Department of Chemistry, Yale University , New Haven, Connecticut 06520-8107, United States.
J Phys Chem B. 2017 Jul 13;121(27):6626-6636. doi: 10.1021/acs.jpcb.7b04233. Epub 2017 Jun 29.
The atomic point-charge model used in most molecular mechanics force fields does not represent well the electronic anisotropy that is featured in many directional noncovalent interactions. Sulfur participates in several types of such interactions with its lone pairs and σ-holes. The current study develops a new model, via the addition of off-atom charged sites, for a variety of sulfur compounds in the OPLS-AA and OPLS/CM5 force fields to address the lack of charge anisotropy. Parameter optimization is carried out to reproduce liquid-state properties, torsional and noncovalent energetics from reliable quantum mechanical calculations, and electrostatic potentials. Significant improvements are obtained for computed free energies of hydration, reducing the mean unsigned errors from ca. 1.4 to 0.4-0.7 kcal/mol. Enhanced accuracy in directionality and energetics is also obtained for molecular complexes with sulfur-containing hydrogen and halogen bonds. Moreover, the new model reproduces the unusual conformational preferences of sulfur-containing compounds with 1,4-intramolecular chalcogen bonds. Transferability of the new force field parameters to cysteine and methionine is verified via molecular dynamic simulations of blocked dipeptides. The study demonstrates the effectiveness of using off-atom charge sites to address electronic anisotropy, and provides a parametrization methodology that can be applied to other systems.
大多数分子力学力场中使用的原子点电荷模型不能很好地表示许多有方向性的非共价相互作用中所具有的电子各向异性。硫通过其孤对电子和σ空穴参与几种类型的这种相互作用。本研究通过在 OPLS-AA 和 OPLS/CM5 力场中为各种硫化合物添加离域电荷位点,开发了一种新模型,以解决电荷各向异性的缺乏问题。通过优化参数以重现液体状态的性质、扭转和非共价的能量,以及静电势来进行参数优化。对于计算水合自由能,得到了显著的改进,将平均未签名误差从约 1.4 降低到 0.4-0.7 kcal/mol。对于含硫氢键和卤键的分子复合物,在方向性和能量方面也得到了增强的准确性。此外,新模型还再现了含 1,4-内分子硫属键的含硫化合物的异常构象偏好。通过受阻二肽的分子动力学模拟验证了新力场参数对半胱氨酸和蛋氨酸的可转移性。该研究证明了使用离域电荷位点来解决电子各向异性的有效性,并提供了一种可应用于其他系统的参数化方法。