QM/CG-MM:在具有精确静电作用的粗粒度环境中对量子力学系统进行系统嵌入。
QM/CG-MM: Systematic Embedding of Quantum Mechanical Systems in a Coarse-Grained Environment with Accurate Electrostatics.
作者信息
Teng Da, Mironenko Alexander V, Voth Gregory A
机构信息
Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, United States.
Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States.
出版信息
J Phys Chem A. 2024 Jul 25;128(29):6061-6071. doi: 10.1021/acs.jpca.4c02906. Epub 2024 Jul 17.
Quantum Mechanics/Molecular Mechanics (QM/MM) can describe chemical reactions in molecular dynamics (MD) simulations at a much lower cost than MD. Still, it is prohibitively expensive for many systems of interest because such systems usually require long simulations for sufficient statistical sampling. Additional MM degrees of freedom are often slow and numerous but secondary in interest. Coarse-graining (CG) is well-known to be able to speed up sampling through both reduction in simulation cost and the ability to accelerate the dynamics. Therefore, embedding a QM system in a CG environment can be a promising way of expediting sampling without compromising the information about the QM subsystem. Sinitskiy and Voth first proposed the theory of Quantum Mechanics/Coarse-grained Molecular Mechanics (QM/CG-MM) with a bottom-up CG mapping. Mironenko and Voth subsequently introduced the DFT-QM/CG-MM formalism to couple a Density Functional Theory (DFT) treated QM system and to an apolar environment. Here, we present a more complete theory that addresses MM environments with significant polarity by explicitly accounting for the electrostatic coupling. We demonstrate our QM/CG-MM method with a chloride-methyl chloride S2 reaction system in acetone, which is sensitive to solvent polarity. The method accurately recapitulates the potential of mean force for the substitution reaction, and the reaction barrier from the best model agrees with the atomistic simulations within sampling error. These models also have generalizability. In two other reactive systems that they have not been trained on, the QM/CG-MM model still achieves the same level of agreement with the atomistic QM/MM models. Finally, we show that in these examples the speed-up in the sampling is proportional to the acceleration of the rotational dynamics of the solvent in the CG system.
量子力学/分子力学(QM/MM)能够在分子动力学(MD)模拟中描述化学反应,其成本远低于MD。然而,对于许多感兴趣的系统来说,它仍然过于昂贵,因为这样的系统通常需要长时间模拟以获得足够的统计采样。额外的分子力学自由度往往速度慢且数量众多,但并非主要关注点。众所周知,粗粒化(CG)能够通过降低模拟成本和加速动力学来加快采样。因此,将量子力学系统嵌入粗粒化环境可能是一种在不损失量子力学子系统信息的情况下加快采样的有效方法。西尼茨基和沃思首先提出了具有自底向上粗粒化映射的量子力学/粗粒化分子力学(QM/CG-MM)理论。米罗年科和沃思随后引入了密度泛函理论(DFT)-QM/CG-MM形式体系,将经密度泛函理论处理的量子力学系统与非极性环境耦合。在此,我们提出一种更完整的理论,通过明确考虑静电耦合来处理具有显著极性的分子力学环境。我们用丙酮中的氯-氯甲烷S2反应系统演示了我们的QM/CG-MM方法,该系统对溶剂极性敏感。该方法准确地再现了取代反应的平均力势,并且最佳模型的反应势垒在采样误差范围内与原子模拟结果一致。这些模型还具有通用性。在另外两个未对其进行训练的反应系统中,QM/CG-MM模型与原子QM/MM模型仍能达到相同程度的一致性。最后,我们表明在这些例子中,采样加速与粗粒化系统中溶剂旋转动力学的加速成正比。