TIP5P-Consistent Treatment of Electrostatics for Biomolecular Simulations.
TIP5P-Consistent Treatment of Electrostatics for Biomolecular Simulations.
复制标题
TIP5P-生物分子模拟静电的一致处理。
DOI：
10.1021/ct700046j
复制
发表时间：
2007
影响因子：
5.5
通讯作者：
Woods,RobertJ
中科院分区：
文献类型：
--
作者：
Tschampel,SarahM;Kennerty,MichaelR;Woods,RobertJ
在分子机械力场中，围绕电负性原子（如氧）的零质量点电荷可以改善氢键的方向性。与此同时，在TIP5P水模型中加入孤独对（lp），相比于其非lp前身TIP3P，提高了其再现气相和凝聚相性质的能力。目前，大多数生物分子参数集通过将经典分子静电势（MEP）拟合到量子力学MEP来计算原子的部分电荷。因此，应用这种方法来优化孤独对描述与当前的静电建模方法是一致的，并且易于实现。在这里，我们提出了一个特定于原子类型的孤独对模型，该模型导致每种原子类型的最优LP位置，并且，值得注意的是，结果再现了TIP5P中存在的孤独对描述。碳水化合物含有丰富的羟基，开发一个包含孤对的碳水化合物力场，与包含孤对的水模型（如TIP5P）一起使用，确保了这两个模型之间的兼容性。该孤对模型的实现改善了一系列氢键团簇的几何形状和能量学，并改善了几种小分子晶体在不含lp力场中的性能。
The inclusion of zero-mass point charges around electronegative atoms, such as oxygen, within molecular mechanical force fields is known to improve hydrogen-bonding directionality. In parallel, inclusion of lone-pairs (LPs) in the TIP5P water model increased its ability to reproduce both gas-phase and condensed-phase properties over its non-LP predecessor, TIP3P. Currently, most biomolecular parameter sets compute partial atomic charges via fitting of the classical molecular electrostatic potential (MEP) to the quantum mechanical MEP. Application of this methodology to optimize lone-pair description is therefore consistent with the current approach to modeling electrostatics and is straightforward to implement. Here, we present an atom-type specific lone-pair model, which leads to the most optimal LP placement for each atom type, and, notably, results in reproduction of the lone-pair description present in TIP5P. Carbohydrates are rich in hydroxyl groups, and development of a lone-pair inclusive carbohydrate force field for use with a lone-pair containing water model, such as TIP5P, ensures the compatibility between these two models. Implementation of this lone-pair model improves the geometry and energetics for a series of hydrogen-bonded clusters and the properties of several small molecule crystals over the non-LP containing force field.