Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castellón, Spain.
Departament de Química Física/IcMol, Universidad de Valencia, 46100 Burjasot, Valencia, Spain.
J Chem Theory Comput. 2005 Sep;1(5):1008-16. doi: 10.1021/ct0501396.
Potential energy surfaces are fundamental tools for the analysis of reaction mechanisms. The accuracy of these surfaces for reactions in very large systems is often limited by the size of the system even if hybrid quantum mechanics/molecular mechanics (QM/MM) strategies are employed. The large number of degrees of freedom of the system requires hundreds or even thousands of optimization steps to reach convergence. Reactions in condensed media (such as enzymes or solutions) are thus usually restricted to be analyzed using low level quantum mechanical methods, thus introducing a source of error in the description of the QM region. In this paper, an alternative method is proposed, coupled to the use of a micro/macroiteration algorithm during the optimization. In these algorithms, the number of microsteps involved in the QM region optimization is usually much smaller than the number of macrosteps required to optimize the MM region. Thus, we define a new potential energy surface in which the gas-phase energy of the QM subsystem and the interaction energy with the MM subsystem are calculated at different computational levels. The high computational level is restricted to the gas-phase energy, which is only requested during the microsteps. The dual level strategy is tested for two reactions in solution (the Menshutkin and the oxy-Cope reactions) and an enzymatic one (the nucleophilic substitution of 1,2-dichloroethane in DhlA). The performance of the proposed computational scheme seems to be quite promising for future applications in other systems.
势能面是分析反应机制的基本工具。即使采用混合量子力学/分子力学(QM/MM)策略,这些表面对于非常大系统中的反应的准确性通常也受到系统大小的限制。系统的自由度数量众多,需要数百甚至数千个优化步骤才能达到收敛。因此,凝聚相(如酶或溶液)中的反应通常仅限于使用低水平的量子力学方法进行分析,从而在QM 区域的描述中引入了误差源。在本文中,提出了一种替代方法,并在优化过程中使用微/宏迭代算法。在这些算法中,QM 区域优化中涉及的微步数通常远小于优化 MM 区域所需的大步数。因此,我们定义了一个新的势能面,其中 QM 子系统的气相能和与 MM 子系统的相互作用能在不同的计算水平上计算。高计算水平仅限于气相能,仅在微步骤中需要。该双重水平策略已针对两个在溶液中进行的反应(Menshutkin 和 oxy-Cope 反应)和一个酶反应(DhlA 中 1,2-二氯乙烷的亲核取代)进行了测试。对于未来在其他系统中的应用,所提出的计算方案的性能似乎很有前途。