A new GROMOS force field for hexopyranose-based carbohydrates

A new parameter set (referred to as 45A4) is developed for the explicit-solvent simulation of hexopyranose-based carbohydrates. This set is compatible with the most recent version of the GROMOS force field for proteins, nucleic acids, and lipids, and the SPC water model. The parametrization procedure relies on: (1) reassigning the atomic partial charges based on a fit to the quantum-mechanical electrostatic potential around a trisaccharide; (2) refining the torsional potential parameters associated with the rotations of the hydroxymethyl, hydroxyl, and anomeric alkoxy groups by fitting to corresponding quantum-mechanical profiles for hexopyranosides; (3) adapting the torsional potential parameters determining the ring conformation so as to stabilize the (experimentally predominant) (4)C(1) chair conformation. The other (van der Waals and nontorsional covalent) parameters and the rules for third and excluded neighbors are taken directly from the most recent version of the GROMOS force field (except for one additional exclusion). The new set is general enough to define parameters for any (unbranched) hexopyranose-based mono-, di-, oligo- or polysaccharide. In the present article, this force field is validated for a limited set of monosaccharides (alpha- and beta-D-glucose, alpha- and beta-D-galactose) and disaccharides (trehalose, maltose, and cellobiose) in solution, by comparing the results of simulations to available experimental data. More extensive validation will be the scope of a forthcoming article. (c) 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1400-1412, 2005.     

Electron–ion recombination in radiation tracks in liquid argon: a computer simulation study

A simulation method is proposed to model electron–ion recombination in radiation tracks in liquid argon at 87 K. The method is applied to calculate the electron escape probability in clusters of up to 20 pairs of electrons and cations that represent a fragment of the track. The results reproduce the basic features of the track recombination in liquid argon observed in experiment.     

质子水合结构的振动态密度分析

使用基于多态经验价键模型的分子动力学模拟, 对水溶液中质子的水合结构及其在质子传递过程中的动力学过程进行了研究. 在价键模型的方法下, 质子的水合结构主要以H₉O₄⁺(Eigen)以及过渡态的H₅O₂⁺(Zundel)结构形态存在, 且在这两种结构中以Eigen的形态表现明显. 通过对质子传递过程中不同水合结构的态密度频谱分析, 发现一个在2000~3000 cm^-1范围内的明显连续的宽吸收谱带, 主要归因于Eigen结构的贡献, 这些特征峰的出现与水合氢离子第一溶剂化层内的强氢键作用密切相关. 对于Zundel的结构, 在1760 cm^-1处出现一个较为明显的肩峰, 归属为质子传递模式的特征振动. 通过对质子水合结构态密度频谱的分析, 可望增强对于稀酸溶液红外光谱中的连续宽吸收带以及质子传递的微观动力学过程的理解.     

离子液体的分子模拟与量化计算

分子模拟方法是研究离子液体结构与性质关系非常有效的方法,可以从分子间相互作用出发研究离子液体的微观结构、热力学和动力学性质;量子化学计算则在分子、电子水平上对离子液体的结构、性能及催化机理进行理论研究。本文综述了分子模拟方法应用于离子液体体系的研究进展,重点介绍了利用分子动力学模拟和量子化学计算方法对不同离子液体进行研究,获得离子液体的结构性质、光谱性质(红外光谱、拉曼光谱)及离子液体催化反应机理等,为探讨离子液体结构-性质的关系、离子对的作用方式、催化反应活性中心、反应途径、反应活化能、振动模式和频率以及设计功能性离子液体提供理论导向。     

增溶性辅料泊洛沙姆188与胆酸聚集形态的介观模拟

为了建立符合中药特点的增溶性药用辅料的筛选与评价方法,本研究以清开灵注射液为研究载体,采用介观动力学方法(MesoDyn)研究其难溶活性成分胆酸与增溶性辅料泊洛沙姆188之间的相互作用,探讨了胆酸对泊洛沙姆188临界胶束浓度的影响及泊洛沙姆188浓度、模拟时间、温度对两者聚集体构型的影响,并采用实验方法验证了部分模拟结果,为中药注射剂增溶性辅料的科学应用提供一定基础.结果表明:在清开灵注射液中活性成分胆酸的存在下,泊洛沙姆188的临界胶束浓度范围为0.6%～0.7%,降低了泊洛沙姆188自身的临界胶束浓度,为使清开灵注射液中的胆酸(3%)全部增溶,泊洛沙姆188浓度应为1.7%.     

Synchrotron X-ray absorption of LaCoO3 perovskite

LaCoO₃ perovskite was prepared at 700°C using citrate precursors. The product was then characterized with X-ray diffraction (XRD) and X-ray absorption spectroscopy (XAS). The powder XRD pattern indicates rhombohedral or its monoclinic I2/a subgroup symmetry. The electronic configuration and the short-range atomic structure of the LaCoO₃ perovskite at room temperature were investigated using synchrotron near-edge X-ray absorption spectroscopy (XANES) and extended X-ray absorption spectroscopy (EXAFS). From the XANES region of the XAS we conclude that Co(III) is at least partly in its intermediate- or high-spin state, which is in accordance with most of the published literature on LaCoO₃ perovskite. The EXAFS region of the LaCoO₃ perovskite spectrum, which up to now was almost not investigated, was simulated satisfactorily for the first two radial structure peaks in terms of the dominant scattering contributions generated with the FEFF8 code and the structural information available from crystallographic data. The best simulation results were obtained with I2/a symmetry. The obtained amplitude reduction factor, zero-energy shift and Debye-Waller factors are useful reference values for data analyses of similar compounds like partly substituted LaCoO₃ perovskite, such as La_1−xCa_xCoO₃ or La_1−xSr_xCoO₃, which are materials of technical interest in catalyst and other applications.     

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.     

热镀铜层冷凝过程的分子动力学模拟

During the hot-dip process of Cu on the surface of the steel,it involves the solidification from liquid to coating. The cooling rate has great influence on the microstructure and the performance. By means of constanttemperature,constant-pressure molecular dynamics simulation technique,the solidification process of the liquid model system made of 500 Cu particles has been studied with the period boundary condition. With the pairs analysis technology and the bond orientational order method,the difference of the structure and energy of the liquid Cu model system between different cooling velocities has been compared. The significant information of microcosmic structural transformation in the solidification process of liquid Cu system has been obtained. The calculation results show that the Finnis-Sinclair（FS）potential works very well in the solidification process of Cu. Cooling slowly the crystal copper layer can be obtained. Cooling quickly the amorphous copper layer can be obtained.     

多壁碳纳米管储氢的物理吸附特性

The physisorption of hydrogen stored in armchair multi-walled carbon nanotubes (MWCNTs) is simulated by the grand canonical Monte Carlo (GCMC) method on the condition of 10 MPa at normalt emperature. Hydrogen-hydrogen and hydrogen-carbon interactions are both modeled with Lennard-Jones potential. The hydrogen storage in double-walled carbon-nanotubes (DWCNTs) has been investigated on the condition that the internal or external radius is changed while the other radius remains constant. The results show that hydrogen molecules are mostly absorbed near the tube walls, and the hydrogens to rage capacityisim proved effectively when the difference between the internal radius and the external radius increases from 0.34 to 0.61 or 0.88 nm. Its simple theoretic explanation also is given. Further more, the capacity of hydrogen physisorbed in there-walled carbon nanotubes (TWCNTs) is calculated when the wall-wall distance is 0.34, 0.61 and 0.88 nm respectively. Then its hydrogen storage capacity is compared with that of single-walled carbon nanotubes (SWCNTs) and DWCNTs, and it is discovered that the capacity of hydrogen physisorbed in MWCNTs decreases as the number of wall increases.