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Articles 1 - 30 of 36
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Heat Capacity Estimators For Random Series Path-Integral Methods By Finite-Difference Schemes, Cristian Predescu, Dubravko Sabo, J. D. Doll, David L. Freeman
Heat Capacity Estimators For Random Series Path-Integral Methods By Finite-Difference Schemes, Cristian Predescu, Dubravko Sabo, J. D. Doll, David L. Freeman
Chemistry Faculty Publications
Previous heat capacity estimators used in path integral simulations either have large variances that grow to infinity with the number of path variables or require the evaluation of first- and second-order derivatives of the potential. In the present paper, we show that the evaluation of the total energy by the T-method estimator and of the heat capacity by the TT-method estimator can be implemented by a finite difference scheme in a stable fashion. As such, the variances of the resulting estimators are finite and the evaluation of the estimators requires the potential function only. By comparison with the task of …
Energy Estimators For Random Series Path-Integral Methods, Cristian Predescu, Dubravko Sabo, J. D. Doll, David L. Freeman
Energy Estimators For Random Series Path-Integral Methods, Cristian Predescu, Dubravko Sabo, J. D. Doll, David L. Freeman
Chemistry Faculty Publications
We perform a thorough analysis on the choice of estimators for random series path integral methods. In particular, we show that both the thermodynamic (T-method)and the direct (H-method)energy estimators have finite variances and are straightforward to implement. It is demonstrated that the agreement between the T-method and the H-method estimators provides an important consistency check on the quality of the path integral simulations. We illustrate the behavior of the various estimators by computing the total, kinetic, and potential energies of a molecular hydrogen cluster using three different path integral techniques. Statistical tests are employed to validate the sampling strategy adopted …
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
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 …
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
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 …
Magnetic Storage Device Using Induced Magnetic Reversal Of A Cobalt, Scott Whittenburg
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 …
Structural Requirements For Expression Of Factor Va Activity, Michael Kalafatis, Daniel O. Beck, Kenneth G. Mann
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 …
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
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 …
Emission Color Tuning In Alq(3) Complexes With Extended Conjugated Chromophores, Radek Pohl, Pavel Anzenbacher Jr.
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.
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
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 …
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
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 …
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
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 …
Thickness Dependence Of Magnetic Blocking In Granular Thin Films, Scott Whittenburg
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 …
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
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 …
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
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 …
Dielectric Constant And Proton Order And Disorder In Ice Ih: Monte Carlo Computer Simulations, Steven W. Rick
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).
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
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 …
Taming The Rugged Landscape: Techniques For The Production, Reordering, And Stabilization Of Selected Cluster Inherent Structures, Dubravko Sabo, J. D. Doll, David L. Freeman
Taming The Rugged Landscape: Techniques For The Production, Reordering, And Stabilization Of Selected Cluster Inherent Structures, Dubravko Sabo, J. D. Doll, David L. Freeman
Chemistry Faculty Publications
We report our studies of the potential energy surface (PES)of selected binary Lennard-Jones clusters. The effect of adding selected impurity atoms to a homogeneous cluster is explored. Inherent structures and transition states are found by combination of conjugate gradient and eigenvector-following methods while the topography of the PES is mapped with the help of a disconnectivity analysis. We show that we can controllably induce new structures as well as reorder and stabilize existing structures that are characteristic of higher-lying minima.
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
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 …
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
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 …
The Solvent Boundary Potential: A New Approach For Computer Simulation Of Large Systems, Valentin Gogonea
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 …
Measurement Of The Anti-Cancer Agent Gemcitabine In Human Plasma By High-Performance Liquid Chromatography, Bruce Keith, Yan Xu, Jean L. Grem
Measurement Of The Anti-Cancer Agent Gemcitabine In Human Plasma By High-Performance Liquid Chromatography, Bruce Keith, Yan Xu, Jean L. Grem
Chemistry Faculty Publications
A reversed-phase HPLC assay has been developed to determine the concentration of the anti-metabolite 2′,2′-difluorodeoxycytidine (gemcitabine, dFdC) in human plasma over the concentration range of 0.5–150 μM (0.13–39.44 μg/ml), and 2′,2′-difluorodeoxyuridine (dFdU), the deaminated, inactive metabolite, over the range of 1.0–227 μM (0.26–60 μg/ml). After the addition of 20 nmol 2′-fluorodeoxycytidine (FdC) as an internal standard, 0.5-ml samples of plasma were subjected to acetonitrile precipitation, followed by analysis using a gradient reversed-phase HPLC assay with UV detection. A Phenomenex Columbus™ C18 column, 5 μm, 150×4.6 mm, and a Waters C18, 4 μm, Nova-Pak Sentry guard column were used to achieve …
Particle Growth In Urban And Industrial Plumes In Texas, Charles A. Brock, Michael Trainer, Thomas B. Ryerson, J. Andrew Neuman, David D. Parrish, John S. Holloway, Dennis K. Nicks, Gregory J. Frost, Gerhard Hübler, Fred C. Fehsenfeld, J. Charles Wilson, J. Michael Reeves, Bernard G. Lafleur, Henrike Hilbert, Elliot L. Atlas, Stephen G. Donnelly Ph.D., Sue M. Schauffler, Verity R. Stroud, Christine Wiedinmyer
Particle Growth In Urban And Industrial Plumes In Texas, Charles A. Brock, Michael Trainer, Thomas B. Ryerson, J. Andrew Neuman, David D. Parrish, John S. Holloway, Dennis K. Nicks, Gregory J. Frost, Gerhard Hübler, Fred C. Fehsenfeld, J. Charles Wilson, J. Michael Reeves, Bernard G. Lafleur, Henrike Hilbert, Elliot L. Atlas, Stephen G. Donnelly Ph.D., Sue M. Schauffler, Verity R. Stroud, Christine Wiedinmyer
Chemistry Faculty Publications
Particle size distributions and gas-phase particle precursors and tracer species were measured aboard an aircraft in the plumes downwind from industrial and urban sources in the vicinity of Houston, TX during the daytime in late August and early September 2000. Plumes originating from the Parish gas-fired and coal-fired power plant, petrochemical industries along the Houston ship channel, the petrochemical facilities near the Gulf coast, and the urban center of Houston were studied. Most of the particle mass flux advected downwind of Houston came from the industries and electrical utilities at the periphery of the city rather than from sources in …
Examination Of The Role Of The Clamp-Loader And Atp Hydrolysis In The Formation Of The Bacteriophage T4 Polymerase Holoenzyme, Michael A. Trakselis, Anthony J. Berdis, Stephen J. Benkovic
Examination Of The Role Of The Clamp-Loader And Atp Hydrolysis In The Formation Of The Bacteriophage T4 Polymerase Holoenzyme, Michael A. Trakselis, Anthony J. Berdis, Stephen J. Benkovic
Chemistry Faculty Publications
Transient kinetic analyses further support the role of the clamp-loader in bacteriophage T4 as a catalyst which loads the clamp onto DNA through the sequential hydrolysis of two molecules of ATP before and after addition of DNA. Additional rapid-quench and pulse-chase experiments have documented this stoichiometry. The events of ATP hydrolysis have been related to the opening/closing of the clamp protein through fluorescence resonance energy transfer (FRET). In the absence of a hydrolysable form of ATP, the distance across the subunit interface of the clamp does not increase as measured by intramolecular FRET, suggesting gp45 cannot be loaded onto DNA. …
Synthesis And Potential Antimetastatic Activity Of Monovalent And Divalent Β-D-Galactopyranosyl-(1→4)-2-Acetamido-2-Deoxy-D-Glucopyranosides, Qin Li, Bin Su, Hui Li, Xiang Bao Meng, Meng Shen Cai, Zhong Jun Li, Rou Li Zhou, Ta Lin Suo
Synthesis And Potential Antimetastatic Activity Of Monovalent And Divalent Β-D-Galactopyranosyl-(1→4)-2-Acetamido-2-Deoxy-D-Glucopyranosides, Qin Li, Bin Su, Hui Li, Xiang Bao Meng, Meng Shen Cai, Zhong Jun Li, Rou Li Zhou, Ta Lin Suo
Chemistry Faculty Publications
Anomers of monovalent and divalent β-d-galactopyranosyl-(1→4)-2-acetamido-2-deoxy-d-gluco-pyranosides were synthesized under different glycosylation conditions, and evaluated for in vitro antimetastatic activity. Three compounds showed promising inhibitory effects on cancer cell attachment, spreading, migration, and invasion. Six divalent O-β-d-galactopyranosyl-(1→4)-2-acetamido-2-deoxy-d-glucopyranosides (29–34) were synthesized and their antimetastatic activities were studied.
Liquid Chromatography–Mass Spectrometry Method For The Analysis Of The Anti-Cancer Agent Capecitabine And Its Nucleoside Metabolites In Human Plasma, Yan Xu, Jean L. Grem
Liquid Chromatography–Mass Spectrometry Method For The Analysis Of The Anti-Cancer Agent Capecitabine And Its Nucleoside Metabolites In Human Plasma, Yan Xu, Jean L. Grem
Chemistry Faculty Publications
A reversed-phase high-performance liquid chromatography method with electrospray ionization and mass spectral detection is described for the determination of capecitabine, 5′-deoxy-5-fluorocytidine and 5′-deoxy-5-fluorouridine in human plasma with 5-chloro-2′-deoxyuridine as the internal standard. An on-line sample clean-up procedure allows dilution of the plasma sample with the initial mobile phase. The linear dynamic range is 0.0500–10.0 μg/ml for capecitabine, and 0.0500–25.0 μg/ml for the metabolites, 5′-deoxy-5-fluorocytidine and 5′-deoxy-5-fluorouridine, respectively. This method has been used to analyze plasma samples from patients receiving capecitabine in combination with oxaliplatin.
Mechanisms For The Oxonolysis Of Ethene And Propene: Reliability Of Quantum Chemical Predictions, Wai-To Chan, Ian P. Hamilton
Mechanisms For The Oxonolysis Of Ethene And Propene: Reliability Of Quantum Chemical Predictions, Wai-To Chan, Ian P. Hamilton
Chemistry Faculty Publications
Reactions of ozone with ethene and propene leading to primary ozonide (concerted and stepwise ozonolysis) or epoxide and singlet molecular oxygen (partial ozonolysis) are studied theoretically. The mechanism of concerted ozonolysis proceeds via a single transition structure which is a partial diradical. The transition structures and intermediates in the stepwise ozonolysis and partial ozonolysis mechanisms are singlet diradicals. Spin-restricted and unrestricted density functional methods are employed to calculate the structures of the closed-shell and diradical species. Although the partial diradicals exhibit moderate to pronounced instability in their RDFT and RHF solutions, RDFT is required to locate the transition structure for …
Response To “Comment On ‘Atomization Energies And Enthalpies Of Formation Of The Snbi[Sub N] (N=1–3) Gaseous Molecules By Knudsen Cell Mass Spectrometry’ ” [J. Chem. Phys. 118, 4766 (2003)], Giovanni Meloni, Karl A. Gingerich
Response To “Comment On ‘Atomization Energies And Enthalpies Of Formation Of The Snbi[Sub N] (N=1–3) Gaseous Molecules By Knudsen Cell Mass Spectrometry’ ” [J. Chem. Phys. 118, 4766 (2003)], Giovanni Meloni, Karl A. Gingerich
Chemistry Faculty Publications
Discusses atomization energies and enthalpies of formation of gaseous molecules of compounds containing tin and bismuth by Knudsen cell mass spectrometry. Procedure followed to evaluate the mass spectrometric equilibrium data regarding these molecules; Statistics of atomization energies and enthalpies calculated; Factors contributing to the necessity of high level of calculations to obtain these figures.
Anion Photoelectron Spectroscopy Of Solvated Transition State Precursors, Harry Gomez, Giovanni Meloni, James Madrid, D M. Neumark
Anion Photoelectron Spectroscopy Of Solvated Transition State Precursors, Harry Gomez, Giovanni Meloni, James Madrid, D M. Neumark
Chemistry Faculty Publications
Photoelectron (PE) spectra have been collected for the clustered bihalide anions XHX−∙(M) (X=Br, I) and BrHI−∙(M), where M=H2O, HBr, and HI, in order to probe the effects of strongly solvating species on the PE spectra of transition state precursor anions. The PE spectra of the XHX−∙(H2O) ions show similar vibrational progressions as the spectra of the bare BrHBr− and IHI− anions, indicating that photodetachment of the bare and hydrated ions accesses similar XHX transition state geometries on the X+HX reactionpotential energy surfaces. These results are consistent with electronic structure calculations that predict a double hydrogen-bonded XHX−∙(H2O) structure in which the …
Photoinduced Electron-Transfer Along Alpha-Helical And Coiled-Coil Metallopeptides, Anna Fedorova, Anita Chaudhari, Michael Y. Ogawa
Photoinduced Electron-Transfer Along Alpha-Helical And Coiled-Coil Metallopeptides, Anna Fedorova, Anita Chaudhari, Michael Y. Ogawa
Chemistry Faculty Publications
A peptide-based electron-transfer system has been designed in which the specific positions of redox-active metal complexes appended to either an a-helix, or an a-helical coiled-coil, can be reversed to test the effect of the helix dipole in controlling photoinduced electron-transfer rates. Two 30-residue apopeptides were prepared having the following sequences: (1) Ac-K-(IEALEGK)(ICALEGK)(IEALEHK)-(IEALEGK)-G-amide, and (II) Ac-K-(IEALEGK)(IHALEGK)-(IEALECK)(IEALEGK)-G-amide. Each apopeptide was reacted first with [Ru(bpy)(2)(phen-ClAc)](2+), where bpy = 2,2'-bipyridine and phen-ClAc = 5-chloroacetamido-1,10-phenanthroline, to attach the ruthenium polypyridyl center to the cysteine side-chain of the polypeptide. The isolated products were then reacted with [Ru(NH3)(5)(H2O)](2+) to yield the binuclear electron-transfer metallopeptides ET-I and ET-II. …
Self-Aggregates Of Cationic Meso-Tetratolylporphyrins In Aqueous Solutions, Pavel Kubat, Kamil Lang, Kristina Prochazkova, Pavel Anzenbacher Jr.
Self-Aggregates Of Cationic Meso-Tetratolylporphyrins In Aqueous Solutions, Pavel Kubat, Kamil Lang, Kristina Prochazkova, Pavel Anzenbacher Jr.
Chemistry Faculty Publications
Aggregation properties of meso-tetratolylporphyrins bearing cationic substituents of a lipophilic nature such as ammonium, pyridinium, phosphonium, sulfonium, and isothiouronium were studied by UV/vis and resonance light scattering spectroscopy. The exciton point-dipole approximation was used to predict the structural alignment of the porphyrin units within the aggregate. The contribution of various types of aggregates depends on the porphyrin substitution, ionic strength, and temperature of aqueous solution of the porphyrin. In general, the preferred structure of an aggregate formed by temperature-induced aggregation is the J-aggregate exhibiting the characteristically narrow, red-shifted Soret band indicating a parallel "side-by-side" arrangement of the porphyrin units. The …