Department of Chemistry and Chemical Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, People's Republic of China.
J Mol Graph Model. 2012 Sep;38:314-23. doi: 10.1016/j.jmgm.2012.07.004. Epub 2012 Jul 27.
Quantitative analysis of molecular surface is a valuable technique for analyzing non-covalent interaction, studying molecular recognition mode, predicting reactive site and reactivity. An efficient way to realize the analysis was first proposed by Bulat et al. (J. Mol. Model., 16, 1679), in which Marching Tetrahedra (MT) approach commonly used in computer graphics is employed to generate vertices on molecular surface. However, it has been found that the computations of the electrostatic potential in the MT vertices are very expensive and some artificial surface extremes will be presented due to the uneven distribution of MT vertices. In this article, we propose a simple and reliable method to eliminate these unreasonably distributed surface vertices generated in the original MT. This treatment can save more than 60% of total analysis time of electrostatic potential, yet the loss in accuracy is almost negligible. The artificial surface extremes are also largely avoided as a byproduct of this algorithm. In addition, the bisection iteration procedure has been exploited to improve accuracy of linear interpolation in MT. The most appropriate grid spacing for surface analysis has also been investigated. 0.25 and 0.20 bohr are recommended to be used for surface analysis of electrostatic potential and average local ionization energy, respectively.
分子表面的定量分析是分析非共价相互作用、研究分子识别模式、预测反应活性位点和反应活性的一种很有价值的技术。Bulat 等人首次提出了一种有效的分析方法（J. Mol. Model.，16，1679），该方法利用计算机图形学中常用的行进四面体（MT）方法在分子表面生成顶点。然而，已经发现 MT 顶点上的静电势计算非常昂贵，并且由于 MT 顶点的不均匀分布，会出现一些人为的表面极值。在本文中，我们提出了一种简单可靠的方法来消除原始 MT 中生成的这些不合理分布的表面顶点。这种处理方法可以节省超过 60%的静电势总分析时间，而准确性的损失几乎可以忽略不计。作为该算法的副产品，人为的表面极值也大大减少。此外，我们还利用二分迭代过程来提高 MT 中线性插值的精度。还研究了最适合表面分析的网格间距。建议分别使用 0.25 和 0.20 bohr 作为静电势能和平均局部电离能的表面分析的合适网格间距。
