Calculation of affinities of peptides for proteins

Several methodologies were employed to calculate the Gibbs standard free energy of binding for a collection of protein-ligand complexes, where the ligand is a peptide and the protein is representative for various protein families. Almost 40 protein-ligand complexes were employed for a continuum approach, which considers the protein and the peptide at the atomic level, but includes solvent as a polarizable continuum. Five protein-ligand complexes were employed for an all-atom approach that relies on a combination of the double decoupling method with thermodynamic integration and molecular dynamics. These affinities were also computed by means of the linear interaction energy method. Although it generally proved rather difficult to predict the absolute free energies correctly, for some protein families the experimental ranking order was correctly reproduced by the continuum and all-atom approach. Considerable attention has also been given to correctly analyze the affinities of charged peptides, where it is required to judge the effect of one or more ions that are being decoupled in an all-atom approach to preserve electroneutrality. The various methods are further judged upon their merits.     

CCl2自由基与H2O分子反应动力学研究

用213 nm激光光解CCl4产生CCl2自由基，用LP LIF技术测定了室温下基态CCl2自由基与H2O分子的反应速率常数为(5.45±0.95)×10－14 cm3•molecule－1•s－1.在G2MP2理论水平上计算了CCl2＋H2O反应的最低单重态势能面，揭示了插入与加成 消除两种反应机理，得到了三个可能的产物通道:HCl＋HClCO、HCl＋trans ClCOH以及HCl＋cis ClCOH.并用RRKM TST和传统过渡态理论计算了这三个通道的分支比及其温度效应.结果说明在低温下（273 K），插入机理的产物通道的分支比远大于加成 消除机理的产物通道， HCl＋HClCO是主要产物，分支比为77.4％，其次是HCl＋cis ClCOH，分支比为22.6％.而在高温下（3000 K），加成 消除机理的反应通道大于插入机理， HCl＋trans ClCOH分支比为82.3％.     

Mass transport in gas channels of electrochemical cells with a solid-oxide electrolyte: Allowing for the electrode reaction rates in numerical calculations

The concentration fields, Nusselt number distributions along the electrode, and ratios of concentrations of electrochemically active components at the entrance into and exit out of an electrochemical cell are determined by numerical integration of the convective-diffusion equation for a broad range of rate constants of electrode reactions, Peclet numbers, and geometrical parameters of channels. Three regions of parameter values are revealed. At low reaction rates (K _l < 0.5), mass transfer is completely determined by electrode kinetics; at high rates (K _l > 20), it is completely determined by the diffusion in the gas phase; and in the intermediate region of values of K _l it is necessary to allow for both the diffusion processes and the electrode reactions.Translated from Elektrokhimiya, Vol. 41, No. 3, 2005, pp. 317–324.Original Russian Text Copyright © 2005 by Ezin, Somov.     

A Theoretical Study on the Conductivity of Carbon Doped BNNT

From the changes in energy band, density of state (DOS) and electronic structure calculated by the DFT/B3LYP method, the conductivity of carbon doped boron‐nitride nanotube (BNNT), which is formed by C‐C bond substituting B‐N bond, was discussed. The results indicate that the substitution will strengthen the conductivity of the tube, and its semi‐conductivity might be adjusted by controlling the substitution.     

第一性原理计算钛酸铅A位掺杂对其负热膨胀性的影响

近年来,实验发现钛酸铅基材料具有负热膨胀性,且其热膨胀程度会受到掺杂元素的影响. 目前所研究的A位掺杂体系中,仅Cd原子掺杂能使钛酸铅负热膨胀性增强. 所以研究A位掺杂钛酸铅,比较Cd原子与其他原子在掺杂钛酸铅时化学键的异同,有助于深刻理解钛酸铅负热膨胀的本质. 本文利用第一性原理,分别优化了Sr、Ba、Cd掺杂钛酸铅的晶格常数,计算了它们的态密度和电荷密度. 结果表明Cd―O键的共价性强于Pb―O键,而Ba―O键和Sr―O键几乎呈离子性,Ba/Sr对Pb的替代削弱了化合物的共价性,降低了自发极化强度. 与实验测量的热膨胀系数对比可以发现,A位原子与氧原子之间的共价性增强,化合物负热膨胀程度升高;若A位原子与氧原子之间的共价性削弱,负热膨胀程度降低. 可见A位原子与氧原子之间的共价性影响了钛酸铅基化合物负热膨胀性.     

低温加氢催化剂的设计: 理论与实践

简要总结了我们在C=C及C=O双键低温加氢双金属催化剂方面的最新研究成果. 首先, 我们以环己烯加氢为探针反应, 证明了平行使用多种研究手段的重要性, 包括单晶表面的基础研究与DFT计算, 多晶表面的合成与表征, 负载型催化剂的制备与性能测试等. 其次, 总结了双金属催化剂在其他加氢反应, 如丙烯醛C=O双键的选择性加氢, 苯的低温加氢, 以及乙炔的选择性加氢等反应中的应用. 最后, 讨论了利用金属碳化物代替贵金属Pt以减少双金属催化剂中Pt用量的可能性.     

Effect of substituents (NH2, OH, F) on structures and stability of lithofluorosilylenoids

Isomeric structures and energies of three kinds of lithofluorosilylenoids, R₂SiLiF (R = NH₂, OH, F) were studied using theab initio molecular orbital theory. The calculations show that thermal stability of the three-membered ring structures of these three kinds of silylenoids decreases in the order of substituents NH₂ > OH > F because of the conjugation between NH₂, OH or F and Si atom. The interaction of substituents R with Li atom makes R₂SiLiF have a structure with two Li-A-Si-F (A = N, O, F) four-membered rings, which is the most stable of the isomers of each of three kinds of silylenoids and whose stability decreases in the order of substituents F > OH > NH₂. Inductive effect of substituents influences the thermal stability of the linear structure of silylenoids.     

A structural analysis of the complexes of (S,S)-dimethylpyridino-18-crown-6 with (R) and (S)-[α-(1-naphthyl)ethyl]ammonium perchlorate by NMR techniques and molecular modeling

Significant - interaction is found in the complexes of (S, S)-dimethylpyridino-18-crown-6 with (R)- and (S)-[-(1-naphthyl)ethyl]ammonium perchlorate. This finding is supported by the¹H NOESY NMR spectral technique, greater chemical shift changes of aromatic protons in both host and guest molecules upon complexation, and by molecular mechanics calculations. Because of the flexibility of the ligand, the tripod hydrogen bonding causes¹³C relaxation times of all periphery carbons to decrease without significant selectivity. Rotational energy barrier calculations of the methyl groups of the complexed ligand also show that the (S, S)-host-(R)-guest is the more stable complex.     

1,1-二氟乙烷和1,2-二氟乙烷分子内原子间非键相互作用

用从头算势诱导极小二乘拟合(PD/LSF)和(exp-6-1)函数研究了1,1-二氟乙烷和1,2-二氟乙烷分子内非键原子间的相互作用。计算结果表明, 同分异构体的能量稳定性差, 在于分子内非键原子间的相互作用。该模式提供了一种简单、实用的研究分子内非键相互作用的方法。     

Synthesis of a new donor, BEDT-HBDST and crystal structures, electrical and magnetic properties of (BEDT-HBDST)2MX4 (M=Fe, Ga, X=Cl, Br), where BEDT-HBDST=2,5-bis(4,5-ethylenedithio-1,3-diselenol-2-ylidene)-2,3,4,5-tetrahydrothiophene

A novel conjugation-elongated bis(ethylenedithio)tetraselenafulvalene (BETS) type donor, 2,5-bis(4,5-ethylenedithio-1,3-diselenol-2-ylidene)-2,3,4,5-tetrahydrothiophene (BEDT-HBDST) and its magnetic and non-magnetic anion salts, (BEDT-HBDST)₂MX₄ (MX₄⁻=FeCl₄⁻, GaCl₄⁻, FeBr₄⁻ and GaBr₄⁻), were prepared. These four salts are isostructural and belong to the space group of P2/c. They showed semiconducting behavior with small activation energies (59-64 meV). The band structures of these salts are quasi one-dimensional and there is a midgap between the upper band and the lower band, since the degree of dimerization is significant in the stacking direction. The MX₄⁻ ions are located between the donor columns and near to the ethylenedithio moieties of the donor molecules. The magnetic susceptibilities of the FeCl₄⁻ and FeBr₄⁻ salts follow the Curie-Weiss law with Curie constants of 4.6 and 4.8 emu K mol⁻¹ (sum of the spins of S=5/2 and S=1/2) and negative Weiss temperatures of θ=−1.2 and −4.9 K, respectively, revealing a weak antiferromagnetic interaction of 3d spins of the FeCl₄⁻ and FeBr₄⁻ anions. The Fe?Fe (6.66-7.60 Å), Cl?Cl (4.81-4.82 Å) and Br?Br (4.74-4.77 Å) distances in the crystal structures of these salts are significantly long. Therefore, the direct magnetic interaction between the 3d spins of the nearest neighboring Fe³⁺ ions appears to be not readily accessible.