分子中原子电荷的一种新的计算法

分子中原子电荷的一种新的计算法王广昌（中国科学院安徽光机所合肥２３００３１）分子的电荷分布是决定分子结构和性质的最重要物理量。原理上，通过求解多体波动方程可以得到分子的电荷分布，但实际上这是极为困难的。因此近似的理论处理或半经验方法就常常被人们用来估...     

原子和分子电荷密度Laplacian量的性质

Morse和Feshbach指出,一个数量场的Laplacian量是非常重要的物理量,它可以直接确定这个场的密集和疏松的准确位置和程度。Bader发现,原子和分子电荷密度ρ(r)的拓扑性质与其Laplacian之间存在着某种内在联系,并且通过其Laplacian的性质,可以在电荷密度分布和支配它的力学性质之间建立一个桥梁。我们知道,维里定理(Virial Theorem)可以表示为 V+2T=0 (1)     

新型掺杂多孔芳香骨架材料的储氢性能模拟

基于PAF-301分子模型通过Li掺杂或B取代等模式设计了几种新型多孔芳香骨架(PAFs)材料,采用量子力学和分子力学方法对新材料的储氢性能进行研究.由量子力学计算得到了不同分子片段与H2之间的结合能,并结合DDEC方法计算了各分子片段的原子电荷分布.利用巨正则蒙特卡洛(GCMC)模拟方法计算了77和298 K下H2在不同PAFs材料中的吸附平衡性质.结果表明,H2直接与苯环的结合能较低,但掺杂Li原子能够提高H2与六元环的结合能,同时Li原子体现出较高的正电性质,B原子取代苯环中的两个C原子后,使得原有C原子电负性增强;77 K下PAF-301Li具有最高的储氢性能,而PAF-C4B2H4-Li2-Si和PAF-C4B2H4-Li2-Ge体现出较好的常温储氢性能,各种材料的常温储氢性能远低于其低温储氢性能.通过77 K下H2在PAFs材料中的等位能面分布和吸附平衡质心密度分布对H2在PAFs材料中的优先吸附位置进行分析,发现在PAF-301和PAF-301Li骨架中,由于中心能量较低的等位能区域范围较宽,H2在其中存在四个明显的吸附高密度分布区域,而其它三种PAFs晶胞中心能量较低的等位能区域范围较窄,使得H2在其中只存在两个明显的吸附高密度分布区域.     

极性分子键角与键偶极矩的关系

研究了基态极性分子的键角和键偶极矩之间的关系。我们采用原子偶极矩校正的Hirshfeld （ADCH）电荷来计算键偶极矩,利用电子的局域函数和键临界点处的局域函数值来分析键的电子结构。通过对IVA族（IVA = C,Si,Ge）、VA族（VA = N,P,As ）、VIA族（VIA = O,S,Se）和VIIA族（VIIA = F,Cl,Br）元素形成的系列共价型基态分子,以及环状基态分子的键角和键偶极矩数据进行分析,发现在键的电子结构类似的情况下,由于键偶极矩的排斥作用,这些分子的键角随键偶极矩的增加而增大。这一发现有助于加深我们对分子几何结构的认识。     

原子-键电负性均衡方法参数的确定与探讨

原子-键电负性均衡方法(ABEEM)是以密度泛函理论(DFT)和电负性均衡原理为基础发展而来，它明确地考虑了化学键是不引入任何实验数据的带纯理论性和计算的方法．使用统一标准并具有代表性和全面性地选择了200多个模型分子，利用可得到较准确结构的MP2／6-31G*优化结构，心／STO-3G单点计算得到Mulliken重叠布居，再用最小二乘法拟合得到许多主族元素在分子体系中的诸原子(包括单、双和叁键等不同成键状态)和化学键的ABEEM参数．所得到的原子的价态电负性可与已提出的其他电负性标度相比拟，计算CO得到的电荷负端为C(与从头计算的结果相反)，结果与实验相符，且原子电荷的正负不完全由原子电负性决定．     

高温超导体的Cu-O键型和氧上的部分电荷

多数钙钛矿型化合物是离子型绝缘体，而高温超导化合物则有金属电性，它们是以什么键型为主？对此等人[1]认为用共价或金属成键图像描述高温超导体在化学上更合理，Nepela等人[2]指出超导体临界温度（Tc）随阴离子平均电负性与阳离子平均电负性之差增大而升高．这意味着离子性较强的超导体有较高的人．杨频等问运用晶型键参数方法估算结果表明高温超导体属干部分离子性与部分共价性键．以上不同的结果都是基丁理论处理或估算得到的·本文试图在实验上通过比较不同成键特征的铜化合物的x光电子能潜（＊P8）来估计对高温超导性起重要作用的C…     

芳甲酰基脲生物活性的量子化学研究

采用密度泛函(DFT)的方法对12个芳甲酰基脲类化合物进行了量子化学计算, 随后讨论了影响化合物生物活性的可能因素. 结果表明, 芳环3, 4, 5号碳原子对HOMO轨道的贡献和芳环上3, 4, 5号碳原子的所带的电荷之和芳环与杂环间的二面角对化合物的活性影响最为重要.     

亲电取代反应中活性位点预测方法的比较

预测发生亲电取代反应的活性位点具有重要的理论和实际意义. 目前已提出了许多基于反应物自身电子结构的预测方法. 本文选择14 个单取代苯和8 个双取代苯作为测试集,对14 种预测方法的可靠性进行了详细的比较分析. 结果表明,福井函数、平均局部离子化能等体现局部电子软度的方法特别适合含有邻对位定位基的单取代苯和双取代苯体系,但对于含有单个间位定位基的体系,这类方法往往预测失败. 基于静电效应的预测方法整体表现明显不如体现局部软度的方法,但更适合含有单个间位定位基的体系. 对所有体系预测能力最稳健的是双描述符,因此可以作为普适性的预测方法.     

亲电取代反应中活性位点预测方法的比较

预测发生亲电取代反应的活性位点具有重要的理论和实际意义.目前已提出了许多基于反应物自身电子结构的预测方法.本文选择14个单取代苯和8个双取代苯作为测试集,对14种预测方法的可靠性进行了详细的比较分析.结果表明,福井函数、平均局部离子化能等体现局部电子软度的方法特别适合含有邻对位定位基的单取代苯和双取代苯体系,但对于含有单个间位定位基的体系,这类方法往往预测失败.基于静电效应的预测方法整体表现明显不如体现局部软度的方法,但更适合含有单个间位定位基的体系.对所有体系预测能力最稳健的是双描述符,因此可以作为普适性的预测方法.     

Restrained point-charge models for disaccharides

Various methods for deriving atomic partial charges from the quantum chemical electrostatic potential and moments have been tested for the sucrose molecule. We show that if no further information is used, the charges on some carbon atoms become large and charge patterns involving these atoms are badly determined and poorly transferable. Adding lone-pairs on the ether oxygen atoms or dividing the molecule into smaller fragments did not cure the instabilities. We develop a method, CHELP-BOW0, that restrains charges toward zero with different weights for different atoms. These harmonic restraints preserve the linear form of the least-squares equations, which are solved in a single step using singular-value decomposition. CHELP-BOW0 improves the chemical transferability of the charges compared to unrestrained methods, and slightly improves their conformational transferability. It introduces a modest degradation of the fit compared to unrestrained CHELP-BOW (mean average deviation of the potential 0.00016 vs. 0.00010 a.u.). A second new method, CHELP-BOWC, avoids the need for restraints by including several conformations in the fit, weighting each according to its estimated energy in solution. CHELP-BOWC charges are more transferable than CHELP-BOW or CHELP-BOW0 charges to conformations not included in the training set. Restraints to zero charge do not further improve transferability of the CHELP-BOWC charges. We, therefore, recommend CHELP-BOW charges for rigid molecules and CHELP-BOWC charges for flexible molecules.     

Automated site-directed drug design: An assessment of the transferability of atomic residual charges (CNDO) for molecular fragments

Summary In this paper a database of atomic residual charges has been constructed for all the molecular fragments defined previously in a combinatorial search of the Cambridge Structural Database. The charges generated for the atoms in each fragment are compared with charges calculated for whole molecules containing those fragments. The fragment atomic charges lie within 1 S.D. of the mean for 68%, and within 2 S.D. for 91%, of the atoms whose charges were computed for whole molecules. The actual charges on any atom are strongly influenced by the adjacent connected atoms. There is a large spread of atomic residual charge within the fragments database.     

Atomic charges for molecular dynamics calculations

Atomic charges obtained with the fit of the ab initio electrostatic potential suffers of several defects, for instance, chemical meaning is not insured. We have employed a method recently put forward for deriving atomic charges which addresses the issue of chemical meaning and conformational transferability to N,N-dibutylacetamide and ethylenediaminetetraacetate. The charges have been used in molecular dynamics calculations where the interaction with a metallic cation is considered. We found structural parameters for the complexes in good agreement with the available experimental results.     

Electron density analyses of opioids: a comparative study

The electron densities of five morphine related molecules (codeine, diprenorphine, naltrexone in the neutral and protonated states, and dextromethorphan) were determined from high-resolution X-ray diffraction experiments (Mo Kalpha and synchrotron primary radiation) at low temperature and CCD area detection techniques. Bond topological analyses were applied, and a partitioning of the molecules into atomic regions making use of Bader's zero flux surfaces yielded atomic volumes and charges. The obtained atom and bonding properties were compared to the results of a previous experimental study of morphine and to theoretical calculations. Experimental and theoretical properties for all chemically equivalent bonds agree within an uncertainty range as is otherwise seen for different theoretical calculations. Hence, the transferability of chemically equivalent submolecular properties, being a key issue of the atoms in molecules (AIM) theory, has been verified experimentally in this class of chemically related molecules. On the other hand, topological differences could clearly be verified in regions with different chemical environments. Electron density differences between the two forms of naltrexone were examined and made visible in an extended region around the nitrogen atom which is once in a neutral state and once in a positively charged state.     

Atomic and bond topological properties of the tripeptide L-alanyl-L-alanyl-L-alanine based on its experimental charge density obtained at 20 K

A 20 K high resolution X-ray data set of L-Ala-L-Ala-L-Ala*1/2 H2O was measured using an ultra-low temperature laboratory setup, that combines area detection and a closed cycle helium cryostat. The charge density determination includes integration of atomic basins and topological analysis according to Bader's quantum theory of atoms in molecules. Two tripeptide units are found in the asymmetric unit, allowing the assessment of transferability of bond topological and atomic properties taking also into consideration previous data of oligopeptides. With respect to invariom modeling the limits of such transferability are investigated and the results of this study show the validity of the nearest/next-nearest neighbour approximation and support the use of database approaches for electron density modeling of macromolecules.     

Electronegativity equalization method: parameterization and validation for organic molecules using the Merz-Kollman-Singh charge distribution scheme

The electronegativity equalization method (EEM) was developed by Mortier et al. as a semiempirical method based on the density-functional theory. After parameterization, in which EEM parameters A(i), B(i), and adjusting factor kappa are obtained, this approach can be used for calculation of average electronegativity and charge distribution in a molecule. The aim of this work is to perform the EEM parameterization using the Merz-Kollman-Singh (MK) charge distribution scheme obtained from B3LYP/6-31G* and HF/6-31G* calculations. To achieve this goal, we selected a set of 380 organic molecules from the Cambridge Structural Database (CSD) and used the methodology, which was recently successfully applied to EEM parameterization to calculate the HF/STO-3G Mulliken charges on large sets of molecules. In the case of B3LYP/6-31G* MK charges, we have improved the EEM parameters for already parameterized elements, specifically C, H, N, O, and F. Moreover, EEM parameters for S, Br, Cl, and Zn, which have not as yet been parameterized for this level of theory and basis set, we also developed. In the case of HF/6-31G* MK charges, we have developed the EEM parameters for C, H, N, O, S, Br, Cl, F, and Zn that have not been parameterized for this level of theory and basis set so far. The obtained EEM parameters were verified by a previously developed validation procedure and used for the charge calculation on a different set of 116 organic molecules from the CSD. The calculated EEM charges are in a very good agreement with the quantum mechanically obtained ab initio charges.     

Atomic properties of N(2)O(4) based on its experimental charge density

Nitrogen dioxide, being known to exist as a dimer N2O4 in the crystal with a very long N-N bond length of 1.76 A, was crystallized at low-temperature conditions on a diffractometer. High-resolution X-ray data (sin(theta/lambda) = 1.249 A-1) were recorded with a CCD area detector to allow the generation of an experimental charge density distribution. By making use of Bader's AIM theory, zero-flux surfaces were calculated, and we examined atomic volumes and atomic charges obtained from this experiment and various theoretical calculations. Four commonly used methods of computing atomic charges (Mulliken, AIM, NPA, and CHELP) were considered. The AIM charges are rather independent from the used basis set. Interestingly, the evaluated atomic volumes are very similar between experiment and theory, although in theory isolated molecules are considered. For the long N-N bond a bond order n of approximately 0.5 was derived from a comparison with appropriate model compounds.