原子-键电负性均衡方法融合进分子力场(ABEEM/MM)应用于蛋白质分子(Crambin)模拟

建立应用于多肽和蛋白质模拟的ABEEM/MM浮动电荷力场.利用该模型和参数,对实际蛋白质分子Crambin(植物种子中的一种小的蛋白质)进行模拟,得到了满意的结果,为其更广泛的应用开辟了道路.     

原子-键电负性均衡方法中的σπ模型及应用

带有双键或共轭双键的化合物可进行加成、氧化和聚合等反应,在有机、生物和制药等领域用途广泛．密度泛函理论下的电负性均衡方法在研讨分子电荷分布和反应性等方面有独特优势［１～４］．在电负性均衡方法中,Ｍｏｒｔｉｅｒ［１］的电负性均衡方法引人注目,但其未考虑分子中化学键的存在．Ｇｈｏｓｈ［２］的半经验电负性均衡方法考虑了化学键电荷,但键电荷取值假定太简单,只能处理双原子分子．Ｙａｎｇ［３,４］等的原子－键电负性均衡方法同时考虑了分子中原子和化学键的存在,取得令人满意的结果．至今尚无人明确地考虑双键的结构…     

应用原子-键电负性均衡方法预测超氧化物歧化酶催化反应的活性部位

应用原子-键电负性均衡方法计算了超氧化物歧化酶的电荷分布和Fukui函数. 结果表明, 超氧化物歧化酶活性中心与超氧阴离子自由基作用时, 金属离子电荷转移在0.1 e～0.3 e之间, 而配体原子等的电荷转移却很小; 同时金属离子的Fukui函数大于配位原子的Fukui函数. 超氧化物歧化酶活性中心与抑制剂作用失活后, 金属离子的Fukui函数小于抑制剂中配位原子的Fukui函数. 电荷转移和Fukui函数表明, Mn, Fe和Cu离子分别是含锰、铁和铜锌超氧化物歧化酶的活性中心部位, 该预测不仅与量子化学理论计算一致, 而且与实验现象相吻合.     

小分子配位对血红素活性影响的原子-键电负性均衡方法研究

应用原子-键电负性均衡方法, 计算了血红素与小分子的配位络合物的电荷分布和Fukui函数. 血红素与氧、水、一氧化碳和一氧化氮结合时, 铁离子电荷转移到配体原子上. 活性中心铁离子的Fukui函数均大于氧和水配体中的配位氧原子, 而小于一氧化碳和一氧化氮配体中的配位碳和配位氮原子的Fukui函数. 从Fukui函数可以得出, 一氧化碳和一氧化氮很难从它们与活性中心血红素结合的配位络合物中解离出来, 而氧和水易于从它们与血红素结合的配位络合物中解离出来, 进而, 血红素可以再与其它配体结合. 血红素与KCN和NaN3抑制剂作用时, 铁离子的Fukui函数均小于与其配位的碳和氮原子, 表明在过氧化氢酶中血红素的活性作用减弱或被抑制.     

密度泛函理论下的分子电负性——Ⅵ.原子键电负性均衡模型

以密度泛函理论和电负性均衡原理为基础 ,将体系的单电子密度分割为原子的单电子密度和键的单电子密度 ,得到了分子总能量、分子中原子以及键的有效电负性的表达式 .基于这些表达式 ,提出了直接计算体系的总能量和体系中电荷分布的新方法 .此模型比其他电负性均衡方法更合理 .对大量分子的总能量和电荷分布所进行的计算结果表明所提出的原子 键电负性均衡模型是可行的 ,可以应用于确定各类生物和有机大分子的总能量和电荷分布 ,给出较EEM和MEEM模型更近于从头计算的结果     

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。     

密度泛函理论下的电负性均衡及应用

以密度泛函理论为框架,综述电负性和电负性均衡理论的发展及其在探讨各种分子性质时的应用。     

密度泛函理论下的分子总体电负性与调和平均电负性的关系

根据密度泛函理论定义的有效原子电负性，讨论了分子中总体电负性与调和平均电负性之间的关系，得到了调和平均电负性非常接近于总体电负性的结论，同时，说明了两者相似的原因，并对一系列分子给出了它们的数值比较．     

基于电负性均衡理论快速计算多肽分子中原子电荷的新方法

Atomic charges play a crucial role in the understanding and modeling of the chemical behavior of proteins. Fast assessment of atomic charge distributions in larger molecules can be performed by implementing the electronegativity equalization method (EEM). To further improve the accuracy of the EEM approach, a novel and efficient method based on Bader's concept of high degree fragment transferability of atomic charges has been proposed for the parameterization of atoms-in-molecules (AIM) charges of polypeptides or proteins. The EEM parameterization method considers both the factors of connectivity and hybridized states, and the effect of the local chemical environment in fragments or groups. The types of atoms were defined on the basis of the local chemical environments of the fragments or functional groups of these atoms. The fragment transferability feature of QTAIM indicates that the atomic properties for the contributing atoms can be reproduced if the chemical environment is comparable. The constituent fragments or functional groups of macromolecules such as polypeptides and proteins can be utilized as building blocks for the additive generation of their electronic densities. The main peptide group (NH―HαCα―C＝O) of the polypeptide in the backbone was used as a building block to model the EEM parameters for reproducing the atomic charges in the polypeptides. A training set of 20 terminally blocked amino acids (Ac-X-NHMe, X = any neutral residue), which recreated the immediate local environment of the main chain fragments or functional groups of the polypeptides, were chosen for the calibration of AIM charges using the differential evolution (DE) algorithm. The effects of the optimized methods on the results were discussed and it was found that the DE algorithm showed a better performance for the objective function. The quality of the AIM charges obtained from the EEM method presented in this study was evaluated by comparison with those obtained from B3LYP/6-31G+(d, p) calculations for the two test tetrapeptides not contained in the training set. It was found that a remarkable improvement was achieved using the EEM model developed in this study as compared to the previous studies. The introduction of Bader's high fragment charge transfer model into the EEM provided a new scheme for its calibration and parameterization for larger systems such as polypeptides or polynucleotides, which possess highly repetitive segments. Among all types of atomic charges, only the AIM charges showed a significant meaning in experiments and could be obtained by X-ray diffraction experiments. Rapidly reproducing the accurate AIM charge for large systems seems to be more meaningful, especially for the prediction of protein-protein, protein-DNA, and drug-receptor recognition and interactions.     

确定大分子体系电荷分布的新方法

近年来，应用密度泛函理论探求电负性和硬度与体系中电荷分布之间的关系，成为令人关注的课题[1~5]．Mortier[1,2]的电负性均衡方法（EEM）没有考虑化学键电荷．Ghosh[4]的半经验电负性均衡方法考虑了化学键电荷，但键电荷取值假设太简单．本文同时考虑了分子中的原子电荷和键电荷的作用，给出了分子中原子和化学键有效电负性的精密公式，这些公式为发展一个系统的精密电负性均衡方法及应用奠定了基础．1理论方法以密度泛函理论[6]为基础，将分子的单电子密度ρmol（r）按式（1）分割：式中ρα（r）是分子中α原子区域的单电子密度，ρα…     

Optimized and parallelized implementation of the electronegativity equalization method and the atom-bond electronegativity equalization method

The most common way to calculate charge distribution in a molecule is ab initio quantum mechanics (QM). Some faster alternatives to QM have also been developed, the so-called "equalization methods" EEM and ABEEM, which are based on DFT. We have implemented and optimized the EEM and ABEEM methods and created the EEM SOLVER and ABEEM SOLVER programs. It has been found that the most time-consuming part of equalization methods is the reduction of the matrix belonging to the equation system generated by the method. Therefore, for both methods this part was replaced by the parallel algorithm WIRS and implemented within the PVM environment. The parallelized versions of the programs EEM SOLVER and ABEEM SOLVER showed promising results, especially on a single computer with several processors (compact PVM). The implemented programs are available through the Web page http://ncbr.chemi.muni.cz/~n19n/eem_abeem.     

Calculation of molecular energies by atom-bond electronegativity equalization method

The atom-bond electronegativity equalization method (ABEEM), based on the equalization of the “effective electronegativity” of an atom or a bond in a molecule, allows the direct calculation of the charge distribution and the molecular electronegativity of a large molecule. We now demonstrate how the another important quantity, the total molecular energy, can be computed directly and rapidly. It is shown that, based on the ABEEM, the corresponding ab initio values of the total molecular energy can be reproduced with very satisfactory accuracy. In addition, it has been found that in the expression of the energy functional E[ρ] of the ABEEM, the charge-dependent term C correlates quite well with the total molecular bonding energy.     

Molecular electronegativity in density functional theory (VI) --Atom-bond electronegativity equalization model

Ｒｅｃｅｎｔｌｙ,ｄｅｖｅｌｏｐｍｅｎｔａｎｄａｐｐｌｉｃａｔｉｏｎｏｆｄｅｎｓｉｔｙｆｕｎｃｔｉｏｎａｌｔｈｅｏｒｙ(ＤＦＴ)ａｒｅｑｕｉｔｅａｔｔｒａｃｔｉｖｅｔｏｓｃｉｅｎｔｉｓｔｓ’ａｔｔｅｎｔｉｏｎ.Ｔｈｅｒｅｌｅｖａｎｔｐａｐｅｒｓａｒｅｉｎｃｒｅａｓｉｎｇｖｅｒｙｑｕｉｃｋｌｙ[1—11].ＳｉｎｃｅｔｈｅｅｌｅｃｔｒｏｎｅｇａｔｉｖｉｔｙｃｏｎｃｅｐｔｗａｓｐｒｏｐｏｓｅｄｂｙＰａｕｌｉｎｇ[12]ｔｏｄｅｓｃｒｉｂｅｔｈｅｐｏｗｅｒｏｆａｎａｔｏｍｉｎａｍｏｌｅｃｕｌｅｔｏａｔｔｒａｃｔｅｌ…     

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.     

Molecular electronegativity in density functional theory (II) --Direct calculation of group electronegativity and the atomic charges in a group

On the basis of a more precise expression of the atomic effective electronegativity deduced from the density functional theory and electronegativity equalization principle, a new scheme for calculating the group electronegativity and the atomic charges in a group is proposed and programed, and various parameters of electronegativity and hardness are given for some common atoms. Through calculation, analysis and comparison of more than one hundred groups, it is shown that the results from this scheme are reasonable and may be extended.     

Systematic formulations for electronegativity and hardness and their atomic scales within density functional softness theory

A unified Mulliken valence with Parr ground‐state electronegativity picture is presented. It provides a useful analytical tool on which the absolute hardness as well ionization potential and electron affinity functionals are based. For all these chemical reactivity indices, systematic approximate density functionals are formulated within density functional softness theory and are applied to atomic systems. For the absolute hardness, a special relationship with the new electronegativity ansatz and a particular atomic trend paralleling the absolute electron affinity are established that should complement and augment the earlier finite‐difference energetic approach. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006