化合物分子表面积计算方法的研究

化合物的分子表面积是重要的物理化学性质参数．根据不同的应用领域及数学方法,提出了多种分子表面积算法[1-10],由此产生了“分子表面积法”,各方法的有效性在各具体应用领域都已被验证．本文将统计方法中的随机变量引入计算化合物分子表面积体系,由分子模型化技术得到化合物分子的原子坐标,不考虑化合物分子中原子的相互作用及分子间近似,直接计算分子表面积．使用该方法可以计算“净”分子表面积、“溶剂可及表面积”、甚至分子结构片段,分子结构中有交叉重叠片段及存在“空洞”的各种分子表面积,该算法及程序较简捷,适应范围广,计算结果较为满意．     

端羧基聚醚聚硅氧烷的制备及其构建超分子的膜形貌与应用性能研究

采用聚醚胺封端聚硅氧烷(BPEAS)与马来酸酐(MAn)开环反应,合成了端羧基聚醚聚硅氧烷(CPSA),分别以CPSA为阴离子构建基元、杀菌性长碳链季铵基聚醚聚硅氧烷(QPEPS)为阳离子构建基元,以异丙醇为介质,通过静电作用进行超分子自组装,构建了一种新型超分子CPSA/QPEPS.通过红外光谱(FTIR)、核磁共振氢谱(~1H-NMR)对CPSA的结构进行表征,用白度仪、柔软度仪、织物折皱弹性仪、接触角仪、酶标仪等仪器对超分子CPSA/QPEPS的应用性能进行了研究,并用场发射扫描电镜(FESEM)、原子力显微镜(AFM)等对CPSA/QPEPS的膜形貌进行了观察.结果表明当m(QPEPS)/m(CPSA)=1∶1时,经CPSA/QPEPS整理过的棉织物,其弯曲刚度显著降低,静态吸水时间仅为4.39 s,且织物对大肠杆菌和金黄色葡萄球菌的抑菌率分别达到了71%.其次,超分子CPSA/QPEPS具有良好的成膜性,AFM观察其膜表面呈现出连续的山脉状形貌,在5μm×5μm扫描范围内CPSA/QPEPS膜的表面均方根粗糙度(R_q)达到了2.57 nm.     

卤代芳烃的脂水分配系数与分子结构的定量关系

本文通过HMO法计算得到了46个卤代芳烃的部分量子化学参数,同时计算了它们的分子总表面积(TSA),以线性溶解能关系(LSER)理论为基础探讨了化合物的正辛醇/水分配系数与其分子结构间的定量关系,建立了一种良好的分配模型,该模型可准确计算出两种溶剂的表面张力之差。     

一种计算多孔固体表面积的新方法

本文提出了一种新的计算多孔固体比表面积的方法。这个方法是根据氮气的脱附等温线求出单分子层饱和吸附量(V_m),然后求出比表面积(S_o)。用该方法的计算结果与用BET方法计算的结果相对误差很小。由于推导该方法需要的假设和近似比BET方程少,所以尤其在多孔固体的表面积测定中显示出它的结果正确性和优越性。     

不同形态水分对煤自燃过程微观作用机制研究

制备不同外在水分和原始赋存水分含量的煤体,通过模拟煤自燃升温氧化过程得到不同温度下的氧化煤样;利用原位傅里叶红外变换光谱仪测定不同氧化煤样中活性官能团的含量,研究形态水分对煤自燃过程微观官能团生成和转化的影响;利用氮吸附仪表征不同氧化煤样中比表面积大小,研究形态水分对煤自燃过程微观孔结构变化的影响;同时结合官能团与比表面积的变化规律,探讨形态水分对煤自燃过程的微观作用机制。形态水分对煤自燃过程的作用机制随着煤自燃状态发展而发生变化,表现出阶段性特征。外来水分含量和原始赋存水分都会促进酚、醇类羟基及含羧基类化合物的生成。外来水分和原始赋存水分的含量对煤自燃过程中微观比表面积、脂肪族C-H组分、含羟基化合物以及含羰基类化合物的生成和转化影响具有差异性;水分形态对微观比表面积和脂肪族C-H组分含量的变化影响具有差异性,而对含羟基化合物以及羧基化合物的生成和转化具有相似性。     

超价化合物的定义和成键特征初探

介绍一些描述超价化合物结构的理论,从改进的8电子规则和分子轨道理论出发,结合计算,对超价化合物结构进行解释.说明了超价化合物结构大量存在非键轨道的特征,同时给出了一个判断超价化合物的方法.     

核自旋偶合常数2JC-C-F的量子化学计算

用密度泛函B3LYP方法,在6-311G基组上对36个化合物进行构型优化、频率分析,计算了C-C-F的核自旋偶合常数^2JC-C-F。由此拟合出一个基于该方法和相同水平上计算^2JC-C-F的公式,选取四种化合物进行验证,计算值与文献值吻合。     

一种计算桥环化合物环数的简便方法

陈亚元同志在“桥环化合物环数的计算方法”一文中,提出了几种如何计算比较复杂的桥环化合物环数的具体方法,同时还介绍了P.A.Reddy对桥环化合物中环数的计算公式c=b-a+1(c为环数,b为环上的键总数,a为环上的原子总数),从而为计算桥环化合物的环数提供了比较简便的方法。由于桥环化合物与桥头原子并存,而化合物中桥头原子的总数目(包括主桥头原子和次桥头原子)又与环数的多少密切相关,所以,可以用桥环化合物中桥头原子的总数来正确计算桥环化合物的环数。设一种桥环化合物中的桥头原子总数为N,环数为M,根据两个桥头原子可以构成一个双环的原则,推导出计算环数的一般公式:     

介孔聚离子液体的可控合成及在常压CO2环加成反应中应用

采用刚性的离子液体聚合单体双-（3-乙烯基-1-咪唑）亚甲基双溴盐（[C₁DVIM]Br）,以聚乙二醇（PEG）为溶剂,能够简单快捷制备出高比表面积的介孔聚离子液体.通过调节PEG的分子量大小,即可有效控制所得聚离子液体的孔结构.介孔聚离子液体由于具有典型的聚阳离子骨架、较高的比表面积以及丰富的卤素位,作为非金属多相催化剂在常压下氧化苯乙烯为底物的CO₂环加成反应中表现出优异的催化活性和良好的回收稳定性,循环使用5次后催化性能基本保持不变.此外,该催化材料还表现出良好的底物兼容性,可以有效转化很难反应的脂肪类环氧化合物.     

毛细管气相色谱程序升温条件下保留值的高精度模拟

本文介绍一种高精度模拟色谱保留值的方法，它以有良好共用性的Ｋｏｖａｔｓ指数为基础数据，辅以在所用色谱柱上恒温下测量的系列正构烷烃保留值，加上所设置的程序升温参数，计算出各化合物在所用色谱柱上的热力学量，再从谱带运动方程出发，用数值方法高精度、快速地计算出各化合物在所用程序升温条件下的保留值。定性工作靠保留值检索而完成。本方法对程序升温的形式和阶数无限制。计算数度为：保留时间优于±１％，保留指数优于     

Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature

New computer programs, SurfRace and FastSurf, perform fast calculations of the solvent accessible and molecular (solvent excluded) surface areas of macromolecules. Program SurfRace also calculates the areas of cavities inaccessible from the outside. We introduce the definition of average curvature of molecular surface and calculate average molecular surface curvatures for each atom in a structure. All surface area and curvature calculations are analytic and therefore yield exact values of these quantities. High calculation speed of this software is achieved primarily by avoiding computationally expensive mathematical procedures wherever possible and by efficient handling of surface data structures. The programs are written initially in the language C for PCs running Windows 2000/98/NT, but their code is portable to other platforms with only minor changes in input-output procedures. The algorithm is robust and does not ignore either multiplicity or degeneracy of atomic overlaps. Fast, memory-efficient and robust execution make this software attractive for applications both in computationally expensive energy minimization algorithms, such as docking or molecular dynamics simulations, and in stand-alone surface area and curvature calculations.     

表面活性剂的QSAR/QSPR研究进展*

本文综述了表面活性剂定量结构-活性/性质相关(QSAR/QSPR)研究的最新进展,以及相关结构描述符在表面活性剂QSAR/QSPR研究中的应用.重点介绍了表面活性剂的cmc和表面张力γ与分子结构的定量关系、离子型表面活性剂电荷分布的定量计算及其对胶体结构与性质的影响.对表面活性剂分子结构与活性/性质的定量相关研究的发展趋势进行了展望.     

Efficient approximate all-atom solvent accessible surface area method parameterized for folded and denatured protein conformations

Continuing advances in computer hardware and software are permitting atomic-resolution molecular simulations for longer time scales and on larger systems. Despite these advances, routinely performing atomistic simulations with explicit water for even small proteins, which reach the folding time of such proteins, remains intractable for the foreseeable future. An implicit approximation of the solvent environment using a solvent accessible surface area (SASA) term in a molecular mechanics potential function allows exclusion of the explicit water molecules in protein simulations. This reduces the number of particles by approximately an order of magnitude. We present a fast and acceptably accurate approximate all-atom SASA method parameterized using a set of folded and heat-denatured conformations of globular proteins. The parameters are shown to be transferable to folded and heat-denatured conformations for another set of proteins. Calculation of the approximate SASA and the associated derivatives with respect to atomic positions for a 4644 atom protein requires only 1/11th the CPU time required for calculation of the nonbonded interactions for this system. On a per atom basis, this algorithm is three times faster than the fastest previously published approximate SASA method and achieves the same level of accuracy.     

Improved strategy in analytic surface calculation for molecular systems: Handling of singularities and computational efficiency

Computer methods for analytic surface calculations of molecular systems suffer from numerical instabilities and are CPU time consuming. In this article, we present proposals toward the solution of both problems. Singularities arise when nearly collinear triples of neighboring atoms or multiple vertices are encountered during the calculation. Topological decisions in analytic surface calculation algorithms (accessibility of vertices and arcs) are based upon the comparison of distances or angles. If two such numbers are nearly equal, then currently used computer programs may not resolve this ambiguity correctly and can subsequently fail. In this article, modifications in the analytic surface calculation algorithm are described that recognize singularities automatically and treat them appropriately without restarting parts of the computation. The computing time required to execute these alterations is minimal. The basic modification consists in defining an accuracy limit within which two values may be assumed as equal. The search algorithm has been reformulated to reduce the computational effort. A new set of formulas makes it possible to avoid mostly the extraction of square roots. Tests for small-and medium-sized intersection circles and for pairs of vertices with small vertex height help recognize fully buried circles and vertex pairs at an early stage. The new program can compute the complete topology of the surface and accessible surface area of the protein crambin in 1.50–4.29 s (on a single R3000 processor of an SGI 4D/480) depending on the compactness of the conformation where the limits correspond to the fully extended or fully folded chain, respectively. The algorithm, implemented in a computer program, will be made available on request. © John Wiley & Sons, Inc.     

Calculation of the average properties of atoms in molecules. II

This article describes an algorithm for the calculation of the average properties of an atom in a molecule. The atom is defined within the topological theory of molecular structure, a theory which defines atoms, bonds, structure, and structural stability in terms of the topological properties of a system's charge distribution. The average properties of the atom so defined are uniquely determined by quantum mechanics. Results for a number of hydrocarbon molecules, obtained by the program PROAIM (properties of atoms in molecules) which implements this algorithm, are given. In general, this program enables one to calculate the average energy of an atom in a molecule to an accuracy of ±1 kcal/mol.     

Develop and test a solvent accessible surface area-based model in conformational entropy calculations

It is of great interest in modern drug design to accurately calculate the free energies of protein-ligand or nucleic acid-ligand binding. MM-PBSA (molecular mechanics Poisson-Boltzmann surface area) and MM-GBSA (molecular mechanics generalized Born surface area) have gained popularity in this field. For both methods, the conformational entropy, which is usually calculated through normal-mode analysis (NMA), is needed to calculate the absolute binding free energies. Unfortunately, NMA is computationally demanding and becomes a bottleneck of the MM-PB/GBSA-NMA methods. In this work, we have developed a fast approach to estimate the conformational entropy based upon solvent accessible surface area calculations. In our approach, the conformational entropy of a molecule, S, can be obtained by summing up the contributions of all atoms, no matter they are buried or exposed. Each atom has two types of surface areas, solvent accessible surface area (SAS) and buried SAS (BSAS). The two types of surface areas are weighted to estimate the contribution of an atom to S. Atoms having the same atom type share the same weight and a general parameter k is applied to balance the contributions of the two types of surface areas. This entropy model was parametrized using a large set of small molecules for which their conformational entropies were calculated at the B3LYP/6-31G* level taking the solvent effect into account. The weighted solvent accessible surface area (WSAS) model was extensively evaluated in three tests. For convenience, TS values, the product of temperature T and conformational entropy S, were calculated in those tests. T was always set to 298.15 K through the text. First of all, good correlations were achieved between WSAS TS and NMA TS for 44 protein or nucleic acid systems sampled with molecular dynamics simulations (10 snapshots were collected for postentropy calculations): the mean correlation coefficient squares (R2) was 0.56. As to the 20 complexes, the TS changes upon binding; TΔS values were also calculated, and the mean R2 was 0.67 between NMA and WSAS. In the second test, TS values were calculated for 12 proteins decoy sets (each set has 31 conformations) generated by the Rosetta software package. Again, good correlations were achieved for all decoy sets: the mean, maximum, and minimum of R2 were 0.73, 0.89, and 0.55, respectively. Finally, binding free energies were calculated for 6 protein systems (the numbers of inhibitors range from 4 to 18) using four scoring functions. Compared to the measured binding free energies, the mean R2 of the six protein systems were 0.51, 0.47, 0.40, and 0.43 for MM-GBSA-WSAS, MM-GBSA-NMA, MM-PBSA-WSAS, and MM-PBSA-NMA, respectively. The mean rms errors of prediction were 1.19, 1.24, 1.41, 1.29 kcal/mol for the four scoring functions, correspondingly. Therefore, the two scoring functions employing WSAS achieved a comparable prediction performance to that of the scoring functions using NMA. It should be emphasized that no minimization was performed prior to the WSAS calculation in the last test. Although WSAS is not as rigorous as physical models such as quasi-harmonic analysis and thermodynamic integration (TI), it is computationally very efficient as only surface area calculation is involved and no structural minimization is required. Moreover, WSAS has achieved a comparable performance to normal-mode analysis. We expect that this model could find its applications in the fields like high throughput screening (HTS), molecular docking, and rational protein design. In those fields, efficiency is crucial since there are a large number of compounds, docking poses, or protein models to be evaluated. A list of acronyms and abbreviations used in this work is provided for quick reference.     

Improved algorithm for accurate computation of molecular solid angles

A new algorithm involving the calculation of the solid angle of a molecule about a point as a measure of steric size has been developed. The algorithm calculates the total solid angle in a stepwise fashion, summing all regions of individual atom solid angles and overlapped atoms, taking into account all orders of possible overlap of multiple atoms. The results for several molecular fragments have been compared to previous solid and cone angle calculations and improved correlations were observed. © 1996 by John Wiley & Sons, Inc.