分子密堆积法及其在B链羧端去六肽(B25—30)胰岛素结构测定中的应用

基于分子密堆积原理我们定义了一个能够表达在单位晶胞中对称相关分子之间堆积相容性的密堆积函数,并在计算机上模拟晶格中的分子密堆积,同时计算该函数在分子的每个旋转及平移位置的值,使分子密堆积定量化。这一方法不仅可以从多个旋转函数或平移函数峰中判断出一个正确的解,而且可能独立地、定量地和快速地解决一些特殊的旋转及平移问题。用已知结构B链羧端去五肽胰岛素作为例子检验了分子密堆积法及其程序的有效性,并用分子密堆积法独立地解决了未知结构B链羧端去六肽胰岛素的平移问题.R因子搜索等方法证实了密堆积法的解的正确性。分子密堆积法可以作为一种既相对独立于分子置换法又与之相辅相承的方法。     

一种改进的分子连接性指数

通过修正分子连接性指数中的点价,使分子轨道理论与分子拓扑理论有机地结合起来,将分子连接性指数改进成为一种量子拓扑指数．实际计算表明,改进后的指数不但保留了原分子连接性指数的优点,而且还弥补了量化指数和分子拓扑指数的一些缺陷。     

原子和简单分子失电子后的体积变化

本文在对比分析一些分子及其一价阳离子的键长的基础上,运用分子轨道理论和共振论成功地解释了实验数据,以及部分分子的阳离子比相应分子的键长大的原因。并对分子失电子后体积变化的规律作了一些有益的探讨     

分子印刷板

分子印刷板是一种主体分子修饰的特制表面,通过超分子相瓦作用在该表面上固定客体分子.在分子印刷板的研究过程中发展的"多重相互作用"理论,可以更好地定量理解分子印刷板与客体分子间的超分子相互作用过程.通过对分子印刷板的广泛研究可以加深人们对超分子化学、表面化学、化学生物学等领域的认识,拓展其在纳米技术、分子的表面定位等方面的应用.     

十七烷基苯酰胺的STM图像分析

通过两种扫描技术,得到不同尺寸下清晰的十七烷基苯酰胺分子图像,这些吸附在高度定向排列石墨基质(HOPG)上的十七烷基苯酰胺分子长轴与石墨表面平行,分子呈首尾一致的定向排列。图中不仅能清楚地识别分子骨架上的甲基或亚甲基,而且较大的苯酰胺基团也能与烷基链清晰地区别开来。     

VRML在分子对称性教学中的应用

以椅式环己烷为例,介绍了如何应用分子模拟软件制作含有分子对称元素的VRML模型的过程。利用VRML的交互性可以帮助学生直观地掌握分子的三维结构以及对称元素的分布,切实提高了分子对称性的教学效果。     

聚合反应条件对渐变型塑料光纤预制棒的折射率分布的影响

用甲基丙烯酸甲酯 (MMA)作为基质 ,采用界面 凝胶聚合技术成功地制备了渐变型塑料光纤预制棒 ,并探讨了掺杂剂浓度及其分子体积以及聚合温度对折射率分布的影响 .观察到聚合温度对折射率分布的影响以及掺杂剂分子的分子体积在极端情况下 (如溴苯与MMA分子的分子体积相似 ,联苯分子体积比MMA则要大的多 )对折射率分布的影响 ,清楚地显示出分子体积在界面 凝胶聚合过程中所起的重要作用 .实验结果表明了高温聚合有利于轴心Δn值的升高 ,可得数值孔径NA较大的预制棒 .低温聚合使得折射率分布趋于平缓化 .     

二维分子的原子不对称性研究

基于分子形状的二进制编码提出了权原子和法来描述原子的不对称环境, 其中权原子和是以相反的方向环绕分子所得原子不对称环境的量度, 分子中一个原子的权原子和与其镜像分子中相应原子的权原子和的大小相等, 符号相反. 权原子和不仅适用于手性分子, 还能描述非手性分子中原子的不对称性. 与Randic′提出的原子和进行比较表明, 权原子和比原子和具有更好地区分能力, 因此, 权原子和能够更好地表征原子的不对称性.     

电负性均衡

电负性是分子中一个原子把电子拉向它自身的能力,是化学理论的基本概念之一。继Pauling建立第一个电负性标度后,提出了众多的电负性标度。只是在密度泛函理论的基础上,电负性概念和电负性均衡原理,才被精密地论证。近二十多年来,电负性理论的重要发展是:应用电负性均衡模型或方法,可以快速地计算分子体系的电荷分布,从而确定分子的其他性质,甚至包括分子的结构和反应性指标。通常的电负性均衡方法只把分子划分到原子区域,虽然简单直观,但其精度和应用范围受到限制。原子与键电负性均衡方法,把分子划分到包括原子区域、化学键区域和孤对电子区域,能够较快速精密地计算分子的电荷分布和其他性质,并被应用到构建新一代可极化或浮动电荷力场的探索中,有广阔的应用前景。     

从LB膜到分子自组装体系——1991年第五届国际LB膜会议追记

LB膜技术是一种分子组装技术,即在力场作用下能将两亲分子加以排列和转移到固体上的一种技术,并可利用这种技术,使各种功能分子或微粒有序地或有控制地排列,成为形成分子器件的一个十分重要的手段。1991年在巴黎召开的第五届国际LB     

Quantifying the symmetry content of the electronic structure of molecules: molecular orbitals and the wave function

A scheme to quantify the symmetry content of the electronic wave function and molecular orbitals for arbitrary molecules is developed within the formalism of Continuous Symmetry Measures (CSMs). After defining the symmetry operation expectation values (SOEVs) as the key quantity to gauge the symmetry content of molecular wavefunctions, we present the working equations to be implemented in order to carry out real calculations using standard quantum chemistry software. The potentialities of a symmetry analysis using this new method are shown by means of some illustrative examples such as the changes induced in the molecular orbitals of a diatomic molecule by an electronegativity perturbation, the breaking of orbital symmetry along the dissociation path of the H(2) molecule, the changes in the molecular orbitals upon a geometrical distortion of the benzene molecule, and the inversion symmetry content in the different spin states of the [Fe(CH(3))(4)](2-) complex.     

Molecular dynamics with helical periodic boundary conditions

Helical symmetry is often encountered in nature and thus also in molecular dynamics (MD) simulations. In many cases, an approximation based on infinite helical periodicity can save a significant amount of computer time. However, standard simulations with the usual periodic boundary conditions (PBC) are not easily compatible with it. In the present study, we propose and investigate an algorithm comprising infinitely propagated helicity, which is compatible with commonly used MD software. The helical twist is introduced as a parametric geometry constraint, and the translational PBC are modified to allow for the helical symmetry via a transitional solvent volume. The algorithm including a parallel code was implemented within the Tinker software. The viability of the helical periodic boundary conditions (HPBC) was verified in test simulations including α‐helical and polyproline II like peptide structures. For an insulin‐based model, the HPBC dynamics made it possible to simulate a fibrillar structure, otherwise not stable within PBC. © 2014 Wiley Periodicals, Inc.     

Maximum overlap symmetry molecular orbitals in conjugated systems

The application of the maximum overlap symmetry orbital (MOSO) method to conjugated systems is discussed briefly. The MOSO method can be employed to construct not only the symmetry orbitals and the molecular orbitais in alternant conjugated systems, but also the symmetry orbitais in non-alternant systems. It is shown that under the Hückel approximation the matrix MM⁺ can be written out directly from the molecular skeleton and may be treated by using chemical graph theory. Because the matrix MM⁺ of a system can be regarded as the Huckel matrix of a smaller system, the maximum overlap symmetry molecular orbital (MOSMO) calculation results can be easily obtained from those of the smaller systems. For homonuclear conjugated systems and for systems in which two kinds of atom appear altemantly, the MOSMOs and the corresponding molecular orbital (MO) energies obtained by the MOSMO calculation are the same as the MOs and the MO energies calculated by the Hückel molecular orbital method.     

Vector algebra and molecular symmetry: a tribute to Professor Josiah Willard Gibbs

Vector algebra, as developed by Josiah Willard Gibbs, is much simpler than matrix or tensor algebra, therefore, it is more suitable to introduce the students of chemistry into the wonderful world of molecular symmetry. A program based on elementary vector algebra has been written to determine all symmetry elements and symmetry operations of rigid molecular structures. The program also contains data for 57 point groups common in chemistry. Therefore, it automatically supplies the particular point group to which the structure belongs. Since the locations of the nuclei related to the symmetry elements are also revealed by the program, even the detailed notation of the framework group of the molecular structure can be deduced. The program can be a great help in determining the symmetries of the normal modes of vibration, too.     

联苯桥联的PPV齐聚物基态构型、电子能级和吸收光谱的理论研究

用密度泛函方法对联苯桥联的PPV齐聚物(TSB)的反式结构进行全优化,得到基态分子的最优几何构型和电子能级,并用ZINDO和TD-DFT方法分别计算其吸收光谱,分析了不同类型的端位取代基团对前线分子轨道能量和能隙的影响. 结果表明,联苯桥联后的PPV齐聚物在结构上形成了链间交叉链内扭曲的构象,这种交叉扭曲的构象降低了分子的对称性,减弱了共轭分子在固体中的π-π堆积作用,这可能是减少荧光猝灭效应,提高固体发光器件效率的重要原因.     

Fuzzy Symmetries for Linear Molecules and their Molecular Orbitals

In this paper, the fuzzy symmetry of some prototypical linear molecules has been analyzed. The results show that some molecular orbitals (MOs) are less symmetrical but some others are more symmetrical than the molecular skeleton, which the MOs correspond to. The membership functions of space inversion for MOs are closely related to the chemical characteristics of the MOs. Sometimes, although the symmetry of a molecular skeleton is not obvious, however that of some MO is quite obvious. The membership functions of the fuzzy inversion symmetry depend on the choice of the position of the center of inversion. As compared to those of diatomic molecules and linear tri-atomic molecules, the linear polyatomic molecules in which a distinctive fuzzy symmetry of space translation may exist, and thus a significant effect on their properties can be expected.     

Implementation of molecular symmetry in valence bond calculation

A novel strategy for the construction of many-electron symmetry-adapted wave function is proposed for ab initio valence bond (VB) calculations and is implemented for valence bond self-consistent filed (VBSCF) and breathing orbital valence bond (BOVB) methods with various orbital optimization algorithms. Symmetry-adapted VB functions are constructed by the projection operator of symmetry group. The many-electron symmetry-adapted wave function is expressed in terms of symmetry-adapted VB functions, and thus the VB calculations can be performed with the molecular symmetry restriction. Test results show that molecular symmetry reduces the computational cost of both the iteration numbers and CPU time. Furthermore, excited states with specific symmetry can be conveniently obtained in VB calculations by using symmetry-adapted VB functions.     

M(o)bius环并苯的分子对称性

一般来说,点群理论认为M(o)bius带环分子最高的对称性只能是C2.本文讨论了由18个苯环组成的环并苯的异构体分子,包括柱面的Hückel型分子(HC-[18])和扭转180°的M(o)bius带环分子(MC-[18]).结果表明除了点对称性外,M(o)bius带环分子还存在一种可称为环面螺旋旋转(TSR)变换的对称性,为此还引用了环面正交曲线坐标系.此外,还讨论了这些分子关于TSR对称性匹配的原子集和原子轨道(AO)集.根据TSR对称性的循环群特征,可以建立此类群的不可约表示及有关特征标.这类分子的分子轨道(MO)关于TSR群的不可约表示是纯的,然而所含的相应的原子轨道对称性匹配的线性组合(SALC-AO)成分可以是多种的.