液体和非晶态Ni64B36合金结构的从头算分子动力学模拟

运用从头算分子动力学模拟了液体以及猝冷后形成的非晶态Ni₆₄B₃₆合金体系, 得到了它们的对相关函数、结构因子、键对分析方面的结构信息, 与实验结果相当一致; 结果表明, 猝冷得到的合金性质与液体合金性质相似, 为非晶态结构. B原子多数以B—B双原子成键形式分散于Ni原子构成的骨架中. 电子态密度分析表明, Ni 3d电子最活泼, 因此在合金中Ni为活性位. 轨道电荷分析从电子结构角度揭示了在NiB 催化剂中B作为修饰剂的机理.     

Local elevation: A method for improving the searching properties of molecular dynamics simulation

Summary The concept of memory has been introduced into a molecular dynamics algorithm. This was done so as to persuade a molecular system to visit new areas of conformational space rather than be confined to a small number of low-energy regions. The method is demonstrated on a simple model system and the 11-residue cyclic peptide cyclosporin A. For comparison, calculations were also performed using simulated temperature annealing and a potential energy annealing scheme. Although the method can only be applied to systems with a small number of degrees of freedom, it offers the chance to generate a multitude of different low-energy structures, where other methods only give a single one or few. This is clearly important in problems such as drug design, where one is interested in the conformational spread of a system.     

Structure-activity relationships of pyrethroid insecticides. Part 2. The use of molecular dynamics for conformation searching and average parameter calculation

Summary Molecular dynamics simulations have been performed on a number of conformationally flexible pyrethroid insecticides. The results indicate that molecular dynamics is a suitable tool for conformational searching of small molecules given suitable simulation parameters. The structures derived from the simulations are compared with the static conformation used in a previous study. Various physicochemical parameters have been calculated for a set of conformations selected from the simulations using multivariate analysis. The averaged values of the parameters over the selected set (and the factors derived from them) are compared with the single conformation values used in the previous study.     

Pu（^7Fg）＋H2（X^1∑g^＋,0,0）的分子反应动力学

基于PuH_2分子基态(X~7A_1)的分析势能函数，用准经典的Monte-Carlo轨线法 对Pu(~7Fg)+H_2(X~1∑_g~+，0，0)的分子反应动力学过程进行了计算。结果表明 ：Pu(~7F_g)与H_2(X~1∑_g~+，0，0)碰撞是弹性碰撞。     

Comparison of the Dynamics of Water Molecules in Crystals of Proton-Ordered Ice IX and Its Proton-Disordered Analog III

A computer simulation of proton-ordered ice IX and its proton-disordered analog III (768 molecules, 90 K) was carried out by the molecular dynamics method using Poltev–Malenkov's potential. For ice IX, the differences in the dynamic characteristics of molecules with O(1) and O(2) are much wider than those in the case of ice III. The libration spectrum of ice IX has a number of distinct acute peaks, and the spectrum of ice III is strongly smoothed. These peculiarities are explained by the proton ordering of ice IX and disordering of ice III. The latter is responsible for the great differences in the short- and especially long-range environment of water molecules in ice crystals and hence for the presence of many molecules with different dynamic characteristics. Thus averaging over a large number of different vibrational spectra of molecules leads to a smoothed total spectrum in the case of the proton-disordered crystal modification of ice.     

The search for a new model structure of β-Factor XIIa

We present the search for a new model of -factor XIIa, a blood coagulation enzyme, with an unknown experimental 3D-structure. We decided to build not one but three different models using different homologous proteins as well as different techniques and different modellers. Additional studies, including extensive molecular dynamics simulations on the solvated state, allowed us to draw several conclusions concerning homology modelling, in general, and -factor XIIa, in particular.     

Influences of local polymer-solvent π-π-interaction on dynamics of phenyl ring rotation and its role on photophysics of conjugated polymer

In this report, the role of local polymer-solvent π-π-interaction on rotational dynamics of phenyl rings of poly[2-methoxy-5-(2′-ethyl-hexyloxy)-1,4-phenylenevinylene] (MEH-PPV) is examined by utilizing nuclear magnetic resonance (NMR) spectroscopy. We have found that an aromatic solvent can couple strongly with the phenyl rings via favorable local π-π-interaction, causing a restriction of the ring rotation. The dynamic process takes place at much faster rate in a non-aromatic solvent. NMR line shape analysis indicates the existence of two side chain configurations with relatively long life-time in toluene and pyridine while a single time-averaged configuration is detected in chloroform and tetrahydrofuran. Addition of chloroform or cyclohexane to a solution of MEH-PPV in toluene is accompanied by an increase of the rotational dynamics. This indicates that the expansion or collapse of main chain upon varying solvent quality play a minor role on the rotational dynamics. The relationship between the dynamics of ring rotation and photophysics of MEH-PPV in solution is discussed.