面心立方C60表面过程的计算机模拟

近年来发现的C60及其金属掺杂化合物形成一个新的材料族，其半导体性质、超导性质及非线性光学性质已受到广泛注意，但目前对这类材料的表面性质尚缺乏研究，我们曾采用参数化的Lenard－Jones6－12模型函数比较不同晶型C6o的相对稳定性　[1]，预测面心立方C60（FccC60）的声子散射频率和态密度[2]，并计算其表面能[3]，取得有意义的结果，表明这一简单模型势能函数是C60分子间有效范德华作用的一种合理抽提．本工作进一步将该势能函数应用于研究fccC60表面吸附分子的迁移机理，并用蒙特卡罗方法模拟fcC（110）及（100）晶面的熔化过程，…     

双嵌段共聚物薄膜介观结构的耗散粒子动力学模拟

采用耗散粒子动力学(Dissipative Particle Dynamics, DPD)方法模拟两平行平板间的双嵌段共聚物体系的介观结构. 模拟结果表明, 随板间距的增大, 体系分层数量的增加是不连续的, 在分层数量的增加过程中, 出现不规则结构的过渡区；聚合物链末端距随板间距的增大呈周期性振荡, 振荡幅度逐渐减小. 对模拟结果的分析表明：层状结构转变点与分层数量之间存在近似线性关系；层状结构转变点近似与共聚物链长的2/3次方成正比.     

“线上线下-虚实结合”在有机化学实验教学中的应用探索——以正溴丁烷的制备实验为例

In response to the impact of the Covid-19 epidemic on organic chemistry laboratory teaching, this article analyzes and discusses the current limitation of traditional organic chemistry laboratory teaching. Taking the "preparation of n-bromobutane" as an example, a new "online-offline and virtual-actual combination" teaching mode with the combination of "Tencent Meeting, MLabs, laboratory and WeChat group" is introduced. The practice of the new mode of teaching includes the following steps: pre-class online guiding by teacher, student preview and practice based on the virtual simulation platform, students and teacher discussion and operation in laboratory, and post-classcomprehensive assessment and Q&A", and good teaching effects have been received. It is significant in cultivating and improving the independent innovation and practical ability, and provides reference for the organic chemistry laboratory teaching reform and also lays a foundation for the construction of "outstanding course" of organic chemistry.     

Computer simulation of electron transfer processes across the electrode|electrolyte interface: a treatment of solvent and electrode polarizability

A polarizable molecular dynamics model for adiabatic electron transfer across the electrode|electrolyte interface is presented. The electronic polarizability of the water and of the metal electrode is accounted for by a dynamical fluctuating charge algorithm, image charges, and the Ewald summation adapted for a conducting interface. The effects of the solvent electronic polarizability are studied by computing the diabatic and adiabatic free energy curves for both polarizable and non-polarizable water models. This represents the first effort to compute the adiabatic free energy curves from simulation for a fully polarizable electrochemical system.     

Factor Xa: Simulation studies with an eye to inhibitor design

Factor Xa is a serine protease which activates thrombin and plays a key regulatory role in the blood-coagulation cascade. Factor Xa is at the crossroads of the extrinsic and intrinsic pathways of coagulation and, hence, has become an important target for the design of anti-thrombotics (inhibitors). It is not known to be involved in other processes than hemostasis and its binding site is different to that of other serine proteases, thus facilitating selective inhibition. The design of high-affinity selective inhibitors of factor Xa requires knowledge of the structural and dynamical characteristics of its active site. The three-dimensional structure of factor Xa was resolved by X-ray crystallography and refined at 2.2 Å resolution by Padmanabhan and collaborators. In this article we present results from molecular dynamics simulations of the catalytic domain of factor Xa in aqueous solution. The simulations were performed to characterise the mobility and flexibility of the residues delimiting the unoccupied binding site of the enzyme, and to determine hydrogen bonding propensities (with protein and with solvent atoms) of those residues in the active site that could interact with a substrate or a potential inhibitor. The simulation data is aimed at facilitating the design of high-affinity selective inhibitors of factor Xa.     

Vibrational spectra of 2-biphenylmethanol. Spectrum simulation and molecular structure

The vibrational spectra of a solid crystalline sample of 2-biphenylmethanol have been measured at room temperature. The IR absorption spectra were recorded in the range 400 cm^–1–3600 cm^–1; Raman spectra were measured in the range 10 cm^–1–1640 cm^–1. The direct mechanical and optoelectronic problems were solved using the fragment method realized as Lev-100 software; the intensity distribution in the IR spectrum of 2-biphenylmethanol was obtained by the same method. The experimental Raman and IR absorption spectra were interpreted by analyzing the calculated data on the frequencies and forms of normal vibrations and their intensities in the IR spectra. IR absorption spectra were simulated for several models of 2-biphenylmethanol conformers that differ in the mutual orientation of fragments. Based on the results of simulation and comparison of the calculated and experimental spectra of conformers we suggested a model for the conformer realized in the solid phase under normal conditions.Original Russian Text Copyright © 2004 by L. M. Babkov, J. Baran, N. A. Davydova, J. I. Kukielskii, and S. V. TrukhachevTranslated from Zhurnal Strukturnoi Khimii, Vol. 45, No. 4, pp. 624–631, July–August, 2004.This revised version was published online in April 2005 with a corrected cover date.     

Mechanism for the inhibition of the acid degradation of ampicillin by 2-hydroxypropyl- β -cyclodextrin

The formation of inclusion complexes between amoxicillin (AMPC) and 2-hydroxypropyl-β-cyclodextrin (HPCD) was investigated by isothermal microcalorimetry and molecular dynamics simulation to evaluate the inhibitory effects on the degradation of AMPC in aqueous solutions at various pH. The process depended significantly on the ionic species of AMPC in the solution. In a strong acid solution, cationic AMPC and HPCD formed two different types of inclusion complexes with a 1:1 stoichiometry: the first-type had a high association constant K ₁ of 4.0-8.0·10³ M^-1 and included the penam ring of AMPC in the HPCD cavity (Mode I), while the second-type with a K ₂ of 1.0·10³ M^-1 contained the phenyl group of AMPC (Mode II). Furthermore, a complex with a 1:2 (AMPC:HPCD) stoichiometry was realized in a two-step reaction and was characterized by a smaller K _1:2of 4.0·10² M^-1 and larger negative enthalpy and entropy changes than the complexes with a 1:1 stoichiometry. Since the β-lactam ring of AMPC could be protected by inclusion with HPCD in the 1:2 complex and Mode I of 1:1 complexes, the degradation of AMPC in the presence of HPCD was approximately four times slower than in its absence at pH 1.2 and 37°C. In weak acid and neutral solutions, zwitterionic AMPC and HPCD formed only one type of inclusion complex with a 1:1 stoichiometry, where the phenyl group was included (Mode II). AMPC was very stable in these solutions (t _1/2=226 h at pH=6.0) and there is little significant difference in the degradation rate between complexed AMPC and uncomplexed AMPC. Thus, the results indicated that the inclusion complex of AMPC with HPCD, effectively increasing the stability of AMPC in a strong acidic solution like that the stomach, would be useful for eradicating Helicobacter pylori infection and as a drug delivery system. This revised version was published online in July 2006 with corrections to the Cover Date.     

Interface motion in a two-dimensional Ising model with a field

We determine by Monte Carlo simulations the width of an interface between the stable phase and the metastable phase in a two-dimensional Ising model with a magnetic field, in the case of nonconversed order parameter (Glauber dynamics). At zero temperature, the width increases ast with–1/3, as predicted by earlier theories. As temperature increases, the value of the effective exponent that we measure decreases toward the value 1/4, which is the value in the absence of magnetic field.     

Metastable systems driven by colored noise: The stationary state

The influence of the Bardeen-Herring back-jump correlations on the Fermi-Dirac statistics of the one-dimensional nonhomogeneous fermionic lattice gas is studied by the Monte Carlo simulation technique and semianalytically. The resulting distribution is obtained, exhibiting increased population of the lower levels in comparison to the Fermi-Dirac statistics.