超临界CO2中甲醇和乙醇无限稀释扩散系数的分子动力学模拟与实验测定

采用分子动力学模拟(MD)方法对甲醇和乙醇在超临界二氧化碳中的无限稀释扩散系数进行了模拟计算, 并应用泰勒分散理论, 采用超临界色谱仪对模拟结果进行了实验验证. 模拟计算值与实验值较吻合, 且变化规律基本一致, 表明采用这种新方法可以准确有效地预测超临界体系的扩散性质, 能够方便地应用于工程设计.     

表皮生长因子受体和抑制剂之间分子对接的研究

研究了表皮生长因子受体(EGFR)和4-苯胺喹唑啉类抑制剂之间的相互作用模式，表皮生长因子受体的三维结构通过同源蛋白模建的方法得到，而抑制剂和靶酶结合复合物结构则通过分子力学和分子动力学结合的方法计算得到。从模拟结果得到的抑制剂和靶酶之间的相互作用模式表明范德华相互作用、疏水相互作用以及氢键相互作用对抑制剂的活性都有重要的影响，抑制剂的苯胺部分位于活性口袋的底部，能够与受体残基的非极性侧链产生很强的范德华和疏水相互作用，抑制剂双环上的取代基团也能和活性口袋外部的部分残基形成一定的范德华和疏水性相互作用，而抑制剂喹唑啉环上的氮原子能和周围的残基形成较强的氢键相互作用，对抑制剂的活性有较大的影响，计算得到抑制剂和靶酶之间的非键相互作用能以及抑制剂和靶酶之间的相互作用信息能够很好地解释抑制剂活性和结构的关系，为全新抑制剂的设计提供了重要的结构信息。     

Structural Studies on Host + Guest Recognition Sensory Systems

Rhodamine B-ethylenediamine--cyclodextrins (RhB--CDen) and rhodamine B--cyclodextrins (RhB--CD) can form inclusive complexes with many guest molecules, a reaction which can be used as a nucleic acid probe. In this paper, the most stable conformations of RhB--CDen and RhB--CD have been determined by fluorescence experiments and analyzed by molecular modeling simulation. The interaction between RhB--CDen and two guest molecules, 1-borneol and cyclohexanol, has also been investigated. The results showed that RhB--CDen has a stronger interaction with 1-borneol than with cyclohexanol. Borneol could push the three aromatic-rings of rhodamine B out of the CD cavity, while the cyclohexanol could not. The interactive sites of host and guest are also presented.     

Structure elucidation and 3D solution conformation of the antibiotic enduracidin determined by NMR spectroscopy and molecular dynamics

Enduracidin and ramoplanin belong to the large family of cyclodepsipeptide antibiotics, highly effective against Gram-positive bacteria. The primary and 3D solution structure of ramoplanin is already well known, and the primary structure of enduracidin has been determined by a combination of chemical and NMR spectroscopic methods. Both antibiotics share a similar peptide core of 17 amino acids and differ mainly in the length of the acyl chain and the presence of two D-mannose moieties in ramoplanin. Based on the high sequence homology with ramoplanin, the structure in solution of enduracidin is modeled as a cyclic peptide. The tertiary structure thus obtained was refined through molecular dynamics (MD) simulation, in which the interatomic NOE-derived distance restraints were imposed. MD simulations yielded a family of representative 3D structures (RMSD = 0.89), which highlighted a backbone geometry similar to that of ramoplanin in its beta-hairpin arrangement. In contrast, enduracidin displays a different arrangement of the side-chain and of the residues forming the hydrophobic core.     

Molecular Dynamics Simulation of the Self-assembled Monolayers of 1-Adamantanethiolate and Its Derivatives on Au（111） Surfaces

The self-assembled monolayers （SAMs） of 1-adamantanethiolate and its derivatives on Au（111） surface were investigated. Density functional theory （DFT） calculation indicates that the most stable configuration for absorption is at the face centered cubic （fcc）-bridge site. Canonical ensemble molecular dynamics （MD） simulations were carried out to study the structures and energies of the SAMs. The ordered structures of the SAMs were analyzed by means of radial distribution function and the relative stability of the SAMs was compared. It was concluded by the comparison of various contributions to the SAM formation energy that the formation of the SAMs was determined by the intermolecular nonbonding interaction and the chemical bonding interaction of sulfur and gold.     

Interconversion behavior of the C-H bond in the CH4+ radical cation: ab initio molecular dynamics study

Thermal motion of CH4+ is investigated by performing an ab initio molecular dynamics method with the second-order M?ller-Plesset (MP2)/6-311G** force field. In the trajectories obtained at 400 K, we have observed rapid interconversion behavior of the geometrical parameters of CH4+ with the frequency of 0.6/ps, where the C-H pair forming the small angle around 55 degrees is switched to another pair on subpicosecond time scale. The switching patterns are found to be classified into the following two types. Type 1: one C-H of the small angled C-H pair is switched to one C-H of the other C-H pair. Type 2: the small angled C-H pair is switched to the other C-H pair, which has been newly observed in the present ab initio MD calculation. The four C-H bonds of CH4+ are characterized by the long and short C-H bonds in a time region of the trajectories, and also for the time-evolution of C-H bonds such interconversion behavior is observed. The switching patterns of the geometrical parameters are compared with those in the interconversion scheme between six equivalent C2v symmetry structures of CH4+ [Paddon-Row, M. N. et al., J Am Chem Soc 1985, 107, 7696]. We have also investigated the electronic energy fluctuation due to thermal motion of CH4+. The standard deviation of total electronic energy at 400 K is evaluated to be 1.2 kcal/mol.     

氢在钯单晶表面的解离与在体相的扩散

氢分子在金属表面的解离吸附与氢原子在金属体相的扩散是个典型的表面过程.前者在甲烷化及合成氨等基础化工反应中起着关键作用;后者常常导致金属材料的脆化与断裂,但过渡金属及其合金是安全和优良的储氢材料.因此,研究氢分子在金属表面的解离吸附与氢原子在金属体相的扩散,是多相催化与金属物理广泛感兴趣的课题,具有重要的理论和应用价值.本文采用分子动力学方法初步探讨了二者之间的关联.分子催化动力学为从微观层次上研究上述课题提供了一种理论方法.本文采用经过我们改进的半经验LEPS方法,计算了氢分子在Pd(100)和(110)晶面的解离和氢原子在钯表面与体相扩散的相互作用位能面,并根据计算结果探讨了其微观机理.     

Methodology for the calculation of the potential of mean force for a cation-pi complex in water.

We report potential of mean force (PMF) calculations on the interaction between the p-sulfonatocalix[4]arene and a monovalent cation (Cs(+)). It has been recently shown from microcalorimetry and (133)Cs NMR experiments that the association with Cs(+) is governed by favourable cation-pi interactions and is characterized by the insertion of the cation into the cavity of the macrocycle. We show that the PMF calculation based upon a classical model is not able to reproduce both the thermodynamic properties of association and the insertion of the cation. In order to take into account the different contributions of the cation-pi interactions, we develop a new methodology consisting of changing the standard PMF by an additional contribution resulting from quantum calculations. The calculated thermodynamic properties of association are thus in line with the microcalorimetry and (133)Cs NMR experiments and the structure of the complex at the Gibbs free-energy minimum shows the insertion of the cation into the cavity of the calixarene.     

Vibrational dynamics of hydrogen‐bonded HCN complexes with OH and NH acids: Computational DFT systematic study

Vibrational properties (band position, infrared [IR], and Raman intensities) of C?N stretching mode were studied in 65 gas phase hydrogen‐bonded 1:1 complexes of HCN with OH acids and NH acids using density functional theory (DFT) calculations at the B3LYP‐6‐311++G(d,p) level. Furthermore, general characteristics of the hydrogen bonds and vibrational changes in acids OH/NH stretching bands were also considered. Experimentally observed blue shift of the C?N stretching band promoted by hydrogen bonding, which shortens the triple bond length, is very well reproduced and quantitatively depends on the hydrogen bond length. Both IR and Raman ν(C?N) band intensities are enhanced, also in good agreement with the experimental results. IR intensity increase is a direct function of the hydrogen bond energy. However, the predicted Raman intensity raise is a more complex function, depending simultaneously on characteristics of both the hydrogen bond (C?N bond length) and the H‐donating acid (polarizability). With these two parameters, ν (C?N) Raman intensities of the complexes are explained with a mean error of ±2.4%. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007