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Free Energy Calculations for DNA Near Surfaces Using an Ellipsoidal Geometry

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Communications in Computational Physics 2008年第5期3卷 1117-1131页

作者： J.Ambia-Garrido B.Montgomery Pettitt departments of Physics University of HoustonHoustonTX 77004USA. departments of chemistry University of HoustonHoustonTX 77004USA.

The change in some thermodynamic quantities such as Gibbs’free energy,entropy and enthalpy of the binding of two DNA strands(forming a double helix),while one is tethered to a surface and are analytically *** particles are submerged in an electrolytic solution;the ionic strength of the media allows the linearized version of the Poisson-Boltzmann equation(from the theory of the double layer interaction)to properly describe the interactions[13].There is experimental and computational evidence that an ion penetrable ellipsoid is an adequate model for the single strand and the double helix[22–25].The analytic solution provides simple calculations useful for DNA chip *** predicted electrostatic effects suggest the feasibility of electronic control and detection of DNA hybridization in the fast growing area of DNA recognition.

关键词： Microarrays genetic analysis analytic Poisson-Boltzmann.

INFLUENCE OF BACKBONE RIGIDITY ON THE LIQUID CRYSTALLINITY OF MESOGEN-CONTAINING POLYACETYLENES

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Chinese Journal of Polymer Science 1998年第2期16卷 185-192页

作者：孔祥兴宛新华郭海成冯新德唐本忠 departments of chemistry Hong Kong University of Science & Technology Clear Water Bay Kowloon Hong Kong departments of Electrical & Electronic Engineering Hong Kong University of Science & Technology Clear Water Bay Kowloon Hong Kong Department of chemistry Peking University Beijing 100871 China

Two acetylene polymers containing cyanobiphenyl-based mesogens, poly{10-[((4'-cyano-4-biphenylyl)oxy)carbonyl]-1-decyne} (PA8CN), which has a relatively flexible polyalkyne backbone, and poly {[4-(((12-((4'-cyano-4-biphenylyl)oxy)dodecyl)oxy) carbonyl) phenyl]-acetylene} (PB12CN), which has a fairly rigid poly(phenylacetylene) backbone, were synthesized using respectively WCl6 and [Rh(nbd)Cl](2) as the catalysts. PA8CN exhibits enantiotropic interdigitated smectic A phase (S-Ad) over a temperature range as wide as ca. 100 degrees C, whereas PB12CN is non-mesomorphic, demonstrating that the backbone rigidity plays an important role in determining the liquid crystallinity of the polyacetylenes.

关键词： polyacetylene polyalkynes poly(phenylacetylene) substituted polyacetylenes liquid crystalline polymers

Calculation and interpretation of classical turning surfaces in solids

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npj Computational Materials 2021年第1期7卷 229-238页

作者： Aaron D.Kaplan Stewart J.Clark Kieron Burke John P.Perdew Department of Physics Temple UniversityPhiladelphiaPA 19122USA Centre for Materials Physics Durham UniversityDurham DH13LEUK departments of chemistry and Physics University of CaliforniaIrvineCA 92697USA departments of Physics and chemistry Temple UniversityPhiladelphiaPA 19122USA

Classical turning surfaces of Kohn–Sham potentials separate classically allowed regions(CARs)from classically forbidden regions(CFRs).They are useful for understanding many chemical properties of molecules but need not exist in solids,where the density never decays to *** equilibrium geometries,we find that CFRs are absent in perfect metals,rare in covalent semiconductors at equilibrium,but common in ionic and molecular *** all materials,CFRs appear or grow as the internuclear distances are uniformly *** can also appear at a monovacancy in a *** with several approximate density functionals and codes confirm these behaviors.A classical picture of conduction suggests that CARs should be connected in metals,and disconnected in wide-gap insulators,and is confirmed in the limits of extreme compression and ***,many semiconductors have no CFR at equilibrium,a key finding for density functional ***,a strong correlation with insulating behavior can still be ***,equilibrium bond lengths for all cases can be estimated from the bond type and the sum of the classical turning radii of the free atoms or ions.

关键词： turning solids expanded

Advances in high-resolution nuclear magnetic resonance methods in inhomogeneous magnetic fields using intermolecular multiple quantum coherences

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Science China(Physics,Mechanics & Astronomy) 2009年第1期52卷 58-69页

作者： CHEN Zhong LIN MeiJin CHEN Xi CAI ShuHui departments of Physics State Key Laboratory of Physical Chemistry of Solid SurfaceXiamen UniversityXiamen 361005China

Strong and extremely homogeneous static magnetic field is usually required for high-resolution nu-clear magnetic resonance (NMR). However, in the cases of in vivo and so on, the magnetic field inho-mogeneity owing to magnetic susceptibility variation in samples is unavoidable and hard to eliminate by conventional methods such as shimming. Recently, intermolecular multiple quantum coherences (iMQCs) have been employed to eliminate inhomogeneous broadening and obtain high-resolution NMR spectra, especially for in vivo samples. Compared to other high-resolution NMR methods, iMQC method exhibits its unique feature and advantage. It simultaneously holds information of chemical shifts, multiplet structures, coupling constants, and relative peak areas. All the information is often used to analyze and characterize molecular structures in conventional one-dimensional NMR spec-troscopy. In this work, recent technical developments including our results in this field are summarized; the high-resolution mechanism is analyzed and comparison with other methods based on interactions between spins is made; comments on the current situation and outlook on the research directions are also made.

关键词： nuclear magnetic resonance high-resolution inhomogeneous magnetic fields intermolecular multiple quantum coherence

The Molecular Mechanism of Interaction between Sushi Peptide and Pseudomonas Endotoxin

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Cellular & Molecular Immunology 2006年第1期3卷 21-28页

作者： Peng Li Miao Sun Thorsten Wohland Bow Ho Jeak Ling Ding departments of Biological Sciences National University of Singapore Singapore 1175431Singapore departments of chemistry National University of Singapore Singapore 117543 Singapore departments of Microbiology National University of Singapore Singapore 117543 Singapore departments of Biological Sciences and Microbiology National University of Singapore 14 Science Drive 4 Singapore 117543 Singapore

Septic shock is caused by Gram-negative bacterial infection. Lipopolysaccharide （LPS） is the bioactive molecule present on the outer membrane of the Gram-negative bacteria. It is generally thought that LPS interacts with sensors on the host cell membrane to activate the intracellular signaling pathway resulting in the overproduction of cytokines such as TNF-α This causes inflammation and ultimately, septic shock. Lipid A is the pharmacophore of the LPS molecule. Thus, developing bio-molecules which are capable of binding LPS at high affinity, especially to the lipid A moiety is an efficient way to neutralize the LPS toxicity. Factor C, a serine protease in the horseshoe crab ameobocytes, is sensitive to trace levels of LPS. We have derived Sushi peptides from the LPS-binding domains of Factor C. Our earlier study showed that the Sushi peptides inhibit LPS-induced septic shock in mice. Here, we demonstrate that the molecular interaction between LPS and Sushi 1 peptide is supported by the hydrophobic interaction between the lipid tail of LPS and Sushi 1 peptide. Furthermore, in the presence of LPS, the peptide transitions from a random structure into an α-helical conformation and it disrupts LPS aggregates, hence, neutralizing the LPS toxicity.

关键词： septic shock Sushi 1 peptide Factor C Pseudomonas endotoxin/LPS LPS binding electrostatic and hydrophobic interaction

Theoretical study of mechanism and kinetics for the addition of hydroxyl radical to phenol

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Science China chemistry 2012年第2期55卷 270-276页

作者： WU PengZhen LI Jian LI ShuJin TAO Fu-Ming College of chemistry Chemical Engineering and Materials Science Soochow University Suzhou 215123 China departments of chemistry and Biochemistry California State University Fullerton CaliJbrnia 92834 USA

The reaction mechanism and kinetics for the addition of hydroxyl radical(OH) to phenol have been investigated using the hybrid density functional(B3LYP) method with the 6-311++G(2dp,2df) basis set and the complete basis set(CBS) method using APNO basis sets,*** equilibrium geometries,energies,and thermodynamics properties of all the stationary points along the addition reaction pathway are *** rate constants and the branching ratios of each channel are evaluated using classical transition state theory(TST) in the temperature range of 210 to 360 K,to simulate temperatures in all parts of the *** ortho addition pathway is dominant and accounts for 99.8% 96.7% of the overall adduct products from 210 to 360 *** calculated rate constants are in good agreement with existing experimental *** addition reaction is irreversible.

关键词：羟基自由基动力学苯酚机制平衡几何结构温度范围速率常数加成反应

Statistical Treatment of Low-Energy Nuclear Level Schemes

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Communications in Theoretical Physics 2007年第2期47卷 303-308页

作者： M. Gholami M. Kildir A.N. Behkami chemistry departments Middle East Technical University Ankara Turkey Physics Department Islamic Azad University Mahabad Iran

水平密度参数和背移动精力 E_1 越过整个周期表与 A 值为原子核被决定从适合在中子束缚能附近在低刺激精力完成水平计划。我们发现精力背移动 E_1 显示出复杂行为并且取决于原子核的类型，弄平甚至，奇怪集体、奇怪奇怪。Thespin 截止... 详细信息

水平密度参数和背移动精力 E_1 越过整个周期表与 A 值为原子核被决定从适合在中子束缚能附近在低刺激精力完成水平计划。我们发现精力背移动 E_1 显示出复杂行为并且取决于原子核的类型，弄平甚至，奇怪集体、奇怪奇怪。Thespin 截止因素也为上面提及的原子核被调查了。结果在水平密度上与以前的结果和不同试验性的数据相比。

关键词：原子核核结构能级密度参数统计处理

Dilute carbon in H_(3)S under pressure

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npj Computational Materials 2022年第1期8卷 806-814页

作者： Xiaoyu Wang Tiange Bi Katerina P.Hilleke Anmol Lamichhane Russell J.Hemley Eva Zurek Department of chemistry State University of New York at BuffaloBuffaloNYUSA Department of Physics University of Illinois ChicagoChicagoILUSA departments of Physics Chemistryand Earth and Environmental SciencesUniversity of Illinois ChicagoChicagoUSA

Recently,room temperature superconductivity was measured in a carbonaceous sulfur hydride material whose identity remains ***,first-principles calculations are performed to provide a chemical basis for structural candidates derived by doping H3S with low levels of *** stabilizes unusual bonding configurations about the carbon atoms,which can be six-fold coordinated as CH_(6) entities within the cubic H_(3)S framework,or four-fold coordinated as methane intercalated into the H-S lattice,with or without an additional hydrogen in the *** doping breaks degenerate bands,lowering the density of states at the Fermi level(NF),and localizing electrons in C-H *** levels of CH_(4) doping do not increase N_(F) to values as high as those calculated for Im3m-H_(3)S,but they can yield a larger logarithmic average phonon frequency,and an electron–phonon coupling parameter comparable to that of R3m-H_(3)*** implications of carbon doping on the superconducting properties are discussed.

关键词： doping phonon carbon

Rates and processes affecting As speciation and mobility in lake sediments during aging

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Journal of Environmental Sciences 2018年第4期30卷 338-347页

作者： Alan Lock Dirk Wallschlager Nelson Belzile Graeme Spiers Celine Gueguen Environmental and Life Sciences Graduate Program Trent University School of the Environment Department of Chemistry and Water Quality CentreTrent University Department of chemistry Laurentian University School of the Environment Departments of Earth Sciences and BiologyLaurentian University School of the Environment and chemistry Department Trent University

Sediments from an arsenic（As） contaminated groundwater vent site were used to investigate As（ Ⅲ） binding, transformation and redistribution in native and iron oxide amended lake sediments using aging spiked batch reactions and a sequential extraction procedure that maintains As（V） and As（ Ⅲ） speciation. In the native sediments, fractionation analysis revealed that 10% of the spiked As（ Ⅲ） remained intact after a 32-day aging experiment and was predominantly adsorbed to the strongly sorbed（NH4H2PO4 extractable） and amorphous Fe oxide bound（H3PO4 extractable） fractions. Kinetic modelling of the experimental results allowed identifying the dominant reaction path for depletion of dissolved As（ Ⅲ） to As（ Ⅲ）absorbed on to the solid phase, followed by oxidation in the solid phase. Arsenite was initially adsorbed primarily to the easily exchangeable fraction（（NH4）2SO4 extractable）, then rapidly transformed into As（V） and redistributed to the strongly sorbed and amorphous Fe oxide bound fractions. Oxidation of As（ Ⅲ） in recalcitrant fractions was less efficient. The iron oxide amendments illustrated the controls that iron oxides can have on As（ Ⅲ） binding and transformation rates. In goethite amended samples As（ Ⅲ） oxidation was faster and primarily occurred in the strongly sorbed and amorphous Fe oxide bound fractions. In these samples,19.3 μg Mn was redistributed（compared to the native sediment） from the easily exchangeable and crystalline Fe oxide bound fractions to the strongly sorbed and amorphous Fe oxide bound fractions, indicating that goethite may act as a catalyst for Mn（Ⅱ） oxidation, thereby producing sorbed Mn（ Ⅲ/Ⅳ ）, which then appears to be involved in rapidly oxidizing As（ Ⅲ）.

关键词： Arsenite Oxidation Fractionation Redistribution Modelling