Laboratoire de chimie , École Normale Supérieure de lyon , 46 allée d'italie , 69007 Lyon , France.
Inorganic Chemistry and Catalysis Group, Debye Institute for Nanomaterials Science , Utrecht University , Universiteitsweg 99 , 3584 CG, Utrecht , The Netherlands.
J Chem Theory Comput. 2018 Aug 14;14(8):3943-3954. doi: 10.1021/acs.jctc.7b01218. Epub 2018 Jul 18.
In recent years, quantum mechanical/molecular mechanical (QM/MM) methods have emerged that are designed specifically for chemical reactions in water. Despite the many advances, a remaining problem is that the patchwork of QM and MM descriptions changes the solvent structure. In a solvent as intricately connected as water, such structural changes can alter a chemical process even across large distances. Examples of structural artifacts in QM/MM water include density accumulation at the QM/MM boundary, decreased order, and density differences between regions. These issues are mostly apparent if the difference between the QM and the MM model is very large, which is often the case with water models. Here, we assess the QM/MM performance of simple MM models that are specifically parametrized to match selected data from a QM simulation of bulk water. To this end, we introduce a novel MM model (PM6-(DH+)-EFF) that reproduces PM6-DH+ water properties. We also assess a recent PBE-DFT-based MM model (PBE-EFF) that reproduces structural properties of bulk water simulated with PBE-DFT. Both models consist solely of tabulated potential energy terms for interactions between atom pairs. We compare the matched QM/MM results (PBE-DFT/PBE-EFF and PM6-DH+/PM6(-DH+)-EFF) with those from mismatched QM/MM simulations (PM6-DH+/PBE-EFF). The mismatched simulations reflect issues similar to those reported for other mismatched QM/MM pairs. The matched simulations yield very good results with water structures that barely deviate from the QM reference. In view of these findings, we strongly recommend adoption of specifically parametrized MM models in the QM/MM simulation of chemical processes in water.
近年来,出现了专门为水中化学反应设计的量子力学/分子力学(QM/MM)方法。尽管取得了许多进展,但仍然存在一个问题,即 QM 和 MM 描述的拼凑会改变溶剂结构。在像水这样错综复杂的溶剂中,这种结构变化即使在很大的距离上也会改变化学反应过程。QM/MM 水中结构人工制品的例子包括在 QM/MM 边界处的密度积累、有序性降低以及区域之间的密度差异。如果 QM 和 MM 模型之间的差异非常大,这些问题通常在水模型中很明显,这些问题在 QM/MM 中最为明显。在这里,我们评估了简单 MM 模型的 QM/MM 性能,这些模型专门针对从 QM 模拟的大块水中选择的数据进行了参数化。为此,我们引入了一种新的 MM 模型(PM6-(DH+)-EFF),该模型再现了 PM6-DH+水的性质。我们还评估了最近基于 PBE-DFT 的 MM 模型(PBE-EFF),该模型再现了用 PBE-DFT 模拟的大块水的结构性质。这两种模型都仅包含用于原子对之间相互作用的表格化势能项。我们将匹配的 QM/MM 结果(PBE-DFT/PBE-EFF 和 PM6-DH+/PM6(-DH+)-EFF)与不匹配的 QM/MM 模拟(PM6-DH+/PBE-EFF)的结果进行了比较。不匹配的模拟反映了与其他不匹配的 QM/MM 对报告的类似问题。匹配的模拟产生了非常好的结果,水中的结构几乎与 QM 参考值没有偏差。鉴于这些发现,我们强烈建议在水中化学过程的 QM/MM 模拟中采用专门参数化的 MM 模型。