Chemistry Commons^™

Characterization Of The Transition State Of Functional Enzyme Dynamics, Evgenii L. Kovrigin, J. Patrick Loria

Chemistry Faculty Research and Publications

Through characterization of the solvent isotope effect on protein dynamics, we have examined determinants of the rate limitation to enzyme catalysis. A global conformational change in Ribonuclease A limits the overall rate of catalytic turnover. Here we show that this motion is sensitive to solvent deuterium content; the isotope effect is 2.2, a value equivalent to the isotope effect on the catalytic rate constant. We further demonstrate that the protein motion possesses a linear proton inventory plot, indicating that a single proton is transferred in the transition state. These results provide compelling evidence for close coupling between enzyme dynamics and …

Programs To Compute Distribution Functions And Critical Values For Extreme Value Ratios For Outlier Detection, George Mcbane

Peer Reviewed Articles

A set of FORTRAN subprograms is presented to compute density and cumulative distribution functions and critical values for the range ratio statistics of Dixon (1951, The Annals of Mathematical Statistics) These statistics are useful for detection of outliers in small samples

Investigations Of Poly[(Styrene-Co-P-Methylstyrene)-Risobutylene- R-(Styrene-Co-P-Methylstyrene)] And Poly[(Acrylic Acid)-5-Styrene-Jb-Is0butylene-5-Styrene-Jb-(Acrylic Acid)], James Grabill Kopchick

Dissertations

The pMe study was conducted to understand the morphological and physical property changes that occur as the ratio of pMe to styrene is increased, effectively increasing the aliphatic units. By the introduction of pMe, the interface region becomes more blended/compatible as the pMe migrates to the interface. These pMe groups are theorized in effect to create multiple ‘anchors’ to distribute the loads experienced at the interface more effectively creating a synergistic effect on the final properties of the copolymers. The primary goals of the pentablock study were the characterization of unique membranes as related to …

Muon-Spin Relaxation Study Of The Spin-(1)(2) Molecular Chain Compound Cu(Hco2)(2)(C4h4n2), T Lancaster, S J. Blundell, M L. Brooks, P J. Baker, F L. Pratt, Jamie L. Manson, C Baines

Chemistry and Biochemistry Faculty Publications

We present the results of a muon-spin relaxation (mu+SR) study of magnetic order in the quasi-one-dimensional spin-1/2 molecular chain compound Cu(HCO2)(2)(C4H4N2). Zero-field mu+SR measurements at low temperatures show oscillations in the measured asymmetry, characteristic of a quasistatic magnetic field at the muon sites. Our measurements provide convincing evidence for long-range magnetic order below a temperature T-N=1.97(8) K. This leads to an estimate of the interchain coupling constant of parallel to J'parallel to/k(B)=1.27 K and to a ratio parallel to J'/J parallel to=1.6x10(-1).

Secondary N-Nitrosocarbamate Anions: Structure And Alkylation Reactions. A Dft Study, Vladimir Benin

Chemistry Faculty Publications

The current article reports theoretical studies (DFT: B3LYP/6-31+G(d)) on the structure and alkylation reactions of the anions of some secondary N-nitrosocarbamates, a class of ambident nucleophiles whose chemistry has been little explored. Several anions (1–4), with an increasing size of the carbamate alkyl (aryl) group were investigated, in an attempt to establish the influence of the size of that group on the thermal stability and regioselectivity of alkylation of the title anions. The conclusion is that thermal stability and the mode of reaction are affected significantly only in the presence of very large and branched carbamate groups. The thermal …

Toward Synthesizing A Selective Dopamine Binding Magnetic Resonance Contrast Agent, Judy Lau

Senior Honors Projects

Magnetic resonance imaging (MRI) is a non-invasive diagnostic methodology used to provide a two-dimensional view of an internal organ or structure, especially the brain and spinal cord. Magnetic resonance contrast agents are usually injected into necessary parts of the body prior to imaging to increase the differences between different tissues or between normal and abnormal tissue, making it easier for a radiologist or doctor to interpret the image that is taken. The development of new and more efficient, effective, and selective contrast agents for various biological processes or chemicals is a growing field of research and study. My project allowed …

Numerical Aspects Of The Saft Equation Of State, Leah M. Octavio

Senior Honors Projects

Equations of states are used to model fluid behavior. At a given temperature and pressure, for example, a mixture of water and alcohol might form a liquid and vapor phase, with the vapor phase being richer in alcohol and the liquid phase richer in water. In many industrial processes, such as distillation or extraction where mixtures of different compounds need to be separated, knowing how the fluid mixture will behave at various conditions helps make the operations more efficient and economical. While many equations of state exist, they differ in their accuracy in modeling systems and in their mathematical complexity. …

A Comparison Of The Imapct Of Environmental Stressors On Blood Parameters Of Captive Harbor Seals (Phoca Vitulina), Maura Allard

Senior Honors Projects

Little research has been established in determining blood chemistry values for harbor seals in Alaska. It has been suggested that various environmental factors can influence the blood chemistry values due to temperature, day length, precipitation, constraint and diet amongst other variables. Currently there are no guidelines for veterinarians and rehabilitators to refer to when analyzing blood chemistry values for sick animals. The hope for this research is that it will aide in establishing guidelines for specific circumstances due to environmental stressors. It is hoped that in the future, this study will be used to create values for which veterinarians can …

Generating Long-Lasting ¹H And ¹³C Hyperpolarization In Small Molecules With Parahydrogen-Induced Polarization, Thorsten Jonischkeit, Ute Bommerich, Jorg Stadler, Klaus Woelk, Heiko G. Niessen, Joachim Bargon

Chemistry Faculty Research & Creative Works

Recently, Levitt and co-workers demonstrated that conserving the population of long-lasting nuclear singlet states in weak magnetic fields can lead to a preservation of nuclear spin information over times substantially longer than governed by the (high-field) spin-lattice relaxation time T₁. Potential benefits of the prolonged spin information for magnetic resonance imaging and spectroscopy were pointed out, particularly when combined with the parahydrogen induced polarization (PHIP) methodology. In this contribution, we demonstrate that an increase of the effective relaxation time by a factor up to three is achieved experimentally, when molecules hyperpolarized by PHIP are kept in a weak …

Magnetic And Electronic Properties Of Eu₄Sr₄Ga₁₆Ge₃₀, Gerald T. Woods, Joshua B. Martin, Matthew Beekman, Raphäel P. Hermann, Fernande Grandjean, Veerle M. Keppens, Olaf Leupold, Gary J. Long, George S. Nolas

Chemistry Faculty Research & Creative Works

Magnetization, static and ac magnetic susceptibility, nuclear forward scattering, and electrical resistivity measurements have been performed on polycrystalline Eu₄Sr₄Ga₁₆Ge₃₀, a type I clathrate that has divalent strontium and europium ions encapsulated within a Ga-Ge framework. These data are compared with those of type I clathrates Eu₈Ga₁₆Ge₃₀ and Eu₆Sr₂Ga₁₆Ge₃₀. The ferromagnetic ordering of these Eu-containing clathrates is substantially altered by the incorporation of strontium, as compared to Eu₈Ga₁₆Ge₃₀. Ferromagnetism, accompanied by a relatively large …

Search For Global-Minimum Geometries Of Medium-Sized Germanium Clusters. Ii. Motif-Based Low-Lying Clusters Ge21–Ge29, S. Yoo, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

We performed a constrained search for the geometries of low-lying neutral germanium clusters GeN in the size range of 21≤N≤29. The basin-hopping global optimization method is employed for the search. The potential-energy surface is computed based on the plane-wave pseudopotential density functional theory. A new series of low-lying clusters is found on the basis of several generic structural motifs identified previously for silicon clusters [S. Yoo and X. C. Zeng, J. Chem. Phys. 124, 054304 (2006)] as well as for smaller-sized germanium clusters [S. Bulusu et al., J. Chem. Phys. 122, 164305 (2005)]. Among the generic motifs examined, …

Faithful Estimation Of Dynamics Parameters From Cpmg Relaxation Dispersion Measurements, Evgenii L. Kovrigin, James G. Kempf, Michael J. Grey, J. Patrick Loria

Chemistry Faculty Research and Publications

This work examines the robustness of fitting of parameters describing conformational exchange (k_ex, p_a/b, and Δω) processes from CPMG relaxation dispersion data. We have analyzed the equations describing conformational exchange processes for the intrinsic inter-dependence of their parameters that leads to the existence of multiple equivalent solutions, which equally satisfy the experimental data. We have used Monte-Carlo simulations and fitting to the synthetic data sets as well as the direct 3-D mapping of the parameter space of k_ex, p_a/b, and Δω to quantitatively assess …

On-Road Remote Sensing Of Automobile Emissions In The Chicago Area: Year 6, September 2004, Gary A. Bishop, Daniel A. Burgard, Donald H. Stedman

Fuel Efficiency Automobile Test Publications

No abstract provided.

On-Road Remote Sensing Of Automobile Emissions In The Denver Area: Year 5, January 2005, Gary A. Bishop, Daniel A. Burgard, Donald H. Stedman

Fuel Efficiency Automobile Test Publications

No abstract provided.

On-Road Remote Sensing Of Automobile Emissions In The Phoenix Area: Year 5, November 2004, Gary A. Bishop, Daniel A. Burgard, Donald H. Stedman

Fuel Efficiency Automobile Test Publications

No abstract provided.

Mechanisms Imposing The Vbeta Bias Of V14a Natural Killer T Cells And Consequences For Microbial Glycolipid Recognition, Paul B. Savage, Dasten G. Wei, Shane A. Curran, Luc Teyton, Albert Bendelac

Faculty Publications

Mouse and human natural killer T (NKT) cells recognize a restricted set of glycosphingolipids presented by CD1d molecules, including self iGb3 and microbial alpha-glycuronosylceramides. The importance of the canonical Valpha 14-Jalpha18 TCR alphachain for antigen recognition by NKT cells is well recognized, but the mechanisms underlying the Vbeta8, Vbeta7, and Vbeta2 bias in mouse have not been explored. To study the influences of thymic selection and the constraints of pairing with Valpha 14-Jalpha 18, we have created a population of mature T cells expressing Valpha 14-Jalpha 18 TCRalpha chain in CD1d-deficient mice and studied its recognition properties in vitro and …

Nocturnal Odd-Oxygen Budget And Its Implications For Ozone Loss In The Lower Troposphere, Steven S. Brown, J. A. Neuman, T. B. Ryerson, M. Trainer, W. P. Dubé, J. S. Holloway, C. Warneke, J. A. De Gouw, Stephen G. Donnelly Ph.D., E. Atlas, B. Matthew, A. M. Middlebrook, R. Peltier, R. J. Weber, A. Stohl, J. F. Meagher, F. C. Fehsenfeld, A. R. Ravishankara

Chemistry Faculty Publications

Nitrogen oxides are important to the regulation of ozone throughout the Earth's atmosphere. Of particular interest for regional air quality is photochemical production and nocturnal destruction Of O3 in the lower troposphere in high NOx(=NO + NO2) environments. Nocturnal tropospheric odd oxygen (Ox), defined as O3 + NO2 + 2NO3 + 3N2O5, is used to assess the impact of NOx emissions on nocturnal O3 loss. Recent aircraft measurements of the components of Ox and HNO3 yield a detailed accounting of the nocturnal Ox budget in a regionally polluted environment. The analysis demonstrates the role of NO3 and N2O5 reactions in …

Protein Structure Similarity Clustering: Dynamic Treatment Of Pdb Structures Facilitates Clustering, Bradley D. Charette, Richard G. Macdonald, Stefan Wetzel, David B. Berkowitz, Herbert Waldmann

David Berkowitz Publications

Protein structure similarity clustering (PSSC) [1]– [3] is one of a number of potential guiding principles [4], [5] that have been introduced to focus combinatorial-library design/ protein targeting. PSSC clusters protein targets with similar ligand-binding cores in which little sequence or functional similarity is evident. Lead compounds for one member of the cluster then provide novel starting points in chemical space for ligand development for other members of the PSSC.

We describe herein a new clustering procedure that lends itself to ligand docking, molecular dynamics (MD), and the vector-alignment-search-tool (VAST) [6] algorithm. This MD-assisted approach offers an alternative to the …

Dactinomycin Impairs Cellular Respiration And Reduces Accompanying Atp Formation, Zhimin Tao, Syed S. Ahmad, Harvey S. Penefsky, Jerry Goodisman, Abdul Kader Souid

Chemistry - All Scholarship

The effect of dactinomycin on cellular respiration and accompanying ATP formation was investigated in Jurkat and HL-60 cells. Cellular mitochondrial oxygen consumption (measured by a homemade phosphorescence analyzer) and ATP content (measured by the luciferin-luciferase bioluminescence system) were determined as functions of time t during continuous exposure to the drug. The rate of respiration, k, was the negative of the slope of [O2] versus t. Oxygen consumption and ATP content were diminished by cyanide, confirming that both processes involved oxidations in the mitochondrial respiratory chain. In the presence of dactinomycin, k decreased gradually with t, the decrease being more pronounced …

Identification Of The Binding Region Of The [2fe-2s] Ferredoxin In Stearoyl-Acyl Carrier Protein Desaturase: Insight Into The Catalytic Complex And Mechanism Of Action, Pablo Sobrado, Karen S. Lyle, Steven P. Kaul, Michelle M. Turco, Ida Arabshahi, Ashok Marwah, Brian G. Fox

Chemistry Faculty Research & Creative Works

Stearoyl-acyl carrier protein desaturase (Δ9D) catalyzes the O 2 and 2e- dependent desaturation of stearoyl-acyl carrier protein (18:0-ACP) to yield oleoyl-ACP (18:1-ACP). The 2e- are provided by essential interactions with reduced plant-type [2Fe-2S] ferredoxin (Fd). We have investigated the protein-protein interface involved in the Fd-Δ9D complex by the use of chemical cross-linking, site-directed mutagenesis, steady-state kinetic approaches, and molecular docking studies. The treatment of the different proteins with 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide and N-hydroxy succinimide revealed that carboxylate residues from Fd and lysine residues from Δ9D contribute to cross-linking. The single substitutions of K60A, K56A, and K230A on Δ9D decreased the k …

Immobilization Of Fission Iodine By Reaction With A Fullerene Containing Carbon Compound And Insoluble Natural Organic Matrix: Quaterly Report January-March 2006, Spencer M. Steinberg

Separations Campaign (TRP)

Project Highlights:

• Established that iodide can be oxidized by MnO₂ to I₂ at pHs of 4-8 and moderate temperature.

• Demonstrated that p-hydroxybenzoic acid can be iodinated by MnO₂ and KI at pHs of 2-8.

• Established that humic acids can be iodinated by MnO₂ and iodide at room temperature in pH range of 4-8.

Gas-Phase Products And Secondary Aerosol Yields From The Ozonolysis Of Ten Different Terpenes, Anita Lee, Allen H. Goldstein, Melita D. Keywood, Song Gao, Varuntida Varutbangkul, Roya Bahreini, Nga L. Ng, Richard C. Flagan, John H. Seinfeld

Chemistry and Physics Faculty Articles

The ozonolyses of six monoterpenes (α-pinene, β-pinene, 3-carene, terpinolene, α-terpinene, and myrcene), two sesquiterpenes (α-humulene and β-caryophyllene), and two oxygenated terpenes (methyl chavicol and linalool) were conducted individually in Teflon chambers to examine the gas-phase oxidation product and secondary organic aerosol (SOA) yields from these reactions. Particle size distribution and number concentration were monitored and allowed for the calculation of the SOA yield from each experiment, which ranged from 1 to 54%. A proton transfer reaction mass spectrometer (PTR-MS) was used to monitor the evolution of gas-phase products, identified by their mass to charge ratio (m/z). …

9-Ethyl-3-(9h-9-Ethyl­Carbazol-3-Yl)-4-Nitro­-9h-Carbazole, Erol Asker, John Masnovi

Chemistry Faculty Publications

In the mol­ecule of the title compound, C₂₈H₂₃N₃O₂, the nitro group is almost perpendicular to the carbazole ring to which it is attached. The crystal packing is determined by C—H⋯O and π–π inter­actions, where the nitrated carbazole ring of one mol­ecule associates in a shifted parallel planar orientation with the centrosymmetrically related non-nitrated carbazole ring of a neighbouring mol­ecule.

Bis(9-Ethyl­Carbazol-3-Yl)Ethane, Erol Asker, John Masnovi

Chemistry Faculty Publications

In the title compound, C₃₀H₂₈N₂, each carbazole skeleton is essentially planar. The planes of the two carbazole ring systems are nearly parallel, with a dihedral angle of 2.33 (19)°. The crystal packing is stabilized only by van der Waals forces and weak C—H⋯π inter­actions.

Erratum: "Hard Sphere Radial Distribution Function Again", Andrij Trokhymchuk, Douglas Henderson, Ivo Nezbeda, Jan Jirsak

Faculty Publications

Some misprints have been found for parameters given by Eqs. 29 and 30 and the relevant equations in the Appendix.

Two New Resorcinarenes: A Pyridine & Acetic Acid Ligand For Metal Coordination And A Deep-Cavity Nitroquinoxaline Resorcinarene, Samantha Sizemore Vernetti

Theses and Dissertations

Functionalizing the upper rim of resorcinarene-based cavitands allows a variety of compounds to be synthesized from a single scaffold. Using the upper-rim moieties as ligands for a variety of transition metal ions further increases the versatility of this class of host compounds. A new resorcinarene-based molecule functionalized with four pyridine and acetic acid ligands has been successfully prepared to explore the properties of metal-assembled complexes. To synthesize this compound, tetra(bromomethyl)cavitand was reacted with N-(2-pyridylmethyl)-N-ethylacetate amine to give ethyl acetate pyridine resorcinarene. Hydrolysis of the ester gave acetic acid pyridine resorcinarene (APRes) in good yield. Complexes with Cu2+, Co2+, and Zn2+ …

2nd Annual Undergraduate Research Conference Abstract Book, University Of Missouri--Rolla

Undergraduate Research Conference at Missouri S&T

No abstract provided.

Chemo-Enzymatic Route To Synthesis Of Biodegradable Polymers And Glycolipid Analogs, Surbhi Bhatt

USF Tampa Graduate Theses and Dissertations

New catalytic synthetic methods in organic chemistry that satisfy increasingly stringent environmental constraints are in great demand by the pharmaceutical and chemical industries. Studies over last 15 years have revealed that activity of enzymes can be increased in organic solvents rather than their natural aqueous environment. Because of their ease of use, high selectivity and environment friendliness, enzymes are enjoying increasing popularity in today's synthesis world.

Chapter 1 describes chemo-enzymatic synthesis of various glycolipid analogs. A highly regioselective macrolactonization was achieved using lipase from Candida antarctica as a catalyst. It also describes evaluation of lipases from different source and their …

Α-Vinylic Amino Acids: Occurrence, Asymmetric Synthesis, And Biochemical Mechanisms, David B. Berkowitz, Bradley D. Charette, Kannan Karukurichi, Jill M. Mcfadden

David Berkowitz Publications

This report presents an overview of the family of naturally occurring “vinylic” amino acids, namely those that feature a C–C double bond directly attached to the α-carbon, along the side chain. Strategies that have been brought to bear on the stereo-controlled synthesis of these olefinic amino acids are surveyed. The mechanistic diversity by which such “vinylic triggers” can be actuated in a PLP (pyridoxal phosphate) enzyme active site is then highlighted by discussion of vinylglycine (VG), its substituted congeners, particularly AVG [4E-(2′-aminoethoxy)vinylglycine], and a naturally occurring VG-progenitor, SMM [(S)-methylmethionine].

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

Chemistry & Biochemistry Newsletter: 2002-2015

Inside:

Page 2-4 Campus Mass Spectrometry Facility

Page 4 Alumni News

Page 5 Alum Featured; Scholarships and Awards

Page 6 Two New Departmental Scholarships; Recent Faculty Publications; Funding

Page 7 2006 Chemistry and Biochemistry Graduates