论文标题

具有构象依赖的分布式电荷的分子动力学

Molecular Dynamics with Conformationally Dependent, Distributed Charges

论文作者

Boittier, Eric D., Devereux, Mike, Meuwly, Markus

论文摘要

计算分子模拟中电子分布的几何变化对于捕获电荷流,电荷各向异性和极化等效果很重要。多极力场已经证明了它们具有定性和正确代表化学重要特征(例如Sigma孔)的能力。还显示,异位点费用提供了一种紧凑的替代方案,其精度相似。在这里,证明,相对于其参考原子,允许在微小分布的电荷模型(MDCM)内搬迁电荷是根据几何形状捕获分子电荷分布变化的可行途径。该方法被称为``灵活的MDCM''(FMDCM)在许多小分子上进行了验证,并且与电子结构计算的参考数据相比,平均具有0.5 kcal/mol的静电电位(ESP)的准确性,而MDCM和点电荷的均方根误差具有2至5级别的均方根误差。此外,使用FMDCM进行$ NVE $集合中的MD模拟,用于周期性边界条件的一盒柔性水分子,在10 ns时间尺度上平均300 K的波动宽度为0.1 kcal/mol。捕获ESP的几何形状依赖性以及能源保存模拟中的长期稳定性的准确性使FMDCM成为将高级静电学引入原子模拟中的有前途的工具。

Accounting for geometry-induced changes in the electronic distribution in molecular simulation is important for capturing effects such as charge flow, charge anisotropy and polarization. Multipolar force fields have demonstrated their ability to qualitatively and correctly represent chemically significant features such as sigma holes. It has also been shown that off-center point charges offer a compact alternative with similar accuracy. Here it is demonstrated that allowing relocation of charges within a minimally distributed charge model (MDCM) with respect to their reference atoms is a viable route to capture changes in the molecular charge distribution depending on geometry. The approach, referred to as ``flexible MDCM'' (fMDCM) is validated on a number of small molecules and provides accuracies in the electrostatic potential (ESP) of 0.5 kcal/mol on average compared with reference data from electronic structure calculations whereas MDCM and point charges have root mean squared errors of a factor of 2 to 5 higher. In addition, MD simulations in the $NVE$ ensemble using fMDCM for a box of flexible water molecules with periodic boundary conditions show a width of 0.1 kcal/mol for the fluctuation around the mean at 300 K on the 10 ns time scale. The accuracy in capturing the geometry dependence of the ESP together with the long-time stability in energy conserving simulations makes fMDCM a promising tool to introduce advanced electrostatics into atomistic simulations.

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