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Molecular Dynamics with Conformationally Dependent, Distributed Charges
Journal of Chemical Theory and Computation ( IF 5.7 ) Pub Date : 2022-11-08 , DOI: 10.1021/acs.jctc.2c00693
Eric D Boittier 1 , Mike Devereux 1 , Markus Meuwly 1
Journal of Chemical Theory and Computation ( IF 5.7 ) Pub Date : 2022-11-08 , DOI: 10.1021/acs.jctc.2c00693
Eric D Boittier 1 , Mike Devereux 1 , Markus Meuwly 1
Affiliation
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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 correctly represent chemically significant features such as anisotropy and 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, i.e., intramolecular polarization. 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. For water, the equilibrium valence angle in the gas phase is found to increase by 2° for simulations in the condensed phase which is consistent with experiment. 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.
中文翻译：
具有构象依赖性分布电荷的分子动力学
在分子模拟中考虑几何引起的电子分布变化对于捕获电荷流动、电荷各向异性和极化等效应非常重要。多极力场已经证明了它们能够正确地表示各向异性和西格玛孔等重要的化学特征。还表明，偏心点电荷提供了一种具有类似精度的紧凑型替代方案。在这里，证明允许在最小分布电荷模型 (MDCM) 内相对于它们的参考原子重新定位电荷是捕获分子电荷分布变化的可行途径，这取决于几何形状，即分子内极化。该方法称为“灵活 MDCM”(fMDCM)，在许多小分子上得到验证，与电子结构计算的参考数据相比，静电势 (ESP) 的平均精度为 0.5 kcal/mol，而 MDCM 和点电荷的均方根误差为 2 至5高。此外，MD模拟中NVE系综使用 fMDCM 对一盒具有周期性边界条件的柔性水分子显示宽度为 0.1 kcal/mol，在 10 ns 时间尺度上在 300 K 的平均值附近波动。对于水，发现气相中的平衡价角对于凝聚相中的模拟增加了 2°，这与实验一致。捕获 ESP 的几何依赖性的准确性以及能量守恒模拟中的长期稳定性使 fMDCM 成为将高级静电学引入原子模拟的有前途的工具。
更新日期：2022-11-08
中文翻译：
具有构象依赖性分布电荷的分子动力学
在分子模拟中考虑几何引起的电子分布变化对于捕获电荷流动、电荷各向异性和极化等效应非常重要。多极力场已经证明了它们能够正确地表示各向异性和西格玛孔等重要的化学特征。还表明，偏心点电荷提供了一种具有类似精度的紧凑型替代方案。在这里，证明允许在最小分布电荷模型 (MDCM) 内相对于它们的参考原子重新定位电荷是捕获分子电荷分布变化的可行途径，这取决于几何形状，即分子内极化。该方法称为“灵活 MDCM”(fMDCM)，在许多小分子上得到验证，与电子结构计算的参考数据相比，静电势 (ESP) 的平均精度为 0.5 kcal/mol，而 MDCM 和点电荷的均方根误差为 2 至5高。此外，MD模拟中NVE系综使用 fMDCM 对一盒具有周期性边界条件的柔性水分子显示宽度为 0.1 kcal/mol，在 10 ns 时间尺度上在 300 K 的平均值附近波动。对于水，发现气相中的平衡价角对于凝聚相中的模拟增加了 2°，这与实验一致。捕获 ESP 的几何依赖性的准确性以及能量守恒模拟中的长期稳定性使 fMDCM 成为将高级静电学引入原子模拟的有前途的工具。
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