influence upon the substrate specificity profile of PC-PLCBc. Here, we report the crystal structures of the native form of several PC-PLCBc variants that exhibited altered substrate specificities for PC, PE, and PS at maximum resolutions of 1.90-2.05 Å. Comparing the structures of these variants to the structure of the wild-type …

The Role Of The Intersection Space In The Photochemistry Of Tricyclo[3.3.0.02,6]Octa-3,7-Diene, Luis Manuel Frutos, Unai Sancho, Marco Garavelli, Massimo Olivucci, Obis Castano

Chemistry Faculty Publications

CASSCF and CASPT2 methods were used to study the photochemistry of tricyclo[3.3.0.0(2,6)]octa-3,7-diene (TOD). The analysis of different S-1 reaction paths as well as the topology of the S-1/S-0 intersection space allows us to establish two novel properties associated with the photochemical behavior of this compound: (i) simple low-lying intersection space domains can mediate different photoproducts, and (ii) TOD photochemistry is probably mediated by two disconnected intersection space domains, related to the formation of cyclooctatetraene and semibulvalene in different time-scales. It is shown that these domains are chemically distinct since the first, leading to COT, mediates barrierless pericyclic reactions while the …

Coupling Photodriven Multielectron Reduction Of Ruthenium Polypyridyl Complexes With Hydrogen Evolving Co-Catalysts, Cale Mcalister

Chemistry & Biochemistry Theses - Archive

With energy demands continuing to increase, the importance of finding a means of converting solar energy into a usable form of chemical energy continues to escalate. Photocatalysis provides a viable approach to harnessing energy from the sun for its use in energy converting reactions such as the water splitting reaction. Ruthenium polypyridyl complexes have played an important role in the growth and advancement of artificial photosynthetic systems, many of which have the ability to utilize solar energy in the process of H2 evolution. This thesis focuses on a biomimetic approach to solar H2 production through multi-electron photocatalysis. The two dinuclear …

Effect Of Structure And Stereochemistry On Cytotoxicity Of Ruthenium Polypyridyl Complexes, Arthi Krishnan

Chemistry & Biochemistry Theses - Archive

Efforts to develop novel non-platinum, metal-based antitumor drugs have been pursued by many groups and ruthenium complexes have drawn a lot of attention as prospective transition metal-based antineoplastic agents. Recently, it was discovered that complex [(phen)2Ru(tatpp)Ru(phen)2]+4 shows biological activity both in vitro and in vivo. Expanding on this area of research, in depth cytotoxicity studies in human lung cancer cells and healthy cells were carried out in five different ruthenium(II) polypyridyl complexes as racemic mixtures and also their enantiopure forms. This study was carried out by performing MTT-cytotoxicity assays on non small cell lung cancer cells (NSCLC), H358 - Human …

Global And Quantitative Gene Expression Analysis Of The Effects Of Drinking Water Exposure To Lead Acetate In Fisher 344 Male Rats Liver, Worlanyo Eric Gato

Dissertations

The primary objective of this research is to analyze global gene expression patterns occurring in Fisher 344 rat livers exposed to varying levels of lead and times. The hypotheses were that: (1) effects associated with Pb exposure are both dose and time dependent and (2) several genes will be over-expressed or repressed including transcripts associated with calcium signaling. Initially, the effects of Pb exposures upon morphometnc indices, liver and kidney tissue histology, Pb distribution, Pb interaction with other trace metals including Zn, Cu, Co, Fe, Ni and Ca were assessed. Results showed a significant accumulation of lead in blood, liver, …

Biochemical Characterization Of Disease-Causing Mutation In N-Terminal Wilson Protein Domain Six, Patrick Ochieng

Masters Theses

Wilson protein (ATP7B) is a copper-transporting P-type ATPase that regulates copper homeostasis and secretion of copper-containing enzymes in the liver. In hepatocytes, ATP7B delivers copper to apoceruloplasmin and mediates the excretion of excess copper into bile. Mutation in the gene coding for Wilson protein leads to Wilson disease. Several mutations in Wilson protein have been identified and of particular interest, mutations affecting the N-metal binding region significantly interfere with the ability of Wilson protein to transport copper to its target in the copper-trafficking pathway. In an attempt to characterize the disease-causing mutation (G591D) in Wilson protein domain 6 (WLN6), we …

Green Chemistry Using Bismuth Salts Bismuth (Iii) Iodide Catalyzed Deprotection Of Acetals And Ketals In H2o, Aaron D. Bailey '07

Honors Projects

Since the Pollution Prevention Act was passed in 1990, synthetic organic chemists have focused on the use of environmentally friendly reagents. Often, many synthetic labs use metal catalysts (compounds containing Hg, Ni, Pb, & Sn) that are toxic to or have detrimental effects on the environment. Unlike many heavy metal compounds, bismuth and its compounds have been found to be relatively non-toxic and environmentally friendly. Due to poor shielding of the nucleus by the f electrons bismuth compounds have been shown to be efficient Lewis acid catalysts for many reactions.

The goal of this project to utilize bismuth compounds, specifically …

Development Of Scanning Electrochemical Microscopy For Studying Electron Transport In Lipid Monolayers And Gold Nanoparticle Films, Violeta Stoycheva

Masters Theses

The focus of this thesis is the scanning electrochemical microscopy (SECM) investigation of the electron transport in lipid monolayers and in films of gold nanoparticles. The quality and stability of lipid monolayers were characterized by various analytical techniques such as fluorescence microscopy and spectroscopy, contact angle, and electrochemistry using a monolayer modified electrode. In the SECM measurement, the monolayer electron transport was not detected. The microscopic monolayer quality turned out to be not suitable for studying the electron transport.

The conductivity of mono layer protected gold clusters (MPCs) with different core sizes (1-3 nm diameter) were investigated using SECM. These …

Transcriptional Regulation Of Glucose-6-Phosphate Dehydrogenase (G6pdh) By Glucose, Pramod U. Thekkat

Masters Theses

In liver, insulin and glucose regulate the expression of important genes for lipid and carbohydrate homeostasis. Studies on the effects of glucose and insulin, including effects on cell signaling, are vital since deficiencies in glucose utilization in cells and/or insulin secretion contribute to conditions like obesity and diabetes. In liver, the pentose phosphate pathway is one of the primary pathways that can utilize the excess carbohydrate. Glucose-6-phosphate dehydrogenase (G6PDH) is an important rate limiting enzyme in this pathway. Our laboratory has shown that both insulin and glucose induce the expression of G6PDH, although the mechanism by which this transcriptional regulation …

Heterogeneous Formation Of Hono On Hno3 Pre-Conditioned Hydrophobic, Hydrophilic And Ionic Surfaces At Various Relative Humidities, Dustin S. Wier

Masters Theses

Nitric acid (HNO₃) is a major sink for NO_x (NO+NO₂ ) and is known to be removed from the atmosphere as a result of wet and dry deposition where it is then deposited on various surfaces in the environment. As these surfaces are photolyzed HONO is produced which affects the overlying troposphere. This study examines the amount of HONO (Nitrous Acid) produced by the photolysis of adsorbed HNO₃ as a function of changing relative humidity on hydrophobic, hydrophilic, and inorganic ionic salt surfaces. The amount of HONO produced was measured in long path cell using …

Jeffress Research Grant - 2005

Virginia Journal of Science

Seven-page list of winners of the Jeffress Research Grant Awards for 2005.

Afci Quarterly Input – Unlv January 1 Through March 31, 2007, 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.

The Role Of Phosducin-Like Protein As A Co-Chaperone With The Cytosolic Chaperonin Complex In Assembly Of The G Protein Βγ Subunit Dimer, Paul Jayson Ludtke

Theses and Dissertations

Phosducin-like protein (PhLP) has been shown to interact with the cytosolic chaperonin containing TCP-1 (CCT), and the βγ subunit dimer of heterotrimeric G proteins (Gβγ). Here we provide details obtained from cryo-electron microscopic and biochemical studies on the structure of the complex between the cytosolic chaperonin CCT and PhLP. Binding of PhLP to CCT occurs through only one of the two chaperonin rings, making multiple contacts with CCT through both its N- and C-terminal domains. In addition, we show that PhLP acts as a co-chaperonin along with CCT in mediating the assembly of the G protein βγ subunit and that …

Size Dependence Of Static And Dynamic Magnetic Properties In Nanoscale Square Permalloy Antidot Arrays, Minghui Yu, Leszek M. Malkinski, Leonard Spinu, Weilie Zhou, Scott L. Whittenburg

Chemistry and Biochemistry Faculty Publications

Permalloy antidot arrays with different square hole sizes ( , , and ) have been fabricated by means of electron-beam lithography and lift-off techniques. The smaller square hole size results in enhanced remanence and reduced coercivity in the antidot array. Multiple resonance modes were clearly observed for the magnetic field applied normal to the array plane, and double uniform resonance modes occurred when the field deviated more than 30° from the normal to the plane. Two distinct dipolar field patterns with different orientations and magnitudes split the uniform resonance into double resonance modes. The double resonance modes show uniaxial in-plane …

The Niemann-Pick Type C2 Protein Loads Isoglobotrihexosylceramide Onto Cd1d Molecules And Contributes To The Thymic Selection Of Nkt Cells, Paul B. Savage, Nicolas Schrantz, Yuval Sagiv, Yang Liu, Albert Bendelac, Luc Teyton

Faculty Publications

The Niemann-Pick type C2 (NPC2) protein is a small, soluble, lysosomal protein important for cholesterol and sphingolipid transport in the lysosome. The immunological phenotype of NPC2-deficient mice was limited to an impaired thymic selection of Valpha 14 natural killer T cells (NKT cells) and a subsequent reduction of NKT cells in the periphery. The remaining NKT cells failed to produce measurable quantities of interferon-gamma in vivo and in vitro after activation with alpha-galactosylceramide. In addition, thymocytes and splenocytes from NPC2-deficient mice were poor presenters of endogenous and exogenous lipids to CD1d-restricted Valpha 14 hybridoma cells. Importantly, we determined that similar …

Nontraditional Synthesis Of Organometallic Compounds And Allylic Alcohols, Andrew J. Hesse

Undergraduate Honors Thesis Collection

One of the central dogmas of chemistry is the use of convection heating to increase rate and yields of reactions. However, other methods for the impartation of energy do exist. Microwave irradiation uses high power waves to directly excite molecule into higher energy states. This speeds up the kinetics of the reaction and thermodynamically favorable products are formed at a higher rate. This project successfully uses microwave irradiation to perform organometallic syntheses of iron based compounds such as ferrocene and iron diene tricarbonyls. Another alternative method involves using mechanical energy as a substitute for thermal energy. By rapidly colliding reactants …

Relativistic Effects In Homogeneous Gold Catalysis, David J. Gorin, F. Dean Toste

Chemistry: Faculty Publications

Transition-metal catalysts containing gold present new opportunities for chemical synthesis, and it is therefore not surprising that these complexes are beginning to capture the attention of the chemical community. Cationic phosphine-gold(i) complexes are especially versatile and selective catalysts for a growing number of synthetic transformations. The reactivity of these species can be understood in the context of theoretical studies on gold; relativistic effects are especially helpful in rationalizing the reaction manifolds available to gold catalysts. This Review draws on experimental and computational data to present our current understanding of homogeneous gold catalysis, focusing on previously unexplored reactivity and its application …

Unraveling The Catalytic Mechanism Of Nitrile Hydratases, Sanghamitra Mitra, Richard C. Holz

Chemistry Faculty Research and Publications

To elucidate a detailed catalytic mechanism for nitrile hydratases (NHases), the pH and temperature dependence of the kinetic constants k_cat and K_m for the cobalt-type NHase from Pseudonocardia thermophila JCM 3095 (PtNHase) were examined. PtNHase was found to exhibit a bell-shaped curve for plots of relative activity versus pH at pH 3.2–11 and was found to display maximal activity between pH 7.2 and 7.8. Fits of these data provided pK_ES1 and pK_ES2 values of 5.9 ± 0.1 and 9.2 ± 0.1 (k_cat′ = 130 ± 1 …

Pyridinium Bis-Retinoids: Extraction, Synthesis, And Folate Coupling, Mary Allison Alvarez

Theses and Dissertations

This thesis is divided into two parts.Part I describes the organic extraction, separation, and liquid chromatographic-mass spectrometric analysis of chromophores from human and bovine retinal pigment epithelium. Flurorophores in the retinal pigment epithelium have been implicated in age related macular degeneration. In addition, the synthesis and characterization of a number of bis-retinoid type compounds that may potentially be found in such extracts, or that may be used for insight into pyridinium bis-retinoid reactivity, was accomplished.Part II describes a study of pyridinium bis-retinoid-folic acid coupling with respect to linker type, linker length, and nature of the linkage. Folic acid has been …

Doping Golden Buckyballs: Cu@Au16- And Cu@Au17- Cluster Anions, Lei-Ming Wang, Satya S. Bulusu, Hua-Jin Zhai, Xiao Cheng Zeng, Wang

Xiao Cheng Zeng Publications

The discovery of the unique catalytic effects of gold nanoparticles on oxide substrates[1] has stimulated a flurry of research into the structures and properties of free gold nanoclusters, which may hold the key to elucidating the catalytic mechanisms of supported gold clusters. One of the most remarkable results has been the discovery of planar gold cluster anions (Au_n^-) of up to twelve gold atoms and the 2D to 3D transition for clusters with n larger than 12.[2]– [4] Among larger gold clusters, Au₂₀ has been found to be a perfect tetrahedron.[5] A more recent study of …

Pressure Dissociation Of Integration Host Factor-Dna Complexes Reveals Flexibility-Dependent Structural Variation At The Protein-Dna Interface, Donald F. Senear, Vira Tretyachenko-Ladokhina, Michael L. Opel, Kimberly A. Aeling, G. Wesley Hatfield, Laurie M. Franklin, Reuben C. Darlington, J. B. A. Ross

Chemistry and Biochemistry Faculty Publications

E. coli Integration host factor (IHF) condenses the bacterial nucleoid by wrapping DNA. Previously, we showed that DNA flexibility compensates for structural characteristics of the four consensus recognition elements associated with specific binding (Aeling et al., J. Biol. Chem. 281, 39236-39248, 2006). If elements are missing, high-affinity binding occurs only if DNA deformation energy is low. In contrast, if all elements are present, net binding energy is unaffected by deformation energy. We tested two hypotheses for this observation: in complexes containing all elements, (1) stiff DNA sequences are less bent upon binding IHF than flexible ones; or (2) DNA sequences …

Dynamic Polarizabilities Of Rare-Earth-Metal Atoms And Dispersion Coefficients For Their Interaction With Helium Atoms, Xi Chu, Alexander Dalgarno, Gerrit C. Groenenboom

Chemistry and Biochemistry Faculty Publications

The dynamic scalar and tensor polarizabilities of the rare-earth-metal atoms are calculated with time-dependent density functional theory. The frequency-dependent polarizabilities at imaginary frequencies are used to determine the isotropic and orientation-dependent van der Waals coefficients for the interactions of the rare-earth-metal atoms with helium atoms. The static polarizabilities are compared with other theoretical values and with experimental results. The agreement is satisfactory in most cases but there are some exceptions where the discrepancy between theory and experiment is significant. The derived isotropic van der Waals coefficients range between 37 and 50 E(H)a(0)(6) and the orientation-dependent coefficients between 2 and -1 …

Modification Of The Active Site Of Mycobacterium Tuberculosis Katg After Disruption Of The Met-Tyr-Trp Cross-Linked Adduct, Sofia M. Kapetanaki, Xiangbo Zhao, Shengwei Yu, Richard S. Magliozzo, Johannes Schelvis

Department of Chemistry and Biochemistry Faculty Scholarship and Creative Works

Mycobacterium tuberculosis catalase-peroxidase (Mtb KatG) is a bifunctional enzyme that possesses both catalase and peroxidase activities and is responsible for the activation of the antituberculosis drug isoniazid. Mtb KatG contains an unusual adduct in its distal heme-pocket that consists of the covalently linked Trp107, Tyr229, and Met255. The KatG(Y229F) mutant lacks this adduct and has decreased steady-state catalase activity and enhanced peroxidase activity. In order to test a potential structural role of the adduct that supports catalase activity, we have used resonance Raman spectroscopy to probe the local heme environment of KatG(Y229F). In comparison to wild-type KatG, resting KatG(Y229F) contains …

Molecular Dynamics Of Homogeneous Nucleation In The Vapor Phase Of Lennard-Jones. Iii. Effect Of Carrier Gas Pressure, Kenji Yasuoka, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

A molecular dynamics simulation of vapor phase nucleation has been performed with 40 000 Lennard-Jones particles for the target gas and 0–160 000 particles for the carrier gas. Three carrier gas models are adopted, including a soft-core model, a Lennard-Jones model, and a modified Lennard-Jones model in which the attractive interaction can be adjusted. The effect of the carrier-gas pressure is assessed through computing and comparing the rate of nucleation and cluster size distribution. It is found that the effect of the carrier-gas pressure can be strongly dependent on the carrier-gas model. A positive effect _enhancement of the nucleation rate_ …

Precision In Imaging Multivariate Optical Computing, Michael N. Simcock, Michael L. Myrick

Faculty Publications

Multivariate optical computing (MOC) is a method of performing chemical analysis using a multilayer thin-film structure known as a multivariate optical element (MOE). Recently we have been advancing MOC for imaging problems by using an imaging MOE (IMOE) in a normal-incidence geometry and employing normalization by the 1-norm. There are several important differences between the previously described 45° and the normal-incidence imaging, one of which is the measurement precision due to photon counting. We compare this precision to 45° MOC. We also discuss how MOE models with similar values of standard errors of calibration and prediction and similar gain values …

Magnetic Order In The S=1/2 Two-Dimensional Molecular Antiferromagnet Copper Pyrazine Perchlorate Cu(Pz)(2)(Clo4)(2), T Lancaster, S J. Blundell, M L. Brooks, P J. Baker, F L. Pratt, Jamie L. Manson, M M. Conner, F Xiao, C P. Landee, F A. Chaves, S Soriano, M A. Novak, T P. Papageorgiou, A D. Bianchi, T Herrmannsdorfer, J Wosnitza, J A. Schlueter

Chemistry and Biochemistry Faculty Publications

We present an investigation of magnetic ordering in the two-dimensional S=1/2 quantum magnet Cu(Pz)(2)(ClO4)(2) using specific heat and zero-field muon-spin relaxation (mu+SR). The magnetic contribution to the specific heat is consistent with an exchange strength of 17.7(3) K. We find unambiguous evidence for a transition to a state of three-dimensional long-range order below a critical temperature T-N=4.21(1) K using mu+SR even though there is no feature in the specific heat at that temperature. The absence of a specific heat anomaly at T-N is consistent with recent theoretical predictions. The ratio of T-N/J=0.24 corresponds to a ratio of intralayer to interlayer …

Hydrogen Storage In Pillared Li-Dispersed Boron Carbide Nanotubes, Xiaojun Wu, Yi Gao, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

Ab initio density-functional theory study suggests that pillared Li-dispersed boron carbide nanotubes is capable of storing hydrogen with a mass density higher than 6.0 weight% and a volumetric density higher than 45 g/L. The boron substitution in carbon nanotube greatly enhances the binding energy of Li atom to the nanotube, and this binding energy (~ 2.7 eV) is greater than the cohesive energy of lithium metal (~1.7 eV), preventing lithium from aggregation (or segregation) at high lithium doping concentration. The adsorption energy of hydrogen on the Li-dispersed boron carbide nanotube is in the range of 10 – 24 kJ/mol, suitable …

Supporting Information For "The Molecular Basis Of High-Altitude Adaptation In Deer Mice", Jay F. Storz, Stephen J. Sabatino, Federico G. Hoffmann, Eben J. Gering, Hideaki Moriyama, Nuno Ferrand, Bruno Monteiro, Michael W. Nachman

Hideaki Moriyama Publications

Figure S1: Variation in Site-Specific Levels of Altitudinal Differentiation across the 5′ α- Globin Gene of P. maniculatus

Figure S2: Relationship between Pairwise Linkage Disequilibrium and Distance in bp

Genbank Accession Numbers

Table S1: Amino Acid Variation in the α-Globin Genes of High- and Low-Altitude Deer Mice: Amino acid replacement polymorphisms in deer mice where the derived variant is present at a frequency of >0.100 in the high-altitude sample.

Table S2: Additional Information on Sequenced Loci: Primer sequences for nuclear loci in P. maniculatus.