Chemistry Commons^™

The Laplacian In Spherical Polar Coordinates, Carl W. David

Chemistry Education Materials

The transformation between Cartesian and Spherical Polar coordinates of the Laplacian is carried out analytically, including two different Maple implementations of the same transformation.

Cost-Effective Engineering Of A Small-Scale Bioreactor, John Tansey, Sadie R. Bartholomew

Chemistry Faculty Scholarship

Several methods exist for increasing the scale of cell culture in the laboratory. While these methods provide significant increases in biomass, they are often prohibitively expensive for many laboratories. We have engineered a small-scale bioreactor with a novel means of introducing oxygen through the catalytic breakdown of hydrogen peroxide using a manganese oxide catalyst. We have also adapted and modified an existing assay for dissolved oxygen to be compatible with culture conditions. In this system we have been able to culture CHO cells at densities of up to 10⁷ cells/mL without the use of automated feedback systems.

Review: A Creationist Review And Preliminary Analysis Of The History, Geology, Climate, And Biology Of The Galápagos Islands, Timothy R. Brophy

Faculty Publications and Presentations

No abstract provided.

Replica Exchange With Dynamical Scaling, Steven W. Rick

Chemistry Faculty Publications

A replica exchange method is presented which requires fewer replicas and is designed to be used for large systems. In this method, dynamically scaled replicas are placed between conventional replicas at broadly spaced temperatures. The potential of the scaled replicas is linearly scaled by a dynamicalvariable which varies between 0 and 1. When the variable is near either end point the replica can undergo exchanges with one of its neighboring replicas. Two different versions of the method are presented for a model system of a small peptide in water. The scaled replica can replace manyreplicas and the method can be …

Density Matrix, Ronald Lovett

Topics in Quantum Mechanics

No abstract provided.

Investigation Of Auni5 Films Deposited By Laser Ablation For Rf Mems Switches, Noha Sameh Ahmed Farghal

Archived Theses and Dissertations

No abstract provided.

Effect Of Surrounding Point Charges On The Density Functional Calculations Of NiXOX Clusters (X = 4–12), Evgueni B. Kadossov, Karen J. Gaskell, Marjorie Langell

Marjorie A. Langell Publications

Embedded Ni_xO_x clusters (x = 4–12) have been studied by the density-functional method using compensating point charges of variable magnitude to calculate the ionic charge, bulk modulus, and lattice binding energy. The computations were found to be strongly dependent on the value of the surrounding point charge array and an optimum value could be found by choosing the point charge to reproduce the experimentally observed Ni–O lattice parameter. This simple, empirical method yields a good match between computed and experimental data, and even small variation from the optimum point charge value produces significant deviation between computed …

Fragmentation Of Methyl Chloride Studied By Partial Positive And Negative Ion Yield Spectroscopy, D. Ceolin, Maria Novella Piancastelli, Renaud Guillemin, Wayne C. Stolte, S-W Yu, Oliver Hemmers, Dennis W. Lindle

Environmental Studies Faculty Publications

The authors present partial-ion-yield experiments on the methyl chloride molecule excited in the vicinity of the Cl2p and C1s inner shells. A large number of fragments, cations produced by dissociation or recombination processes, as well as anionic species, have been detected. Although the spectra exhibit different intensity distributions depending on the core-excited atom, general observations include strong site-selective fragmentation along the C–Cl bond axis and a strong intensity dependence of transitions involving Rydberg series on fragment size.

Basic Research Needs For Geosciences: Facilitating 21st Century Energy Systems, U.S. Department Of Energy, Office Of Basic Energy Sciences, Donald J. Depaolo, Franklin M. Orr Jr.

Publications (YM)

Executive Summary

Serious challenges must be faced in this century as the world seeks to meet global energy needs and at the same time reduce emissions of greenhouse gases to the atmosphere. Even with a growing energy supply from alternative sources, fossil carbon resources will remain in heavy use and will generate large volumes of carbon dioxide (CO₂). To reduce the atmospheric impact of this fossil energy use, it is necessary to capture and sequester a substantial fraction of the produced CO₂. Subsurface geologic formations offer a potential location for long-term storage of the requisite large …

The Structure And Function Of Small Nucleolar Ribonucleoproteins, Steve Reichow, Tomoko Hamma, Adrian R. Ferré-D’Amaré, Gabriele Varani

Chemistry Faculty Publications and Presentations

Eukaryotes and archaea use two sets of specialized ribonucleoproteins (RNPs) to carry out sequencespecific methylation and pseudouridylation of RNA, the two most abundant types of modifications of cellular RNAs. In eukaryotes, these protein–RNA complexes localize to the nucleolus and are called small nucleolar RNPs (snoRNPs), while in archaea they are known as small RNPs (sRNP). The C/D class of sno(s)RNPs carries out ribose- 20-O-methylation, while the H/ACA class is responsible for pseudouridylation of their RNA targets. Here, we review the recent advances in the structure, assembly and function of the conserved C/D and H/ACA sno(s)RNPs. Structures of each of the …

Development Of Enzymatic Biofuel Cell Based On Carbon Nanotube Electrodes On Porous Silicon, Fan Yang

Theses

The work presented in this thesis has focused on designing and characterizing biofuel cell electrodes using porous silicon (p-Si) as the substrate or current collecting platform on which carbon nanotubes (CNTs), both single-walled carbon nanotubes (SWNTs) and multi-walled carbon nanotubes (MiWNTs), were synthesized directly, followed by enzyme catalyst immobilization on the CNTs. Laccase and glucose oxidase (GOx) were used as enzymatic biocatalysts, which were immobilized on the CNT walls and tips using an electrochemical technique. Cyclic voltammetry showed well-defined redox peaks which indicated that the enzyme (GOx and laccase) were successfully immobilized on the CNTs. The amperometric responses of the …

Catalytic Cleavage Of Phosphate Ester Bonds By Boron Chelates, David A. Atwood

Chemistry Faculty Patents

Novel chemical compounds are disclosed having the general formula L{YX_m}_n, wherein X is selected from the Group 13 elements, Y is a halide, and L is a chelating ligand containing at least one binding atom contacting the Group 13 element, the atom being selected from the group consisting of C, N, O, and S, and m and n are integers having a value of at least 1. L may be a Schiff base type ligand, such as a salen ligand. The compositions of the present invention may be bidentate, quadridentate, or greater. The compositions may be …

High-Resolution Structure Of A Beta-Peptide Bundle, Douglas S. Daniels, E. James Petersson, Jade X. Qiu, Alanna S. Schepartz

Chemistry Faculty Publications

We recently reported that β-peptides can form discrete hetero-oligomers in aqueous solution. Here we describe the structure of such an oligomer as determined by X-ray crystallography. The structure of Zwit-1F reveals a homo-octamer of two cupped “hands” composed of both parallel and antiparallel 314-helices. The core of the assembly is composed entirely of solvent-excluded β3-homoleucine residues. The Zwit-1F assembly shares many of the physical characteristics of natural proteins.

Examination Of The New Α-(2′Z-Fluoro)Vinyl Trigger With Lysine Decarboxylase: The Absolute Stereochemistry Dictates The Reaction Course, Kannan R. Karukurichi, Roberto De La Salud-Bea, Wan Jin Jahng, David B. Berkowitz

David Berkowitz Publications

The first examination of a terminal α-fluorovinyl trigger in an amino acid decarboxylase active site is reported. To investigate the enantiospecifity of inactivation with this new AADC trigger, an enantioselective synthesis of L-α-(2′Z-fluoro)vinyllysine and its D-antipode has been developed. Control of stereochemistry is achieved through introduction of the amino acid side chain via alkylation of a chiral vinylglycine-derived dienolate. Facial selectivity is conferred by a trans-2′(β- naphthyl)-2′-propylcyclohexyl ester auxiliary, available in both antipodal forms (Comins protocol). The alkylation employs a new electrophile, N-p-methoxybenzyl-N-(2′- trimethylsilylethanesulfonyl)-4-iodobutylamine, for convergent installation of the lysine side chain. Vinyl to 2′-fluorovinyl interconversion then provides L- …

Rank-Ordering Protein-Ligand Binding Affinity By A Quantum Mechanics/ Molecular Mechanics/Poisson-Boltzmann-Surface Area Model, Mingliang Wang, Chung Wong

Chemistry & Biochemistry Faculty Works

The authors describe a quantum mechanics/molecular mechanics/Poisson-Boltzmann-surface area model for rank-ordering protein-ligand binding affinity in aqueous solution. Unlike many classical continuum electrostatics calculations in which the protein and ligand are treated as a uniform dielectric, this model uses quantum mechanics to explicitly describe the electronic polarization of the ligand by its environment. In solving the Poisson-Boltzmann equation, the authors use the quantum mechanical charge density directly rather than the common point-charge approximation. The authors show that useful results can be obtained by using experimental structure, by choosing a protein dielectric constant that is smaller than that typically used in classical …

Catena-Poly[[Diaquadinitratozinc(Ii)]Bis(Μ-1,4-Di-3-Pyridyl-2,3-Diaza-1,3-Butadiene)], Shakoya Paulin, Pierre Kelly, Kenneth B. Williams, Andrea M. Goforth, Mark D. Smith, Leroy Peterson Jr., Hans-Conrad Zur Loye

Faculty Publications

The polymeric title complex, [Zn(NO₃)₂(C₂₄H₂₀N₈)(H₂O)₂]_n, features distorted ZnN₂O₄ octahedra with each Zn^II atom being located on an inversion center. Adjacent Zn ions are doubly bridged by two equivalent 1,4-di-3-pyridyl-2,3-diaza-1,3-butadiene ligands to form linear chains.

Catena-Poly[[Bis(Α-Thenoyltrifluoroacetonato-Κ2O,O')Copper(Ii)]-Μ-1,4-Di-3-Pyridyl-2,3-Diaza-1,3-Butadiene-Κ2N:N'], William J. Perkins, Tamar Maxwell, Ken B. Williams, Andrea M. Goforth, Mark D. Smith, Leroy Peterson Jr., Hans-Conrad Zur Loye

Faculty Publications

The title compound, [Cu(C₈H₄F₃O₂S)₂(C₁₂H₁₀N₄)]_n or [Cu(tta)₂(L2)₂]_n (L2 = 1,4-di-3-pyridyl-2,3-diaza-1,3-butadiene and tta = -thenoyltrifluoroacetonate), consists of undulating chains containing two crystallographically distinct Cu^II centers that are each located on inversion centers. Each Cu^II center exhibits distorted octahedral coordination provided by two pyridyl N atoms from two equivalent L2 ligands and four O atoms from two equivalent tta ligands. The chains interact through weak C-FH-C contacts.

Water Borne Film-Forming Compositions, Michael R. Van-De-Mark, Nantana Jiratumnukul

Chemistry Faculty Research & Creative Works

The present invention provides a film-forming composition comprising a particulate polymer or emulsified liquid prepolymer, water and a coalescent aid comprising an ester having the formula RCOOX wherein R and X are independently hydrocarbyl or substituted hydrocarbyl, and at least one of R and X contain at least two unsaturated carbon— carbon bonds. The coalescent aid helps lower the minimum film formation temperature of low glass transition temperature coatings and high glass transition temperature coatings and allows optimum film formation at ambient temperatures. The coalescent aid of this coating composition is not volatile like conventional coalescent aids but rather remains …

Searching For Smart Durable Coatings To Promote Bone Marrow Stromal Cell Growth While Preventing Biofilm Formation, Fereydoon Namavar, John D. Jackson, J. Graham Sharp, Ethan E. Mann, Kenneth W. Bayles, Chin Li Cheung, Connie A. Feschuk, Shailaja Varma, Hani Haider, Kevin L. Garvin

Barry Chin Li Cheung Publications

There is a great need to develop methods to regulate cellular growth in order to enhance or prevent cell proliferation, as needed, to either improve health or prevent disease. In this work we evaluated the adhesion, survival and growth of bone marrow stromal cells on the surface of several new ion beam engineered nano-crystals of ceramic hard coatings such as zirconium, titanium, tantalum and cerium oxides. Cell adhesion and growth on the ceramic coatings were compared to adhesion and growth on a nano-crystalline silver coating which is known to possess antibacterial properties. The initial results of a study to determine …

13C Nmr Analysis Of Biologically Produced Pyrene Residues By Mycobacterium Sp. Kms In The Presence Of Humic Acid, J. Karl C. Nieman, Richard C. Holz, Ronald C. Sims

Chemistry Faculty Research and Publications

Cultures of the pyrene degrading Mycobacterium sp. KMS were incubated with [4-¹³C]pyrene or [4,5,9,10-¹⁴C]pyrene with and without a soil humic acid standard to characterize the chemical nature of the produced residues and evaluate the potential for bonding reactions with humic acid. Cultures were subjected to a “humic acid/humin” separation at acidic pH, a duplicate separation followed by solvent extraction of the humic acid/humin fraction, and a high pH separation. ¹³C NMR analysis was conducted on the resulting solid extracts. Results indicated that the activity associated with solid extracts did not depend on pH and that …

Intellectual Property Management In Health And Agricultural Innovation: A Handbook Of Best Practices, Vol. 2, Anatole Krattiger, Richard T. Mahoney, Lita Nelsen, Jennifer A. Thomson, Alan B. Bennett, Kanikaram Satyanarayana, Gregory D. Graff, Carlos Fernandez, Stanley Kowalski

Law Faculty Scholarship

Prepared by and for policy-makers, leaders of public sector research establishments, technology transfer professionals, licensing executives, and scientists, this online resource offers up-to-date information and strategies for utilizing the power of both intellectual property and the public domain. Emphasis is placed on advancing innovation in health and agriculture, though many of the principles outlined here are broadly applicable across technology fields. Eschewing ideological debates and general proclamations, the authors always keep their eye on the practical side of IP management. The site is based on a comprehensive Handbook and Executive Guide that provide substantive discussions and analysis of the opportunities …

Apparatus And Method For Growing Crystal, And Apparatus And Method For Analyzing Crystal: United States Patent No. 7,156,917 B2, Hideaki Moriyama, Norio Sugi, Kazunori Kawasaki, Shoji Muramatsu

Hideaki Moriyama Publications

An apparatus for growing a biological macromolecular crystal by vaporizing biological macromolecular solution into an oversaturated state. The apparatus includes a first sealed room that receives first crystallizing agent solution, and a communicating tube that communicates with the first sealed room and has a small sectional area for suppressing convection of air. A plurality of droplets of solution dissolving a biological macromolecule and a crystallizing agent therein are held in the communicating tube with the plurality of droplets being separated from each other.

Synthesis And X-Ray Crystal Structure Of [(C5ph5)Crcl(Μ-Cl)2tl]2: An Example Of The Rare M-X-Tli Linkage (X = Halide), K. Brian Davis, T. David Harris, Michael Castellani, James A. Golen, Arnold L. Rheingold

Chemistry Faculty Research

Reaction of solid TlCl with [(C5Ph5)CrCl(m-Cl)]2 in CH2Cl2 solvent yields the monomeric complex (C5Ph5)CrCl(m-Cl)2Tl in 80% isolated yield. The C5H5 and C5Me5 analogues do not react with TlCl suggesting a steric basis for the reaction of the C5Ph5 material. An X-ray crystal structure of [(C5Ph5)CrCl(m-Cl)2Tl]2•2CH2Cl2 was obtained.

Selective Synthesis Of Oxacalix[6]Arenes And Mixed Oxacalix[4]Arenes, Christian Crannell

Undergraduate Research Symposium (UGRS)

Calixarenesare macrocycles composed of benzene rings meta linked to each other by one carbon atom. These exotic compounds can be used for a variety of purposes including metalleaching for environmental cleanup, surface technology, luminescent probes, nuclear waste treatment, among others. A variety of calixarenesexist, including azacalix[n]arenesthiocalix[n]arenes(where n = the number of benzene rings) and oxacalix[n]arenes; these macrocycles use nitrogen, sulfur and oxygen, respectively, as the atom whichlinks the benzene rings together. My research has focused on synthesizing oxacalix[6]arenes (“hexamer”) in high yield, which is a synthetic challenge because it is generally accepted that oxacalix[n>4]arenes will thermodynamically decompose to the …

Investigating The Spring Bloom In San Francisco Bay: Links Between Water Chemistry, Metal Cycling, Mercury Speciation, And Phytoplankton Community Composition, Allison C. Luengen

Environmental Science

Investigating the spring bloom in San Francisco Bay: Links between water chemistry, metal cycling, mercury speciation, and phytoplankton community composition This dissertation addresses the relationship between two problems facing estuaries nationwide: nutrient enrichment and metal contamination. The focus is on the southern reach of San Francisco Bay, where high nutrient concentrations can control the magnitude of the predictably occurring spring phytoplankton bloom. The bloom in this study, in spring 2003, was one of the largest blooms on record, exceeding 150 μg L ^-1 of chlorophyll α. As the bloom grew, diatoms (e.g. Thalassiosira punctigera ) depleted dissolved nutrients from the …

The Visual Image Of Chemistry: Perspectives From The History Of Art And Science, Joachim Schummer, Tami I. Spector

Chemistry Faculty Publications

In this paper we investigate the most important visual stereotypes of chemistry as they occur in current portraits of chemists, depictions of chemical plants, and images of chemical glassware and apparatus. By studying the historical origin and development of these stereotypes within the broader context of the history of art and science, and by applying aesthetic and cultural theories, we explore what these images implicitly communicate about the chemical profession to the public. We conclude that chemists, along with commercial artists, have unknowingly created a visual image of chemistry that frequently conveys negative historical associations, ranging from imposture to kitsch. …

Sol-Gel Technology In Enhancing The Filtration Of Semi-Volatile Organic Compounds, David T. Nguyen, Jennie Ash, Chastity Ellison

The Corinthian

For the past several years, the field of sol-gel technology has undergone remarkable growth in areas ranging from micro-fibers to chemical sensors. Incorporating an organic phase into the colloidal mixture via pre- or post-doping can modify sol-gels, and manipulation of the size of the pores can be used in developing 'eco-friendly' water filters, particularly for filtering semi-volatile organic compounds in water. In this research project, various forms of sol-gels were made to see which is more efficient for certain semi-volatile chemicals that can be found in diverse sources of water. Organically modified silicates and different structurally sound sol-gels were made …

Purification And Study Of Phosphoglucose Isomerase In Cauliflower, Shanti Shrestha

Capstone Research Projects

Phosphoglucose isomerase (PGI), an important enzyme in the glycolytic pathway, catalyzes the conversion of glucose-6-phosphate to fructose-6-phosphate and vice versa. The purpose of this research was to isolate PGI from cauliflower using a shortened procedure through column chromatography and characterize it through absorbance readings, enzyme activity measurements, and SDS-PAGE (sodium dodecyl sulfate-polyacrylamide gel electrophoresis). PGI was successfully isolated from cauliflower using ion-exchange chromatography. Absorbance and enzyme activity were determined at 280nm and 340nm respectively. There appeared to be one main absorbance peak for the protein at fraction 31, as well as a maximum peak for enzyme activity. SDS-PAGE was conducted …

Intellectual Property Management In Health And Agricultural Innovation: Executive Guide, Anatole Krattiger, Richard T. Mahoney, Lita Nelsen, Jennifer A. Thomson, Alan B. Bennett, Kanikaram Satyanarayana, Gregory D. Graff, Carlos Fernandez, Stanley Kowalski

Law Faculty Scholarship

Prepared by and for policy-makers, leaders of public sector research establishments, technology transfer professionals, licensing executives, and scientists, this online resource offers up-to-date information and strategies for utilizing the power of both intellectual property and the public domain. Emphasis is placed on advancing innovation in health and agriculture, though many of the principles outlined here are broadly applicable across technology fields. Eschewing ideological debates and general proclamations, the authors always keep their eye on the practical side of IP management. The site is based on a comprehensive Handbook and Executive Guide that provide substantive discussions and analysis of the opportunities …

Intellectual Property Management In Health And Agricultural Innovation: A Handbook Of Best Practices, Vol. 1, Anatole Krattiger, Richard T. Mahoney, Lita Nelsen, Jennifer A. Thomson, Alan B. Bennett, Kanikaram Satyanarayana, Gregory D. Graff, Carlos Fernandez, Stanley Kowalski

Law Faculty Scholarship

Prepared by and for policy-makers, leaders of public sector research establishments, technology transfer professionals, licensing executives, and scientists, this online resource offers up-to-date information and strategies for utilizing the power of both intellectual property and the public domain. Emphasis is placed on advancing innovation in health and agriculture, though many of the principles outlined here are broadly applicable across technology fields. Eschewing ideological debates and general proclamations, the authors always keep their eye on the practical side of IP management. The site is based on a comprehensive Handbook and Executive Guide that provide substantive discussions and analysis of the opportunities …