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Chemistry Faculty Publications

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Articles 931 - 960 of 1129

Full-Text Articles in Chemistry

Thickness Dependence Of Magneto-Transport In Cu-Co Granular Thin Films, Scott Whittenburg Jun 2004

Thickness Dependence Of Magneto-Transport In Cu-Co Granular Thin Films, Scott Whittenburg

Chemistry Faculty Publications

This work explores the thickness dependence of magneto-transport properties in Cu80Co20 granular thin films with different thickness. These results are compared with silver-based film series studied earlier. It was observed that the thickness dependence of the GMR effect was sensitive to the surface chemistry of the films. The extraordinary Hall effect (EHE) in these films was measured and found to be different from the Ag-based system. In the Cu-based system, the EHE is a weak function of film thickness over the range studied. When the variation of the spontaneous magnetization is taken into account the effective EHE has a universal …

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Evaluating The Contributions Of Desolvation And Base-Stacking During Translesion Dna Synthesis, Xuemei Zhang, Irene Lee, Anthony J. Berdis May 2004

Evaluating The Contributions Of Desolvation And Base-Stacking During Translesion Dna Synthesis, Xuemei Zhang, Irene Lee, Anthony J. Berdis

Chemistry Faculty Publications

DNA polymerases catalyze the insertion of a nucleoside triphosphate into the growing polymer chain using the template strand as a guide. Numerous factors such as hydrogen bonding interactions, base-stacking contributions, and desolvation play important roles in controlling the efficiency and fidelity of this process. We previously demonstrated that 5-nitro-indolyl-2′-deoxyriboside triphosphate, a non-natural nucleobase with enhanced base-stacking properties, was more efficiently inserted opposite a non-templating DNA lesion compared to natural templating nucleobases (E. Z. Reineks and A. J. Berdis, Biochemistry, 2004, 43, 393–404). The catalytic enhancement was proposed to reflect increased base-stacking interactions of the non-natural nucleobase with the polymerase and …

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Measurement Of The Anticancer Agent Gemcitabine And Its Deaminated Metabolite At Low Concentrations In Human Plasma By Liquid Chromatography-Mass Spectrometry, Yan Xu, Bruce Keith, Jean L. Grem Apr 2004

Measurement Of The Anticancer Agent Gemcitabine And Its Deaminated Metabolite At Low Concentrations In Human Plasma By Liquid Chromatography-Mass Spectrometry, Yan Xu, Bruce Keith, Jean L. Grem

Chemistry Faculty Publications

A liquid chromatography/mass spectrometry (LC-MS) method has been developed and validated for the determination of the anticancer agent gemcitabine (dFdC) and its metabolite 2′,2′-difluoro-2′-deoxyuridine (dFdU) in human plasma. An Oasis® HLB solid phase extraction cartridge was used for plasma sample preparation. Separation of the analytes was achieved with a YMC ODS-AQ (5 μm, 120 Å, mm) column. The initial composition of the mobile phase was 2% methanol/98% 5 mM ammonium acetate at pH 6.8 (v/v), and the flow rate was 0.2 ml/min. An isocratic gradient was used for 3 min, followed by a linear gradient over 4 min to 30% …

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Sensing Of Aqueous Phosphates By Polymers With Dual Modes Of Signal Transduction, Dmitry Aldakov, Pavel Anzenbacher Jr. Apr 2004

Sensing Of Aqueous Phosphates By Polymers With Dual Modes Of Signal Transduction, Dmitry Aldakov, Pavel Anzenbacher Jr.

Chemistry Faculty Publications

A new approach to sensing of aqueous phosphate-related anions based on chromogenic conductive polymers is demonstrated. This method utilizes synergy between low-level p-doping in a polythiophene polymer and hydrogen bonding to increase anion-sensor affinity. These chromogenic conductive polymers show anion-specific changes both in color and in conductivity upon increasing concentration of anions, thus providing two independent modes of signal transduction.

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A Reoptimization Of The Five-Site Water Potential (Tip5p) For Use With Ewald Sums, Steven W. Rick Apr 2004

A Reoptimization Of The Five-Site Water Potential (Tip5p) For Use With Ewald Sums, Steven W. Rick

Chemistry Faculty Publications

The five-site transferable interaction potential (TIP5P) for water [M. W. Mahoney and W. L. Jorgensen, J. Chem. Phys. 112, 8910 (2000)] is most accurate at reproducing experimental data when used with a simple spherical cutoff for the long-ranged electrostatic interactions. When used with other methods for treating long-ranged interactions, the model is considerably less accurate. With small modifications, a new TIP5P-like potential can be made which is very accurate for liquid water when used with Ewald sums, a more physical and increasingly more commonly used method for treating long-ranged electrostatic interactions. The new model demonstrates a density maximum near 4 …

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Red−Green−Blue Emission From Tris(5-Aryl-8-Quinolinolate)Al(Iii) Complexes, Radek Pohl, Victor A. Montes, Joseph Shinar, Pavel Anzenbacher Jr. Mar 2004

Red−Green−Blue Emission From Tris(5-Aryl-8-Quinolinolate)Al(Iii) Complexes, Radek Pohl, Victor A. Montes, Joseph Shinar, Pavel Anzenbacher Jr.

Chemistry Faculty Publications

A simple yet effective strategy for synthesis of 5-aryl-8-quinolinolate-based electroluminophores with tunable emission wavelengths is presented. Two different pathways for the attachment of electron-donating or electron-withdrawing aryl groups to the 5-position of the quinolinolate ligand via Suzuki coupling were developed. A successful tuning in the emission color was achieved: the emission wavelength was found to correlate with the Hammett constant of the respective substituents, providing a powerful strategy for prediction of the optical properties of new electroluminophores.

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New Magnetic Materials Obtained By Ion-Exchange Reactions From Non-Magnetic Layered Perovskites, H Kageyama, L Viciu, Gabriel Caruntu, Y Ueda, John B. Wiley Mar 2004

New Magnetic Materials Obtained By Ion-Exchange Reactions From Non-Magnetic Layered Perovskites, H Kageyama, L Viciu, Gabriel Caruntu, Y Ueda, John B. Wiley

Chemistry Faculty Publications

New layered magnetic materials, (MCl)Ca2Ta3O10 (M = Cu, Fe), have been prepared by ion-exchange reactions of non-magnetic perovskite derivatives, ACa2Ta3O10 (A = Rb, Li), in corresponding anhydrous molten salts. Powder x-ray diffraction patterns of the products are successfully indexed assuming tetragonal symmetry with cell dimensions a = 3.829 Å and c = 15.533 Å for Cu, and a = 3.822 Å and c = 15.672 Å for Fe. Being separated by the Ca2Ta3O10 triple-layer perovskite slabs, the transition-metal chloride (MCl) network provides a two-dimensional magnetic lattice. Magnetic susceptibility measurements …

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The Contribution Of Amino Acid Region Asp695-Tyr698 Of Factor V To Procofactor Activation And Factor Va Function, Daniel O. Beck, Michael A. Bukys, Lisam S. Singh, Katalin A. Szabo, Michael Kalafatis Jan 2004

The Contribution Of Amino Acid Region Asp695-Tyr698 Of Factor V To Procofactor Activation And Factor Va Function, Daniel O. Beck, Michael A. Bukys, Lisam S. Singh, Katalin A. Szabo, Michael Kalafatis

Chemistry Faculty Publications

There is strong evidence that a functionally important cluster of amino acids is located on the COOH-terminal portion of the heavy chain of factor Va, between amino acid residues 680 and 709. To ascertain the importance of this region for cofactor activity, we have synthesized five overlapping peptides representing this amino acid stretch (10 amino acids each, HC1-HC5) and tested them for inhibition of prothrombinase assembly and function. Two peptides, HC3 (spanning amino acid region 690-699) and HC4 (containing amino acid residues 695-704), were found to be potent inhibitors of prothrombinase activity with IC(50) values of approximately 12 and approximately …

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Gated Electron Transfer As A Probe Of The Configurational Dynamics Of Peptide−Protein Complexes, Liu Liu, Jing Hong, Michael Y. Ogawa Jan 2004

Gated Electron Transfer As A Probe Of The Configurational Dynamics Of Peptide−Protein Complexes, Liu Liu, Jing Hong, Michael Y. Ogawa

Chemistry Faculty Publications

Gated electron-transfer measurements are used to probe the configurational dynamics of complexes formed between small metallopeptides and cytochrome c. The results show that that an apparently subtle chemical alteration of the metallopeptide produces significant changes to the dynamics of the peptide−protein complex.

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Characterization Of Drawn And Undrawn Poly-L-Lactide Films By Differential Scanning Calorimetry, John F. Turner Ii, A. Riga, Anne O'Connor, Jing Zhang, Jennifer Collis Jan 2004

Characterization Of Drawn And Undrawn Poly-L-Lactide Films By Differential Scanning Calorimetry, John F. Turner Ii, A. Riga, Anne O'Connor, Jing Zhang, Jennifer Collis

Chemistry Faculty Publications

Poly-L-lactic acid (PLLA) is an optically active, biocompatible and biodegradable polymer that has been widely investigated as an artificial cell scaffold material. In its most crystalline form, PLLA is highly anisotropic and is one of the most piezoelectric polymers known. Conversely, amorphous PLLA exhibits little, if any, piezoelectric behavior. Compression molded PLLA films can be endowed with varying amounts of crystalline character and piezoelectricity by uniaxially stretching the polymer in a hot air bath. Understanding the precise crystalline architecture of PLLA that results from tensile drawing is important for constructing cell scaffolds that have highly tailored biodegradation and cell guiding …

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Evaluation Of A Simple Carrier Molecule To Enhance Drug Penetration Of Dermal Layers By Utilizing Multivariate Methods, Structure Property Correlations, And Continuous System Modeling, Ronald Bartzatt Jan 2004

Evaluation Of A Simple Carrier Molecule To Enhance Drug Penetration Of Dermal Layers By Utilizing Multivariate Methods, Structure Property Correlations, And Continuous System Modeling, Ronald Bartzatt

Chemistry Faculty Publications

Nicotinic acid is shown to be comparable to dihydropyridine in its capacity to facilitate penetration of an attached antibacterial drug through dermal layers. Antibacterial drugs examined with nicotinic acid or dihydropyridine carriers were b-lactam antibiotics: methicillin, oxacillin, benzylpenicillin, penicillin F, penicillin dihydro F, propicillin, carbenicillin, penicillin K, penicillin X, and ampicillin. An oxymethyl (-O-CH2-) group is inserted as the linker between the antibiotic and the carrier group. Structure Property Correlations and multivariate methods such as regression analysis, cluster analysis, principal component analysis, discriminate analysis, self-organizing tree algorithm, and factor analysis clearly showed that nicotinic acid performs as an effective carrier …

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Determination Of Crystalline Content Gradients In Cold-Drawn Poly-L-Lactic Acid Films By Dsc, Anne O'Connor, A. Riga, John F. Turner Ii Jan 2004

Determination Of Crystalline Content Gradients In Cold-Drawn Poly-L-Lactic Acid Films By Dsc, Anne O'Connor, A. Riga, John F. Turner Ii

Chemistry Faculty Publications

Poly-L-lactic acid (PLLA) is a semi-crystalline, optically active, biodegradable, and biocompatible polymer that has been utilized extensively in biomedical applications as an implantable artificial cell scaffold material. In its crystalline form, PLLA is piezoelectric and it has been implicated in the enhancement of electromechanically induced osteogenesis in vivo. In its amorphous state, however, PLLA does not exhibit piezoelectricity. By uniaxially cold-drawing the polymer, PLLA can be endowed with varying degrees of piezoelectricity. It is important to understand the crystalline architecture of drawn PLLA so that the osteogenic potential imparted by piezoelectricity, if any, can be differentiated from the effects of …

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Lipid-Lowering Effects Of Ethyl 2-Phenacyl-3-Aryl-1h-Pyrrole- 4-Carboxylates In Rodents, Justin M. Holub, Kathy O'Toole-Colin, Adam Getzel, Anthony Argenti, Michael A. Evans, Daniel C. Smith, Gerard A. Dalglish, Shahzad Rifat, Donna L. Wilson, Brett M, Taylor, Ulander Miott, Josephine Glersaye, Kam Suet Lam, Bryan J. Mccranor, Joshua D. Berkowitz, Robert B. Miller, John R. Lukens, Keith Krumpe, John T. Gupton, Bruce S. Burnham Jan 2004

Lipid-Lowering Effects Of Ethyl 2-Phenacyl-3-Aryl-1h-Pyrrole- 4-Carboxylates In Rodents, Justin M. Holub, Kathy O'Toole-Colin, Adam Getzel, Anthony Argenti, Michael A. Evans, Daniel C. Smith, Gerard A. Dalglish, Shahzad Rifat, Donna L. Wilson, Brett M, Taylor, Ulander Miott, Josephine Glersaye, Kam Suet Lam, Bryan J. Mccranor, Joshua D. Berkowitz, Robert B. Miller, John R. Lukens, Keith Krumpe, John T. Gupton, Bruce S. Burnham

Chemistry Faculty Publications

A series of substituted 2-phenacyl-3-phenyl-1H-pyrrole-4-carboxylates were prepared from substituted acetophenones in 6 steps. The final condensations between a chloroenal and an aminoketone were carried out under neutral conditions in parallel to yield the series listed below. Selected pyrrole derivatives proved to be potent hypolipidemic agents lowering serum triglyceride concentrations in CF-1 male mice after 14 days of I.P. administration. One agent orally lowered serum cholesterol in Sprague-Dawley male rats at 2mg/kg/day after 14 days. The agents demonstrated a lowering of mouse serum LDL- cholesterol levels and selected compounds showed an elevation of serum HDL-cholesterol levels. The cholesterol concentrations in the …

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Distance-Dependent Electron Hopping Conductivity And Nanoscale Lithography Of Chemically-Linked Gold Monolayer Protected Cluster Films, Francis P. Zamborini, Laura E. Smart, Michael C. Leopold, Royce W. Murray Oct 2003

Distance-Dependent Electron Hopping Conductivity And Nanoscale Lithography Of Chemically-Linked Gold Monolayer Protected Cluster Films, Francis P. Zamborini, Laura E. Smart, Michael C. Leopold, Royce W. Murray

Chemistry Faculty Publications

Films of monolayer protected Au clusters (MPCs) with mixed alkanethiolate and ω-carboxylate alkanethiolate monolayers, linked together by carboxylate–Cu2+–carboxylate bridges, exhibit average edge-to-edge cluster spacings that vary with the numbers of methylene segments in the alkanethiolate ligand as determined by a combined atomic force microscopy (AFM)/UV-Vis spectroscopy method. The electronic conductivity (σEL) of dry films is exponentially dependent on the cluster spacing, consistent with electron tunneling through the alkanethiolate chains and non-bonded contacts between those chains on individual, adjacent MPCs. The calculated electronic coupling factor (β) for tunneling between MPCs is 1.2 Å−1, which is similar to …

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Measurement Of Anti-Cancer Agent Methoxyamine In Plasma By Tandem Mass Spectrometry With On-Line Sample Extraction, Shuming Yang, Lili Liu, Stanton L. Gerson, Yan Xu Oct 2003

Measurement Of Anti-Cancer Agent Methoxyamine In Plasma By Tandem Mass Spectrometry With On-Line Sample Extraction, Shuming Yang, Lili Liu, Stanton L. Gerson, Yan Xu

Chemistry Faculty Publications

In this work, we present the development and validation of a tandem mass spectrometry method for the quantitative determination of methoxyamine (CH3ONH2), a potential new chemotherapeutic agent, in human and mouse plasma. Methoxyamine together with the internal standard (I.S.) methoxyl-D3-amine was directly derivatized in plasma sample with a novel chemical agent 4-(N,N-diethylamino)benzaldehyde. The product solution was injected into an on-line Oasis® HLB extraction column ( mm) for analyte extraction. After the elution of extractives, the derivatized analytes were monitored by the positive-electrospray-ionization mass spectrometry (ESI-MS-MS). The structures of derivatized analytes were elucidated by fragmentation. Quantitation of plasma methoxyamine was carried …

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Magnetic Storage Device Using Induced Magnetic Reversal Of A Cobalt, Scott Whittenburg Oct 2003

Magnetic Storage Device Using Induced Magnetic Reversal Of A Cobalt, Scott Whittenburg

Chemistry Faculty Publications

The effects of the applied field, cell size, and cutting area on the ‘‘seed’’ induced magnetic reversal of a cobalt element array have been studied by a stochastic dynamic micromagnetics code using the Laudau–Lifshitz–Gilbert equation. Three magnetic reversal mechanisms under different magnitudes of the applied field have been investigated by examining the energy profiles. To minimize the effect of the thermal fluctuations on the switching time, an applied field with magnitude around 0.7 or 0.8 T and an element array with cutting area less than 10 nm310 nm are required. By using the smaller cellsize, the switching time and the …

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Structural Requirements For Expression Of Factor Va Activity, Michael Kalafatis, Daniel O. Beck, Kenneth G. Mann Aug 2003

Structural Requirements For Expression Of Factor Va Activity, Michael Kalafatis, Daniel O. Beck, Kenneth G. Mann

Chemistry Faculty Publications

Thrombin activated factor Va (factor VIIa, residues 1-709 and 1546-2196) has an apparent dissociation constant (Kd,app) for factor Xa within prothrombinase of approximately 0.5 nM. A protease (NN) purified from the venom of the snake Naja nigricollis nigricollis, cleaves human factor V at Asp697, Asp1509, and Asp1514 to produce a molecule (factor VNN) that is composed of a Mr 100,000 heavy chain (amino acid residues 1-696) and a Mr 80,000 light chain (amino acid residues 1509/1514-2196). Factor VNN, has a Kd,app for factor Xa of 4 nm and reduced clotting activity. Cleavage of factor VIIa by NN at Asp697 results …

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Growth, Conductivity, And Vapor Response Properties Of Metal Ion-Carboxylate Linked Nanoparticle Films, Michael C. Leopold, Robert L. Donkers, Dimitra Georganopoulou, Megan Fisher, Francis P. Zamborini, Royce W. Murray Aug 2003

Growth, Conductivity, And Vapor Response Properties Of Metal Ion-Carboxylate Linked Nanoparticle Films, Michael C. Leopold, Robert L. Donkers, Dimitra Georganopoulou, Megan Fisher, Francis P. Zamborini, Royce W. Murray

Chemistry Faculty Publications

Nanoparticles of metals (Au, Ag, Pd, alloys) in the size range 1–3 nm diameter can be stabilized against aggregation of the metal particles by coating the metal surface with a dense monolayer of ligands (thiolates). The stabilization makes it possible to analytically define the nanoparticle composition (for example, Au140(hexanethiolate)53, I) and to elaborate the chemical functionality of the protecting monolayer (for example, Au140(C6)35(MUA)18, II, where C6 = hexanethiolate and MUA = mercaptoundecanoic acid). Network polymer films (IIfilm) on interdigitated array electrodes can be prepared from II, based on cation coordination (i.e., Cu2+, Zn2+, Ag+, methyl viologen) by the …

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Emission Color Tuning In Alq(3) Complexes With Extended Conjugated Chromophores, Radek Pohl, Pavel Anzenbacher Jr. Aug 2003

Emission Color Tuning In Alq(3) Complexes With Extended Conjugated Chromophores, Radek Pohl, Pavel Anzenbacher Jr.

Chemistry Faculty Publications

GraphicsA new method for the synthesis of 5-arylethynyl-8-hydroxyquinoline ligands using Sonogashira-Hagihara coupling was developed. The electronic nature of arylethynyl substituents affects the emission color and quantum yield of the resulting Al(III) complex. Photophysical properties of the metallocomplexes correspond to the electron-withdrawing/-donating character of the arylethynyl substituents. Optical properties of such AI(Ill) complexes correlate with the Hammett constant values of the respective substituents. This strategy offers a powerful tool for the preparation of electroluminophores with predictable photophysical properties.

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Amino Acids Glu323, Tyr324, Glu330, And Val331 Of Factor Va Heavy Chain Are Essential For Expression Of Cofactor Activity, Lisam S. Singh, Michael A. Bukys, Daniel O. Beck, Michael Kalafatis Jul 2003

Amino Acids Glu323, Tyr324, Glu330, And Val331 Of Factor Va Heavy Chain Are Essential For Expression Of Cofactor Activity, Lisam S. Singh, Michael A. Bukys, Daniel O. Beck, Michael Kalafatis

Chemistry Faculty Publications

We have recently demonstrated that amino acid region 323-331 of factor Va heavy chain (9 amino acids, AP4') contains a binding site for factor Xa (Kalafatis, M., and Beck, D. O. (2002) Biochemistry 41, 12715-12728). To ascertain which amino acids within this region are important for the effector and receptor properties of the cofactor with respect to factor Xa, we have synthesized three overlapping peptides (5 amino acids each) spanning the amino acid region 323-331 and tested them for their effect on prothrombinase complex assembly and function. Peptide containing amino acids 323EYFIA327 alone was found to increase the catalytic efficiency …

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Tools For The Automatic Identification And Classification Of Rna Base Pairs, Neocles B. Leontis, Huanwang Yang, Fabrice Jossinet, Li Chen, John Westbrook, Helen Berman, Eric Westhof Jun 2003

Tools For The Automatic Identification And Classification Of Rna Base Pairs, Neocles B. Leontis, Huanwang Yang, Fabrice Jossinet, Li Chen, John Westbrook, Helen Berman, Eric Westhof

Chemistry Faculty Publications

Three programs have been developed to aid in the classification and visualization of RNA structure. BPViewer provides a web interface for displaying three-dimensional (3D) coordinates of individual base pairs or base pair collections. A web server, RNAview, automatically identifies and classifies the types of base pairs that are formed in nucleic acid structures by various combinations of the three edges, Watson-Crick, Hoogsteen and the Sugar edge. RNAView produces two-dimensional (2D) diagrams of secondary and tertiary structure in either Postscript, VRML or RNAML formats. The application RNAMLview can be used to rearrange various parts of the RNAView 2D diagram to generate …

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Non-Watson-Crick Basepairing And Hydration In Rna Motifs: Molecular Dynamics Of 5s Rrna Loop E, Neocles B. Leontis, Kamila Réblová, Nad'a Špačková, Richard Štefl, Kristina Csaszar, Jaroslav Koča, J Sponer Jun 2003

Non-Watson-Crick Basepairing And Hydration In Rna Motifs: Molecular Dynamics Of 5s Rrna Loop E, Neocles B. Leontis, Kamila Réblová, Nad'a Špačková, Richard Štefl, Kristina Csaszar, Jaroslav Koča, J Sponer

Chemistry Faculty Publications

Explicit solvent and counterion molecular dynamics simulations have been carried out for a total of > 80 ns on the bacterial and spinach chloroplast 5S rRNA Loop E motifs. The Loop E sequences form unique duplex architectures composed of seven consecutive non-Watson-Crick basepairs. The starting structure of spinach chloroplast Loop E was modeled using isostericity principles, and the simulations refined the geometries of the three non-Watson-Crick basepairs that differ from the consensus bacterial sequence. The deep groove of Loop E motifs provides unique sites for cation binding. Binding of Mg2+ rigidifies Loop E and stabilizes its major groove at an intermediate …

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Thickness Dependence Of Magnetic Blocking In Granular Thin Films, Scott Whittenburg Jun 2003

Thickness Dependence Of Magnetic Blocking In Granular Thin Films, Scott Whittenburg

Chemistry Faculty Publications

Interparticle interaction among single domain nanosize magnetic particles embedded in nonmagnetic matrix was studied. Attention was paid to concentrated Cu–Co granular thin films with a fixed magnetic volume fraction 20%. By analyzing theoretical models and comparing with experimental results, a dimensional constraint on the magnetic properties was found. As the film thickness reduces toward the thin limit the interparticle interaction plays important roles in modifying the magnetic behavior. The dipolar interaction energy was calculated among magnetic particles including far-neighbor interaction for films with different thickness values. When magnetization variation is included in the calculation, the resulting calculated interaction energy versus …

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Rnase L Mediates Transient Control Of The Interferon Response Through Modulation Of The Double-Stranded Rna-Dependent Protein Kinase Pkr, Khalid S.A. Khabar, Yunus M. Siddiqui, Fahad Al-Zoghaibi, Latifa Al-Haj, Mohammed Dhalla, Aimin Zhou, Beihua Dong, Mark Whitmore, Jayashree Paranjape, Mohammed N. Al-Ahdal, Futwan Al-Mohanna, Bryan R.G. Williams, Robert H. Silverman May 2003

Rnase L Mediates Transient Control Of The Interferon Response Through Modulation Of The Double-Stranded Rna-Dependent Protein Kinase Pkr, Khalid S.A. Khabar, Yunus M. Siddiqui, Fahad Al-Zoghaibi, Latifa Al-Haj, Mohammed Dhalla, Aimin Zhou, Beihua Dong, Mark Whitmore, Jayashree Paranjape, Mohammed N. Al-Ahdal, Futwan Al-Mohanna, Bryan R.G. Williams, Robert H. Silverman

Chemistry Faculty Publications

The transient control of diverse biological responses that occurs in response to varied forms of stress is often a highly regulated process. During the interferon (IFN) response, translational repression due to phosphorylation of eukaryotic initiation factor 2α, eIF2α, by the double-stranded RNA-dependent protein kinase, PKR, constitutes a means of inhibiting viral replication. Here we show that the transient nature of the IFN response against acute viral infections is regulated, at least in part, by RNase L. During the IFN antiviral response in RNase L-null cells, PKR mRNA stability was enhanced, PKR induction was increased, and the phosphorylated form of eIF2α …

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Evaluating The Effects Of Enhanced Processivity And Metal Ions On Translesion Dna Replication Catalyzed By The Bacteriophage T4 Dna Polymerase, Edmunds Z. Reineks, Anthony J. Berdis May 2003

Evaluating The Effects Of Enhanced Processivity And Metal Ions On Translesion Dna Replication Catalyzed By The Bacteriophage T4 Dna Polymerase, Edmunds Z. Reineks, Anthony J. Berdis

Chemistry Faculty Publications

The fidelity of DNA replication is achieved in a multiplicative process encompassing nucleobase selection and insertion, removal of misinserted nucleotides by exonuclease activity, and enzyme dissociation from primer/templates that are misaligned due to mispairing. In this study, we have evaluated the effect of altering these kinetic processes on the dynamics of translesion DNA replication using the bacteriophage T4 replication apparatus as a model system. The effect of enhancing the processivity of the T4 DNA polymerase, gp43, on translesion DNA replication was evaluated using a defined in vitro assay system. While the T4 replicase (gp43 in complex with gp45) can perform …

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Dielectric Constant And Proton Order And Disorder In Ice Ih: Monte Carlo Computer Simulations, Steven W. Rick May 2003

Dielectric Constant And Proton Order And Disorder In Ice Ih: Monte Carlo Computer Simulations, Steven W. Rick

Chemistry Faculty Publications

The dielectric properties of ice Ih are studied using a Monte Carlo algorithm for sampling over proton configurations. The algorithm makes possible the calculation of the dielectric constant and other properties of the proton-disordered crystal. Results are presented for three classical models of water, two commonly used nonpolarizable models (SPC/E and TIP4P) and a polarizable model
(TIP4P-FQ).

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Effect Of Petrochemical Industrial Emissions Of Reactive Alkenes And NoX On Tropospheric Ozone Formation In Houston, Texas, T. B. Ryerson, M. Trainer, W. M. Angevine, C. A. Brock, R. W. Dissly, F. C. Fehsenfeld, G. J. Frost, P. D. Goldan, J. S. Holloway, G. Hübler, R. O. Jakoubek, W. C. Kuster, J. A. Neuman, D. K. Nicks, D. D. Parrish, J. M. Roberts, D. T. Sueper, E. L. Atlas, Stephen G. Donnelly Ph.D., F. Flocke, A. Fried, W. T. Potter, S. Schauffler, V. Stroud, A. J. Weinheimer, B. P. Wert, C. Wiedinmyer, R. J. Alvarez, R. M. Banta, L. S. Darby, C. J. Senff Apr 2003

Effect Of Petrochemical Industrial Emissions Of Reactive Alkenes And NoX On Tropospheric Ozone Formation In Houston, Texas, T. B. Ryerson, M. Trainer, W. M. Angevine, C. A. Brock, R. W. Dissly, F. C. Fehsenfeld, G. J. Frost, P. D. Goldan, J. S. Holloway, G. Hübler, R. O. Jakoubek, W. C. Kuster, J. A. Neuman, D. K. Nicks, D. D. Parrish, J. M. Roberts, D. T. Sueper, E. L. Atlas, Stephen G. Donnelly Ph.D., F. Flocke, A. Fried, W. T. Potter, S. Schauffler, V. Stroud, A. J. Weinheimer, B. P. Wert, C. Wiedinmyer, R. J. Alvarez, R. M. Banta, L. S. Darby, C. J. Senff

Chemistry Faculty Publications

Petrochemical industrial facilities can emit large amounts of highly reactive hydrocarbons and NOx to the atmosphere; in the summertime, such colocated emissions are shown to consistently result in rapid and efficient ozone (O3) formation downwind. Airborne measurements show initial hydrocarbon reactivity in petrochemical source plumes in the Houston, TX, metropolitan area is primarily due to routine emissions of the alkenes propene and ethene. Reported emissions of these highly reactive compounds are substantially lower than emissions inferred from measurements in the plumes from these sources. Net O3 formation rates and yields per NOx molecule oxidized in these petrochemical industrial source plumes …

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Peptide−Protein Interactions: Photoinduced Electron-Transfer Within The Preformed And Encounter Complexes Of A Designed Metallopeptide And Cytochrome C, Robin C. Lasey, Liu Liu, Ling Zang, Michael Y. Ogawa Apr 2003

Peptide−Protein Interactions: Photoinduced Electron-Transfer Within The Preformed And Encounter Complexes Of A Designed Metallopeptide And Cytochrome C, Robin C. Lasey, Liu Liu, Ling Zang, Michael Y. Ogawa

Chemistry Faculty Publications

Photoinduced electron-transfer (ET) occurs between a negatively charged metallopeptide, [Ru(bpy)2(phen-am)-Cys-(Glu)(5)-Gly](3-) = RuCE(5)G, and ferricytochrome c = Cyt c. In the presence of Cyt c, the triplet state lifetime of the ruthenium metallopeptide is shortened, and the emission decays via biexponential kinetics, which indicates the existence of two excited-state populations of ruthenium peptides. The faster decay component displays concentration-independent kinetics demonstrating the presence of a preformed peptide-protein complex that undergoes intra-complex electron-transfer. Values of K-b = (3.5 +/- 0.2) x 10(4) M-1 and k(ET)(obs) = (2.7 +/- 0.4) x 10(6) s(-1) were observed at ambient temperatures. The magnitude of k(ET)(obs) decreases …

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Chlorine Budget And Partitioning During The Stratospheric Aerosol And Gas Experiment (Sage) Iii Ozone Loss And Validation Experiment (Solve), S. M. Schauffler, E. L. Atlas, Stephen G. Donnelly Ph.D., A. Andrews, S. A. Montzka, J. W. Elkins, D. F. Hurst, P. A. Romashkin, G. S. Dutton, V. Stroud Mar 2003

Chlorine Budget And Partitioning During The Stratospheric Aerosol And Gas Experiment (Sage) Iii Ozone Loss And Validation Experiment (Solve), S. M. Schauffler, E. L. Atlas, Stephen G. Donnelly Ph.D., A. Andrews, S. A. Montzka, J. W. Elkins, D. F. Hurst, P. A. Romashkin, G. S. Dutton, V. Stroud

Chemistry Faculty Publications

The amount of chlorine in the stratosphere has a direct influence on the magnitude of chlorine-catalyzed ozone loss. A comprehensive suite of organic source gases of chlorine in the stratosphere was measured during the NASA Stratospheric Aerosol and Gas Experiment (SAGE) III Ozone Loss and Validation Experiment (SOLVE) campaign in the arctic winter of 2000. Measurements included chlorofluorocarbons (CFCs), hydrochlorofluorocarbons (HCFCs), halon 1211, solvents, methyl chloride, N2O, and CH4. Inorganic chlorine contributions from each compound were calculated using the organic chlorine measurements, mean age of air, tropospheric trends, and a method to account for mixing in the stratosphere. Total organic …

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The Solvent Boundary Potential: A New Approach For Computer Simulation Of Large Systems, Valentin Gogonea Mar 2003

The Solvent Boundary Potential: A New Approach For Computer Simulation Of Large Systems, Valentin Gogonea

Chemistry Faculty Publications

The paper presents the theoretical framework for the development of a new solvent boundary method for computer simulations and its possible application to the simulation of nitric oxide synthase. Different approaches for the construction of a solvent boundary potential are reviewed and their strengths and weaknesses are discussed. A new solvent boundary potential is proposed which combines the mean field force approximation with the Green's function approach for treating long-range electrostatic interactions, and introduces a novel strategy to treat electrostriction effects due to ions crossing the solvent boundary. Finally, a series of computational tests are devised in order to assess …

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