Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota , 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, United States.
Acc Chem Res. 2014 Sep 16;47(9):2731-8. doi: 10.1021/ar500068a. Epub 2014 May 19.
Conspectus The development of more efficient and more accurate ways to represent reactive potential energy surfaces is a requirement for extending the simulation of large systems to more complex systems, longer-time dynamical processes, and more complete statistical mechanical sampling. One way to treat large systems is by direct dynamics fragment methods. Another way is by fitting system-specific analytic potential energy functions with methods adapted to large systems. Here we consider both approaches. First we consider three fragment methods that allow a given monomer to appear in more than one fragment. The first two approaches are the electrostatically embedded many-body (EE-MB) expansion and the electrostatically embedded many-body expansion of the correlation energy (EE-MB-CE), which we have shown to yield quite accurate results even when one restricts the calculations to include only electrostatically embedded dimers. The third fragment method is the electrostatically embedded molecular tailoring approach (EE-MTA), which is more flexible than EE-MB and EE-MB-CE. We show that electrostatic embedding greatly improves the accuracy of these approaches compared with the original unembedded approaches. Quantum mechanical fragment methods share with combined quantum mechanical/molecular mechanical (QM/MM) methods the need to treat a quantum mechanical fragment in the presence of the rest of the system, which is especially challenging for those parts of the rest of the system that are close to the boundary of the quantum mechanical fragment. This is a delicate matter even for fragments that are not covalently bonded to the rest of the system, but it becomes even more difficult when the boundary of the quantum mechanical fragment cuts a bond. We have developed a suite of methods for more realistically treating interactions across such boundaries. These methods include redistributing and balancing the external partial atomic charges and the use of tuned fluorine atoms for capping dangling bonds, and we have shown that they can greatly improve the accuracy. Finally we present a new approach that goes beyond QM/MM by combining the convenience of molecular mechanics with the accuracy of fitting a potential function to electronic structure calculations on a specific system. To make the latter practical for systems with a large number of degrees of freedom, we developed a method to interpolate between local internal-coordinate fits to the potential energy. A key issue for the application to large systems is that rather than assigning the atoms or monomers to fragments, we assign the internal coordinates to reaction, secondary, and tertiary sets. Thus, we make a partition in coordinate space rather than atom space. Fits to the local dependence of the potential energy on tertiary coordinates are arrayed along a preselected reaction coordinate at a sequence of geometries called anchor points; the potential energy function is called an anchor points reactive potential. Electrostatically embedded fragment methods and the anchor points reactive potential, because they are based on treating an entire system by quantum mechanical electronic structure methods but are affordable for large and complex systems, have the potential to open new areas for accurate simulations where combined QM/MM methods are inadequate.
概要 开发更高效、更准确的方法来表示反应势能面是将大规模系统的模拟扩展到更复杂的系统、更长时间的动力学过程和更完整的统计力学采样的要求。处理大规模系统的一种方法是通过直接动力学片段方法。另一种方法是通过拟合特定于系统的解析势能函数,采用适用于大规模系统的方法。在这里,我们同时考虑这两种方法。首先,我们考虑三种允许给定单体出现在多个片段中的片段方法。前两种方法是静电嵌入多体(EE-MB)扩展和静电嵌入相关能(EE-MB-CE)的多体扩展,我们已经证明,即使将计算限制为仅包括静电嵌入的二聚体,这些方法也能得到相当准确的结果。第三种片段方法是静电嵌入分子剪裁方法(EE-MTA),它比 EE-MB 和 EE-MB-CE 更灵活。我们表明,与原始非嵌入方法相比,静电嵌入大大提高了这些方法的准确性。量子力学片段方法与组合量子力学/分子力学(QM/MM)方法一样,需要在存在系统其余部分的情况下处理量子力学片段,这对于靠近量子力学片段边界的系统其余部分尤其具有挑战性。即使对于与系统其余部分没有共价键的片段,这也是一个微妙的问题,但当量子力学片段的边界切割键时,情况会变得更加困难。我们已经开发了一套方法来更真实地处理这种边界处的相互作用。这些方法包括重新分配和平衡外部部分原子电荷以及使用调谐氟原子来封端悬空键,我们已经表明,它们可以大大提高准确性。最后,我们提出了一种新方法,通过将分子力学的便利性与拟合特定系统电子结构计算的势能函数的准确性相结合,超越了 QM/MM。为了使后者适用于具有大量自由度的系统,我们开发了一种在局部内部坐标与势能的拟合之间进行插值的方法。应用于大规模系统的一个关键问题是,我们不是将原子或单体分配给片段,而是将内部坐标分配给反应、次要和次要集。因此,我们在坐标空间而不是原子空间中进行分区。沿着一系列称为锚定点的预先选择的反应坐标排列对局部依赖于三级坐标的势能的拟合;势能函数称为锚定点反应势能。静电嵌入片段方法和锚定点反应势能,因为它们基于通过量子力学电子结构方法处理整个系统,但对于大规模和复杂系统来说是可行的,因此有可能在组合 QM/MM 方法不足的情况下为准确模拟开辟新的领域。