求助：QM/MM MD的隧穿效应和中间体寿命

霜晨月

我用QM/MM MD计算一个酶催化反应，包含2步：质子转移和负氢转移，方法是1维与2维伞形采样，作出PMF与2维自由能面，结果显示2步反应是分步进行（stepwize）的。
但审稿人坚持认为这2步反应是协同（concerted）过程，审稿意见这样说：

A reaction is either concerted, or stepwise, depending on whether an intermediate has a significant lifetime at that temperature. ... Concertedness of reaction and lifetimes of intermediates will also be significantly affected by quantum effects such as tunnelling and zero-point energy for proton and hydride transfers, as found by previous simulations. Quantum effects are not included in the current work, which applies only classical dynamics simulations (with a QM/MM potential). In this case, so-called intermediates 1 and 2 are predicted to have negligible lifetime even without zero-point and tunnelling corrections. Therefore these are not actually intermediates and the conclusions are incorrect. The results indicate that the reaction is concerted.

我的疑问是：
1. QM/MM MD模拟，应该如何考虑隧穿效应和ZPE呢？（他这里说的ZPE，指的是用量化方法计算自由能时的热力学校正ZPE吗？）如果用的是簇模型，当然可以考虑隧穿效应；但QM/MM MD该如何考虑呢？（话说，我从前用簇模型计算酶催化反应时，经常被审稿人建议用QM/MM MD）
2. 中间体的lifetime该如何计算？审稿人又是如何从2维自由能面看出中间体的lifetime的呢？

请老师们多加指教！
另外，不确定这个求助帖是该发在量化版还是分子模拟版，如有不当，还烦请管理员代为移动。
多谢多谢！

ene

那你是基于什么现象判断你的反应一定是分步的？因为某个中间构像的自由能比较低？

霜晨月

ene 发表于 2022-7-20 04:02
那你是基于什么现象判断你的反应一定是分步的？因为某个中间构像的自由能比较低？

是，反应路径中间有两个明显的能量极小点，能垒4-6kcal/mol