Department of Chemistry and Chemical Biology, Department of Physics and Astronomy, and Center for Quantum Information and Control, University of New Mexico, Albuquerque, New Mexico 87131, United States.
J Phys Chem A. 2021 May 6;125(17):3760-3775. doi: 10.1021/acs.jpca.1c00164. Epub 2021 Apr 23.
Quantum-mechanically driven charge polarization and charge transfer are ubiquitous in biomolecular systems, controlling reaction rates, allosteric interactions, ligand-protein binding, membrane transport, and dynamically driven structural transformations. Molecular dynamics (MD) simulations of these processes require quantum mechanical (QM) information in order to accurately describe their reactive dynamics. However, current techniques-empirical force fields, subsystem approaches, MD, and machine learning-vary in their ability to achieve a consistent chemical description across multiple atom types, and at scale. Here we present a physics-based, atomistic force field, the , in which QM forces are described at a uniform level of theory across all atoms, avoiding the need for explicit solution of the Schrödinger equation or large, precomputed training data sets. Coupling between the electronic and atomistic length scales is effected through an ensemble density functional theory formulation of the embedded-atom method originally developed for elemental materials. Charge transfer is expressed in terms of ensembles of state basis densities of individual atoms, and charge polarization, in terms of atomic -state basis densities. This provides a highly compact yet general representation of the force field, encompassing both local and system-wide effects. Charge rearrangement is realized through the evolution of ensemble weights, adjusted at each dynamical time step via chemical potential equalization.
量子力学驱动的电荷极化和电荷转移在生物分子系统中普遍存在，控制着反应速率、变构相互作用、配体-蛋白结合、膜转运以及动态驱动的结构转变。为了准确描述这些过程的反应动力学，这些过程的分子动力学 (MD) 模拟需要量子力学 (QM) 信息。然而，当前的技术——经验力场、子系统方法、MD 和机器学习——在跨越多种原子类型和大规模实现一致化学描述的能力上存在差异。在这里，我们提出了一种基于物理的原子力场，即 ，其中在所有原子上以统一的理论水平描述 QM 力，避免了对薛定谔方程的显式求解或大型预计算训练数据集的需求。电子和原子长度尺度之间的耦合通过最初为元素材料开发的嵌入原子方法的集合密度泛函理论公式来实现。电荷转移用单个原子的 态基密度的集合来表示，电荷极化用原子 态基密度来表示。这提供了一种高度紧凑但通用的力场表示，包含局部和系统范围的效应。通过集合权重的演化来实现电荷重排，并通过化学势均衡在每个动力学时间步进行调整。
