Energy decomposition in molecular complexes: implications for the treatment of polarization in molecular simulations

This study examines the contribution of electrostatic and polarization to the interaction energy in a variety of molecular complexes. The results obtained from the Kitaura-Morokuma (KM) energy decomposition analysis at the HF/6-31G(d) level indicate that, for intermolecular distances around the equilibrium geometries, the polarization energy can be determined as the addition of the polarization energies of interacting blocks, as the mixed polarization term is typically negligible. Comparison of KM and QM/MM results shows that the electrostatic energy determined in the KM method is underestimated (in absolute value) by QM/MM methods. The reason of such underestimation can be attributed to the simplified representation of treating the interaction between overlapping charge distribution by the interaction of a QM molecule with a set of point charges. Nevertheless, the polarization energies calculated by KM and QM/MM methods are in close agreement. Finally, a consistent, automated strategy to derive charge distributions that include implicitly polarization effects in pairwise, additive force fields is presented. The strategy relies in the simultaneous fitting of electrostatic and polarization energies computed by placing a suitable perturbing particle at selected points around the molecule. The suitability of these charges to describe molecular interactions is discussed.     

Chemical shift driven geometry optimization

A new method for refinement of 3D molecular structures by geometry optimization is presented. Prerequisites are a force field and a very fast procedure for the calculation of chemical shifts in every step of optimization. To the energy, provided by the force field (COSMOS force field), a pseudoenergy, depending on the difference between experimental and calculated chemical shifts, is added. In addition to the energy gradients, pseudoforces are computed. This requires the derivatives of the chemical shifts with respect to the coordinates. The pseudoforces are analytically derived from the integral expressions of the bond polarization theory. Single chemical shift values attributed to corresponding atoms are considered for structural correction. As a first example, this method is applied for proton position refinement of the D-mannitol X-ray structure. A crystal structure refinement with 13C chemical shift pseudoforces is carried out.     

Some thermodynamic aspects of highT c superconductors

Thermochemical and thermodynamical properties of HTSC phases are reviewed for the Y-Ba-Cu-O system and also presented for the newly calculated Bi-Sr-Cu-O system stressing out stoichiometric and phenomenological viewpoints. Simulated data are listed for (H ₂₉₈ ^o -H _o ^o , phase transformation temperatures, standard entropies, standard enthalpies of formation, heat capacities in crystalline phase, etc. Pseudobinary phase diagrams are treated showing the effect of oxygen partial pressure particularly illustrated on the (Sr, Bi, Ba)-Cu-O system.The work was carried out under the project No. A 2010532 supported by the Grant Agency of Academy of Sciences of the Czech Republic and the grant No. 104/97/0589 financed by the Grant Agency of the Czech Republic.     

GROMACS: fast, flexible, and free

This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor searching and of inner loop performance, GROMACS is a very fast program for molecular dynamics simulation. It does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. In addition, it can handle polarizable shell models and flexible constraints. The program is versatile, as force routines can be added by the user, tabulated functions can be specified, and analyses can be easily customized. Nonequilibrium dynamics and free energy determinations are incorporated. Interfaces with popular quantum-chemical packages (MOPAC, GAMES-UK, GAUSSIAN) are provided to perform mixed MM/QM simulations. The package includes about 100 utility and analysis programs. GROMACS is in the public domain and distributed (with source code and documentation) under the GNU General Public License. It is maintained by a group of developers from the Universities of Groningen, Uppsala, and Stockholm, and the Max Planck Institute for Polymer Research in Mainz. Its Web site is http://www.gromacs.org.     

剪应力下弱作用势胶体颗粒聚团的特点

探讨了不同剪应力下，具有Ｌｅｎｎａｒｄ－Ｊｏｎｅｓ势的胶体颗粒聚团的结构特性，包括簇团的大小分布，径向分布函数，分形维数和原子配位数。研究表明，在弱作用力下，胶体簇团的分布随剪应力的增加而趋向小簇团一边；径向分布函数曲线随剪应力的增加而降低，胡在近程距离内降低得最多；分形维数随剪应力的增加表现为先增加后减小的趋势，其值随模拟条件的不同而在１．９－２．４之间变动。剪应力“场”对分形维数的大小没有太大     

共聚物配体交替结构与其催化活性关系的理论研究

本文采用以ASED-MO(含原子对排斥的EHMO法)为基础的结构自动优化的EHTOPT法及Monte-Carlo法, 对甲醇羰基化制乙酸催化剂的共聚物配体交替结构进行了理论研究。计算了AA, AB, BB, BA二聚反应的反应途径, 找出了过渡态, 并确定了反应活化势垒。在假设两反应频率因子相同的前提下, 求出竞聚率, 采用Monte-Carlo法模拟共聚物结构, 计算出共聚物配体中起催化活性的AB交替结构所占比率。比较不同共聚物配体的活性, 并研究了温度及单体配比对共聚物配体交替结构的影响。     

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，…     

“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.