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Full-Text Articles in Chemistry

Reexamine Structures And Relative Stability Of Medium-Sized Silicon Clusters: Low-Lying Endohedral Fullerene-Like Clusters Si30-Si38, Soohaeng Yoo, Nan Shao, Xiao Cheng Zeng Oct 2009

Reexamine Structures And Relative Stability Of Medium-Sized Silicon Clusters: Low-Lying Endohedral Fullerene-Like Clusters Si30-Si38, Soohaeng Yoo, Nan Shao, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

We report improved results of lowest-lying silicon clusters Si31–Si38. A large population of low-energy clusters are collected from previous searches by several research groups and the binding energies of these clusters are computed using density-functional theory (DFT) methods. Best candidates (isomers with high binding energies) are identified from the screening calculations. Additional constrained search is then performed for the best candidates using the basin-hopping method combined with DFT geometry optimization. The obtained low-lying clusters are classified according to binding energies computed using either the Perdew–Burke–Ernzerhof (PBE) functional or the Becke exchange and Lee–Yang–Parr correlation (BLYP) functional. …

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The Α,Α-Difluorinated Phosphonate L-Pser-Analogue: An Accessible Chemical Tool For Studying Kinase-Dependent Signal Transduction In Vitro, And In Living Cells, Kaushik Panigrahi, Marijean Eggen, Jun-Ho Maeng, Quanrong Shen, David B. Berkowitz Sep 2009

The Α,Α-Difluorinated Phosphonate L-Pser-Analogue: An Accessible Chemical Tool For Studying Kinase-Dependent Signal Transduction In Vitro, And In Living Cells, Kaushik Panigrahi, Marijean Eggen, Jun-Ho Maeng, Quanrong Shen, David B. Berkowitz

David Berkowitz Publications

This overview focuses on the (α,α-difluoromethylene)phosphonate mimic of phosphoserine (pCF2Ser) and its application to the study of kinase-mediated signal transduction – pathways of great interest to drug development. The most versatile modes of access to these chemical biological tools are discussed, organized by method of PCF2-C bond. The pCF2-Ser mimic may be site-specifically incorporated into peptides (SPPS) and proteins (expressed protein ligation). This isopolar, dianionic pSer mimic results in a “constitutive phosphorylation” phenotype, and is seen to support native protein-protein interactions that depend upon serine phosphorylation. Signal transduction pathways studied with this chemical biological …

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Chemically Decorated Boron-Nitride Nanoribbons, Xiao-Jun Wu, Men-Hao Wu, Xiao Cheng Zeng Sep 2009

Chemically Decorated Boron-Nitride Nanoribbons, Xiao-Jun Wu, Men-Hao Wu, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

Motivated by recent studies of graphenen nanoribbons (GNRs), we explored electronic properties of pure and chemically modified boron nitride nanoribbons (BNNRs) using the density functional theory method. Pure BNNRs with both edges fully saturated by hydrogen are semiconducting with wide band gaps. Values of the band gap depend on the width and the type of edge. The chemical decoration of BNNRs’ edges with four different functional groups, including -F, -Cl, -OH, and -NO2, was investigated. The band-gap modulation by chemical decoration may be exploited for nanoelectronic applications.

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Spiroadamantyl 1,2,4-Trioxolane, 1,2,4-Trioxane, And 1,2,4-Trioxepane Pairs: Relationship Between Peroxide Bond Iron(Ii) Reactivity, Heme Alkylation Efficiency, And Antimalarial Activity, Xiaofang Wang, Darren J. Creek, Charles E. Schiaffo, Yuxiang Dong, Jacques Chollet, Christian Scheurer, Segio Wittlin, Susan A. Charman, Patrick Dussault, James K. Wood, Jonathan L. Vennerstrom Aug 2009

Spiroadamantyl 1,2,4-Trioxolane, 1,2,4-Trioxane, And 1,2,4-Trioxepane Pairs: Relationship Between Peroxide Bond Iron(Ii) Reactivity, Heme Alkylation Efficiency, And Antimalarial Activity, Xiaofang Wang, Darren J. Creek, Charles E. Schiaffo, Yuxiang Dong, Jacques Chollet, Christian Scheurer, Segio Wittlin, Susan A. Charman, Patrick Dussault, James K. Wood, Jonathan L. Vennerstrom

Patrick Dussault Publications

These data suggest that iron(II) reactivity for a set of homologous spiroadamantyl 1,2,4-trioxolane, 1,2,4-trioxane, and 1,2,4-trioxepane peroxide heterocycles is a necessary, but insufficient, property of animalarial peroxides. Heme alkylation efficiency appears to give a more accurate prediction of antimalarial activity than FeSO4-mediated reaction rates, suggesting that antimalarial activity is not merely dependent on peroxide bond cleavage, but also on the ability of reactive intermediates to alkylate heme or other proximal targets.

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Coexistence And Transition Between Cassie And Wenzel State On Pillared Hydrophobic Surface, Takahiro Koishi, Kenji Yasuoka, Shigenori Fujikawa, Toshikazu Ebisuzaki, Xiao Cheng Zeng May 2009

Coexistence And Transition Between Cassie And Wenzel State On Pillared Hydrophobic Surface, Takahiro Koishi, Kenji Yasuoka, Shigenori Fujikawa, Toshikazu Ebisuzaki, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

Water droplets on rugged hydrophobic surfaces typically exhibit one of the following two states: (i) the Wenzel state [Wenzel RN (1936) Ind Eng Chem 28:988–994] in which water droplets are in full contact with the rugged surface (referred as the wetted contact) or (ii) the Cassie state [Cassie, ABD, Baxter S (1944) Trans Faraday Soc 40:546–551] in which water droplets are in contact with peaks of the rugged surface as well as the “air pockets” trapped between surface grooves (the composite contact). Here, we show large-scale molecular dynamics simulation of transition between Wenzel state and Cassie state of water droplets …

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N- And C-Terminal Domains In Human Holocarboxylase Synthetase Participate In Substrate Recognition, Yousef I. Hassan, Hideaki Moriyama, Lars J. Olsen, Xin Bi, Janos Zempleni Apr 2009

N- And C-Terminal Domains In Human Holocarboxylase Synthetase Participate In Substrate Recognition, Yousef I. Hassan, Hideaki Moriyama, Lars J. Olsen, Xin Bi, Janos Zempleni

Hideaki Moriyama Publications

Holocarboxylase synthetase (HCS) catalyzes the binding of the vitamin biotin to carboxylases and histones. Carboxylases mediate essential steps in macronutrient metabolism. For example, propionyl- CoA carboxylase (PCC) catalyzes the carboxylation of propionyl-CoA in the metabolism of oddchain fatty acids. HCS comprises four putative domains, i.e., the N-terminus, the biotin transfer/ATP binding domain, a putative linker domain, and the C-terminus. Both N- and C-termini are essential for biotinylation of carboxylases by HCS, but the exact functions of these two domains in enzyme catalysis are unknown. Here we tested the hypothesis that N- and C-termini play roles in substrate recognition by HCS. …

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One-Pot Formation Of Large Macrocycles With Modifiable Peripheries And Internal Cavities, Joseph S. Ferguson, Kazuhiro Yamato, Rui Liu, Lan He, Xiao Cheng Zeng, Bing Gong Mar 2009

One-Pot Formation Of Large Macrocycles With Modifiable Peripheries And Internal Cavities, Joseph S. Ferguson, Kazuhiro Yamato, Rui Liu, Lan He, Xiao Cheng Zeng, Bing Gong

Xiao Cheng Zeng Publications

Macrocycles with persistent shape and large, noncollapsible lumens have attracted increasing interest because of their unique properties and potential applications.[1] Although most of the macrocycles with well-defined shape have hydrocarbon backbones formed from the stepwise coupling of sp- or sp2-hybridized carbon atoms,[1a,b,d, 2] macrocycles with other rigid backbones have also been reported.[3] For example, we discovered a series of aromatic oligoamide macrocycles that could be generated in high yield by a one-pot macrocyclization process.[4] These readily available macrocycles contain hydrophilic cavities that are rich in carbonyl oxygen atoms. With their persistent shape and noncollapsible cavities, these macrocycles have demonstrated unique …

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Asymmetric Synthesis Of 1,2-Dioxanes: Approaches To The Peroxyplakoric Acids, Chunping Xu, Chris Schwartz, Joseph Raible, Patrick Dussault Jan 2009

Asymmetric Synthesis Of 1,2-Dioxanes: Approaches To The Peroxyplakoric Acids, Chunping Xu, Chris Schwartz, Joseph Raible, Patrick Dussault

Patrick Dussault Publications

The stereospecific intramolecular alkylation of a hydroperoxyacetal provides the basis for the first asymmetric synthesis of the dioxane propionate core of the peroxyplakorates. Chemoselective hydrometallation of an alkyne in the presence of a peroxide is used to introduce a synthon for the polyunsaturated side chains of the peroxyplakorates. The route suggests a general solution for the 1,2-dioxane unit in many peroxide natural products.

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Evaluation Of Silica Monoliths In Affinity Microcolumns For High-Throughput Analysis Of Drug–Protein Interactions, Michelle J. Yoo, David S. Hage Jan 2009

Evaluation Of Silica Monoliths In Affinity Microcolumns For High-Throughput Analysis Of Drug–Protein Interactions, Michelle J. Yoo, David S. Hage

David Hage Publications

Silica monoliths in affinity microcolumns were tested for the high-throughput analysis of drug–protein interactions. HSA was used as a model protein for this work, while carbamazepine and R-warfarin were used as model analytes. A comparison of HSA silica monoliths of various lengths indicated columns as short as 1 to 3 mm could be used to provide reproducible estimates of retention factors or plate heights. Benefits of using smaller columns for this work included the lower retention times and lower back pressures that could be obtained versus traditional HPLC affinity columns, as well as the smaller amount of protein that …

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N- And C-Terminal Domains In Human Holocarboxylase Synthetase Participate In Substrate Recognition, Yousef I. Hassan, Hideaki Moriyama, Lars J. Olsen, Xin Bi, Janos Zempleni Jan 2009

N- And C-Terminal Domains In Human Holocarboxylase Synthetase Participate In Substrate Recognition, Yousef I. Hassan, Hideaki Moriyama, Lars J. Olsen, Xin Bi, Janos Zempleni

Hideaki Moriyama Publications

Holocarboxylase synthetase (HCS) catalyzes the binding of the vitamin biotin to carboxylases and histones. Carboxylases mediate essential steps in macronutrient metabolism. For example, propionyl- CoA carboxylase (PCC) catalyzes the carboxylation of propionyl-CoA in the metabolism of oddchain fatty acids. HCS comprises four putative domains, i.e., the N-terminus, the biotin transfer/ATP binding domain, a putative linker domain, and the C-terminus. Both N- and C-termini are essential for biotinylation of carboxylases by HCS, but the exact functions of these two domains in enzyme catalysis are unknown. Here we tested the hypothesis that N- and C-termini play roles in substrate recognition by HCS. …

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Allosteric Regulation Of The Primase (Dnag) Activity By The Clamp-Loader (Τ) In Vitro, Kiran Chintakayala, Cristina Machón, Anna Haroniti, Marilyn A. Larson, Steven H. Hinrichs, Mark A. Griep, Panos Soultanas Jan 2009

Allosteric Regulation Of The Primase (Dnag) Activity By The Clamp-Loader (Τ) In Vitro, Kiran Chintakayala, Cristina Machón, Anna Haroniti, Marilyn A. Larson, Steven H. Hinrichs, Mark A. Griep, Panos Soultanas

Mark A. Griep Publications

During DNA replication the helicase (DnaB) recruits the primase (DnaG) in the replisome to initiate the polymerization of new DNA strands. DnaB is attached to the τ subunit of the clamp-loader that loads the β clamp and interconnects the core polymerases on the leading and lagging strands. The τ–DnaB−DnaG ternary complex is at the heart of the replisome and its function is likely to be modulated by a complex network of allosteric interactions. Using a stable ternary complex comprising the primase and helicase from Geobacillus stearothermophilus and the τ subunit of the clamp-loader from Bacillus subtilis we show that changes …

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Steel Hull Corrosion Of Uss Arizona With Applications To Submerged Resources, D. L. Johnson, D. J. Medlin, M. A. Russell, D. L. Conlin, L. E. Murphy, J. D. Carr Jan 2009

Steel Hull Corrosion Of Uss Arizona With Applications To Submerged Resources, D. L. Johnson, D. J. Medlin, M. A. Russell, D. L. Conlin, L. E. Murphy, J. D. Carr

Department of Chemistry: Faculty Publications

The USS Arizona Preservation project is a multi-year, interdisciplinary and cumulative effort with each discipline contributing to basic research required to make informed management decisions for long-term preservation. Three significant issues include: (1) USS Arizona is a grave site for 900 or more Navy and Marine personal lost with the USS Arizona when Japanese forces attacked Pearl Harbor on Dec 7, 1941. (2) Minimizing environmental hazard from a potential fuel oil release of an estimated 500,000 gallons remaining in fuel bunkers or compartment overheads. A cross section view of the ship and bunkers before and after the attack is shown …

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Quantum Mechanical/Molecular Mechanical/Continuum Style Solvation Model: Linear Response Theory, Variational Treatment, And Nuclear Gradients, Hui Li Jan 2009

Quantum Mechanical/Molecular Mechanical/Continuum Style Solvation Model: Linear Response Theory, Variational Treatment, And Nuclear Gradients, Hui Li

Department of Chemistry: Faculty Publications

Linear response and variational treatment are formulated for Hartree–Fock (HF) and Kohn–Sham density functional theory (DFT) methods and combined discrete-continuum solvation models that incorporate self-consistently induced dipoles and charges. Due to the variational treatment, analytic nuclear gradients can be evaluated efficiently for these discrete and continuum solvation models. The forces and torques on the induced point dipoles and point charges can be evaluated using simple electrostatic formulas as for permanent point dipoles and point charges, in accordance with the electrostatic nature of these methods. Implementation and tests using the effective fragment potential (EFP, a polarizable force field) method and the …

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Tuning The Electronic Properties Of The Golden Buckyball By Endohedral Doping: M@Au16− (M=Ag,Zn, In), Lei-Ming Wang, Rhitankar Pal, Wei Huang, Xiao Cheng Zeng, Lai-Sheng Wang Jan 2009

Tuning The Electronic Properties Of The Golden Buckyball By Endohedral Doping: M@Au16− (M=Ag,Zn, In), Lei-Ming Wang, Rhitankar Pal, Wei Huang, Xiao Cheng Zeng, Lai-Sheng Wang

Xiao Cheng Zeng Publications

The golden Au16- cage is doped systematically with an external atom of different valence electrons: Ag, Zn, and In. The electronic and structural properties of the doped clusters, MAu16- (M =Ag,Zn, In), are investigated by photoelectron spectroscopy and theoretical calculations. It is observed that the characteristic spectral features of 16-, reflecting its near tetrahedral (Td) symmetry, are retained in the photoelectron spectra of MAu16-, suggesting endohedral structures with little distortion from the parent Au16- cage for the doped clusters. Density functional calculations show that …

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Magnetic Doping Of The Golden Cage Cluster M@Au16− (M=Fe,Co,Ni), Lei-Ming Wang, Jaeil Bai, Anne Lechtken, Wei Huang, Detlef Schooss, Manfred Kappes, Xiao Cheng Zeng, Lai-Sheng Wang Jan 2009

Magnetic Doping Of The Golden Cage Cluster M@Au16− (M=Fe,Co,Ni), Lei-Ming Wang, Jaeil Bai, Anne Lechtken, Wei Huang, Detlef Schooss, Manfred Kappes, Xiao Cheng Zeng, Lai-Sheng Wang

Xiao Cheng Zeng Publications

Structural, electronic, and magnetic properties of the golden cage doped with a transition-metal atom, MAu16- (M =Fe,Co,Ni), are investigated using trapped ion electron diffraction, photoelectron spectroscopy, and density-functional theory. The best agreement to experiment is obtained for endohedral M@Au16- structures but with considerable distortions to the parent Au16- cage. Fe@Au16- and Co@Au16- are found to have similar structures with C2 symmetry while a C1 structure is obtained for Ni@Au16-. The 4s electrons are observed to transfer to the Au16 cage, whereas atomiclike …

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Classification And Cluster Analysis Of Complex Time-Of-Flight Secondary Ion Mass Spectrometry For Biological Samples, Stephen E. Reichenbach, Xue Tian, Qingping Tao, Alex Henderson Jan 2009

Classification And Cluster Analysis Of Complex Time-Of-Flight Secondary Ion Mass Spectrometry For Biological Samples, Stephen E. Reichenbach, Xue Tian, Qingping Tao, Alex Henderson

School of Computing: Conference and Workshop Papers

Identifying and separating subtly different biological samples is one of the most critical tasks in biological analysis. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is becoming a popular and important technique in the analysis of biological samples, because it can detect molecular information and characterize chemical composition. ToF-SIMS spectra of biological samples are enormously complex with large mass ranges and many peaks. As a result the classification and cluster analysis are challenging. This study presents a new classification algorithm, the most similar neighbor with a probability-based spectrum similarity measure (MSN- PSSM), which uses all the information in the entire ToF- SIMS …

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Co Chemisorption On The Surfaces Of The Golden Cages, Wei Huang, Satya S. Bulusu, Rhitankar Pal, Xiao Cheng Zeng, Lai-Sheng Wang Jan 2009

Co Chemisorption On The Surfaces Of The Golden Cages, Wei Huang, Satya S. Bulusu, Rhitankar Pal, Xiao Cheng Zeng, Lai-Sheng Wang

Xiao Cheng Zeng Publications

We report a joint experimental and theoretical study of CO chemisorption on the golden cages. We find that the Au17 − cage is highly robust and retains its cage structure in Au17 − (CO)−. On the other hand, the Au16 − cage is transformed to a structure similar to Au17 − upon the adsorption of CO. Au18 − is known to consist of two nearly degenerate structures, i.e., a cage and a pyramidal isomer, which coexist in the cluster beam. However, upon CO chemisorption only the cage isomer is observed while the pyramidal …

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The Tata-Binding Protein Core Domain In Solution Variably Bends Tata Sequences Via A Three-Step Binding Mechanism [Tables & Figures], Roberto F. Delgadillo, Jodell E. Whittington, Laura K. Parkhurst, Lawrence J. Parkhurst Jan 2009

The Tata-Binding Protein Core Domain In Solution Variably Bends Tata Sequences Via A Three-Step Binding Mechanism [Tables & Figures], Roberto F. Delgadillo, Jodell E. Whittington, Laura K. Parkhurst, Lawrence J. Parkhurst

Lawrence Parkhurst Publications

Studies of the binding and bending of the AdMLP TATA sequence (TATAAAAG) by the core domain of yeast TBP allow quantitation of the roles of the N-terminal domains of yeast and human TBP. All three proteins bind DNA via a three-step mechanism with no evidence for an initially bound but unbent DNA. The large enthalpy and entropy of activation for the first step in yTBP binding can now be assigned to movement of the NTD from the DNA binding pocket and not to energetics of DNA bending. The energetic patterns for hTBP and cTBP suggest that the …

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Energy Decomposition Analysis Of Covalent Bonds And Intermolecular Interactions, Peifeng Su, Hui Li Jan 2009

Energy Decomposition Analysis Of Covalent Bonds And Intermolecular Interactions, Peifeng Su, Hui Li

Department of Chemistry: Faculty Publications

An energy decomposition analysis method is implemented for the analysis of both covalent bonds and intermolecular interactions on the basis of single-determinant Hartree–Fock (HF) (restricted closed shell HF, restricted open shell HF, and unrestricted open shell HF) wavefunctions and their density functional theory analogs. For HF methods, the total interaction energy from a supermolecule calculation is decomposed into electrostatic, exchange, repulsion, and polarization terms. Dispersion energy is obtained from second-order Møller–Plesset perturbation theory and coupled-cluster methods such as CCSD and CCSD(T). Similar to the HF methods, Kohn–Sham density functional interaction energy is decomposed into electrostatic, exchange, repulsion, polarization, and dispersion …

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Immobilization Method For Producing Active Α1-Acid Glycoprotein, David S. Hage, Hai Xuan Jan 2009

Immobilization Method For Producing Active Α1-Acid Glycoprotein, David S. Hage, Hai Xuan

Department of Chemistry: Faculty Publications

A method and kit for immobilization of a glycoprotein. The method may include activating an affinity Support. The affinity Support may be activated by reacting the affinity Support with a compound that is reactive with one or more functional groups included within the glycoprotein. The method may also include oxidizing the glycoprotein in which oxidation conditions are selected to yield an oxidized glycoprotein that is biologically active and contains a Sufficient number of reactive aldehyde groups for coupling to a Support. For example, the oxidized glycoprotein may include five reactive aldehyde groups. In addition, the method may include reacting the …

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Heterogeneous Conductorlike Solvation Model, Hui Li, Dejun Si Jan 2009

Heterogeneous Conductorlike Solvation Model, Hui Li, Dejun Si

Department of Chemistry: Faculty Publications

A heterogeneous conductorlike solvation model (conductorlike screening model/conductorlike polarizable continuum model) that uses different local effective dielectrics for different portions of the solute cavity surface is implemented for quantum chemical Hartree–Fock and Kohn–Sham methods. A variational treatment is used to form the heterogeneous solvation operator, so a simple analytic expression of the energy gradients, which are vital for geometry optimization and molecular dynamics simulation, is derived and implemented. Using the new Fixed Points with Variable Areas surface tessellation scheme, continuous and smooth potential energy surfaces as well as analytic gradients are obtained for this heterogeneous model.

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Techniques For Consecutive Tem And Atom Probe Tomography Analysis Of Nanowires, D. R. Diercks, B. P. Gorman, Chin Li Cheung, G. Wang Jan 2009

Techniques For Consecutive Tem And Atom Probe Tomography Analysis Of Nanowires, D. R. Diercks, B. P. Gorman, Chin Li Cheung, G. Wang

Department of Chemistry: Faculty Publications

Nanowires show great promise for development in many technological applications including electronics, photonics, and displays . Due to the fine scale of nanowires, transmission electron microscopy (TEM) and atom probe tomography (APT) are among a limited number of techniques that can measure the crystallographic and chemical nature of these structures which ultimately define their performance.

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Dipole-Induced, Thermally Stable Lamellar Structure By Polar Aromatic Silane, Jinyue Jiang, Ocelio V. Lima, Yong Pei, Xiao Cheng Zeng, Li Tan, Eric Forsythe Jan 2009

Dipole-Induced, Thermally Stable Lamellar Structure By Polar Aromatic Silane, Jinyue Jiang, Ocelio V. Lima, Yong Pei, Xiao Cheng Zeng, Li Tan, Eric Forsythe

Xiao Cheng Zeng Publications

Lamellar structures, consisting of alternating inorganic layers separated by organic moieties, have attracted much attention over a wide range of applications, such as polymer-clay composites, rheology control, and optoelectronic devices. Organosilanes are ideal candidates for such efforts due to their ability to self-assemble and the intrinsic hybrid configuration of organic/inorganic moieties. Yet, the main emphasis has been focused on alkylsilane, where an alkyl group is linked with a silane terminal, i.e., R-SiX3 (R is alkane and X can be halogen or alkoxy). Construction of stacked monolayers of alkylsilane through chemisorption is possible. The demonstrated pathway usually takes place after …

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Materials Design Of Half-Metallic Graphene And Graphene Nanoribbons, Menghao Wu, Xiaojun Wu, Yi Gao, Xiao Cheng Zeng Jan 2009

Materials Design Of Half-Metallic Graphene And Graphene Nanoribbons, Menghao Wu, Xiaojun Wu, Yi Gao, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

Through patterned chemical modification, we show that both graphene sheets and zigzag-edged graphene nanoribbons (ZGNRs) can be converted to half-metals as long as the unmodified carbon strip (or width of ZGNRs) is sufficiently wide. Periodically functionalized graphene can mimic electronic behavior of edge-modified ZGNRs as the edge-modified zigzag carbon chains effectively divide a graphene sheet into a series of identical ZGNRs.

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First-Principles Study Of Methane Dehydrogenation On A Bimetallic Cu/N(111) Surface, Wei An, Xiao Cheng Zeng, C. Heath Turner Jan 2009

First-Principles Study Of Methane Dehydrogenation On A Bimetallic Cu/N(111) Surface, Wei An, Xiao Cheng Zeng, C. Heath Turner

Xiao Cheng Zeng Publications

We present density-functional theory calculations of the dehydrogenation of methane and CHx (x = 1 – 3) on a Cu/Ni(111) surface, where Cu atoms are substituted on the Ni surface at a coverage of 1/4 monolayer.

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On The Phase Diagram Of Water With Density Functional Theory Potentials: The Melting Temperature Of Ice /H With The Perdew–Burke–Ernzerhof And Becke–Lee–Yang–Parr Functionals, Soohaeng Yoo, Xiao Cheng Zeng, Sotiris C. Xantheas Jan 2009

On The Phase Diagram Of Water With Density Functional Theory Potentials: The Melting Temperature Of Ice /H With The Perdew–Burke–Ernzerhof And Becke–Lee–Yang–Parr Functionals, Soohaeng Yoo, Xiao Cheng Zeng, Sotiris C. Xantheas

Xiao Cheng Zeng Publications

The melting temperature (Tm) of ice Ih was determined from constant enthalpy and pressure (NPH) Born–Oppenheimer molecular dynamics simulations to be 417±3 K for the Perdew–Burke– Ernzerhof and 411±4 K for the Becke–Lee–Yang–Parr density functionals using a coexisting ice (Ih)-liquid phase at constant pressures of P=2500 and 10 000 bar and a density p=1 g/cm3, respectively.

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Noncovalent Interactions In The Asymmetric Synthesis Of Rigid, Conjugated Helical Structures, Makoto Miyasaka, Maren Pink, Suchada Rajca, Andrzej Rajca Jan 2009

Noncovalent Interactions In The Asymmetric Synthesis Of Rigid, Conjugated Helical Structures, Makoto Miyasaka, Maren Pink, Suchada Rajca, Andrzej Rajca

Andrzej Rajca Publications

Helical supramolecular architecture, such as helical foldamers, supramolecular helicates and aggregates, helical molecules, macromolecules, and oligomers, is a fascinating topic of interest in chemistry and materials science. Although such supramolecular structures may provide advantages in the design of stimuli-responsive and functional materials, the weak nature of the noncovalent forces, as well as the dependency of the dynamic process on their local environments, may hinder their possible applications because of their limited structural stability and processibility. Stabilization of these supramolecular structures could be achieved by modification of the molecular backbone with specific functional groups that permit intramolecular cross-linking, in which covalent …

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Androgen-Stimulated Udp-Glucose Dehydrogenase Expression Limits Prostate Androgen Availability Without Impacting Hyaluronan Levels, Qin Wei, Robert Galbenus, Ashraf Raza, Ronald Cerny, Melanie A. Simpson Jan 2009

Androgen-Stimulated Udp-Glucose Dehydrogenase Expression Limits Prostate Androgen Availability Without Impacting Hyaluronan Levels, Qin Wei, Robert Galbenus, Ashraf Raza, Ronald Cerny, Melanie A. Simpson

Ronald Cerny Publications

UDP-glucose dehydrogenase (UGDH) oxidizes UDP-glucose to UDP-glucuronate, an essential precursor for production of hyaluronan (HA), proteoglycans, and xenobiotic glucuronides. High levels of HA turnover in prostate cancer are correlated with aggressive progression. UGDH expression is high in the normal prostate even though HA accumulation is virtually undetectable. Thus, its normal role in the prostate may be to provide precursors for glucuronosyltransferase enzymes, which inactivate and solubilize androgens by glucuronidation. In this report, we quantified androgen dependence of UGDH, glucuronosyltransferase, and HA synthase expression. Androgen dependent and independent human prostate cancer cell lines were used to test the effects of UGDH …

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Continuous And Smooth Potential Energy Surface For Conductorlike Screening Solvation Model Using Fixed Points With Variable Areas, Peifeng Su, Hui Li Jan 2009

Continuous And Smooth Potential Energy Surface For Conductorlike Screening Solvation Model Using Fixed Points With Variable Areas, Peifeng Su, Hui Li

Department of Chemistry: Faculty Publications

Rigorously continuous and smooth potential energy surfaces, as well as exact analytic gradients, are obtained for a conductorlike screening solvation model (CPCM, a variant of the general COSMO) with Hartree–Fock (RHF, ROHF, UHF, and MCSCF) and density functional theory (R-DFT, RO-DFT, and U-DFT) methods using a new tessellation scheme, fixed points with variable areas (FIXPVA). In FIXPVA, spheres centered at atoms are used to define the molecular cavity and surface. The surface of each sphere is divided into 60, 240, or 960 tesserae, which have positions fixed relative to the sphere center and areas scaled by switching functions of their …

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Smooth Potential Energy Surface For Cavitation, Dispersion, And Repulsion Free Energies In Polarizable Continuum Model, Yali Wang, Hui Li Jan 2009

Smooth Potential Energy Surface For Cavitation, Dispersion, And Repulsion Free Energies In Polarizable Continuum Model, Yali Wang, Hui Li

Department of Chemistry: Faculty Publications

The fixed points with variable areas [FIXPVA (Ref. 1)] tessellation scheme is used to obtain smooth potential energy surfaces for the cavitation Gcav, dispersion Gdis, and repulsion Grep free energies in the polarizable continuum model (PCM). It is shown that FIXPVA can reproduce the standard GEPOL (Ref. 4) results to within 1 kcal/mol.

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