Reaction Path-Force Matching in Collective Variables: Determining Ab Initio QM/MM Free Energy Profiles by Fitting Mean Force.
Reaction Path-Force Matching in Collective Variables: Determining Ab Initio QM/MM Free Energy Profiles by Fitting Mean Force.
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集体变量中的反应路径-力匹配：通过拟合平均力确定从头算QM/MM自由能分布。
DOI：
10.1021/acs.jctc.1c00245
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发表时间：
2021-08-10
影响因子：
5.5
通讯作者：
Pu, Jingzhi
中科院分区：
文献类型：
--
作者：
Kim, Bryant;Snyder, Ryan;Nagaraju, Mulpuri;Zhou, Yan;Ojeda-May, Pedro;Keeton, Seth;Hege, Mellisa;Shao, Yihan;Pu, Jingzhi
凝聚相化学反应自由能分布的第一性原理测定受到与从头算量子力学/分子力学（AI/MM）势能表面上的构型取样相关的令人生畏的成本的阻碍。在这里，我们报告了一种新方法，通过平均力拟合实现高效的AI/MM自由能模拟。在该方法中，集体变量（CV）中的自由能路径首先在有效的无功辅助电位上确定。基于沿自由能路径沿着采样的配置，通过力匹配确定用于在CV上再现AI/MM力的校正力。AI/MM自由能分布，然后预测从模拟上的援助潜力结合校正力。这样的校正-预测循环被重复，直到建立收敛。由于拟合了沿自由能路径沿着在平衡系综中采样的CV上的瞬时力，因此此过程通过再现自由能平均力忠实地恢复目标自由能剖面。由于它与我们最近提出的反应路径-力匹配（RP-FM）框架有着密切的联系，我们将这种新方法命名为集合变量RP-FM（RP-FM-CV）。我们证明了这种方法的有效性上的II型溶液相SN2反应，NH 3 + CH 3Cl（Menshutkin反应），模拟与明确的水溶剂。为了得到Al/MM自由能分布，我们采用半经验的AM1/MM哈密顿量作为确定弦最小自由能路径的基础水平，沿着自由能平均力被拟合到各种目标Al/MM水平使用Hartree-Fock（HF）理论，密度泛函理论（DFT），和二阶Müller-Plesset微扰（MP2）理论作为AI方法。在基础和目标水平上的键断裂和键形成CV上的力通过在Wilson B-矩阵形式主义下从笛卡尔到冗余内部坐标的力变换来获得，其中线性化FM通过使用样条函数来促进。对于所测试的Menshutkin反应，我们的FM处理大大减小了CV力的偏差，原来在12~33至102 kcal/mol/cm的范围内。与实验和基准AI/MM结果的比较，各种模拟协议下的新方法的测试，以及溶质-溶剂径向分布函数的分析表明，RP-FM-CV可以用作模拟溶液相化学反应的高效，准确和稳健的方法。
First-principles determination of free energy profiles for condensed-phase chemical reactions is hampered by the daunting costs associated with configurational sampling on ab initio quantum mechanical/molecular mechanical (AI/MM) potential energy surfaces. Here, we report a new method that enables efficient AI/MM free energy simulations through mean force fitting. In this method, a free energy path in collective variables (CVs) is first determined on an efficient reactive aiding potential. Based on the configurations sampled along the free energy path, correcting forces to reproduce the AI/MM forces on the CVs are determined through force matching. The AI/MM free energy profile is then predicted from simulations on the aiding potential in conjunction with the correcting forces. Such cycles of correction-prediction are repeated until convergence is established. As the instantaneous forces on the CVs sampled in equilibrium ensembles along the free energy path are fitted, this procedure faithfully restores the target free energy profile by reproducing the free energy mean forces. Due to its close connection with the reaction path-force matching (RP-FM) framework recently introduced by us, we designate the new method as RP-FM in collective variables (RP-FM-CV). We demonstrate the effectiveness of this method on a type-II solution-phase SN2 reaction, NH3 + CH3Cl (the Menshutkin reaction), simulated with an explicit water solvent. To obtain the AI/MM free energy profiles, we employed the semiempirical AM1/MM Hamiltonian as the base level for determining the string minimum free energy pathway, along which the free energy mean forces are fitted to various target AI/MM levels using the Hartree-Fock (HF) theory, density functional theory (DFT), and the second-order MØller-Plesset perturbation (MP2) theory as the AI method. The forces on the bond-breaking and bond-forming CVs at both the base and target levels are obtained by force transformation from Cartesian to redundant internal coordinates under the Wilson B-matrix formalism, where the linearized FM is facilitated by the use of spline functions. For the Menshutkin reaction tested, our FM treatment greatly reduces the deviations on the CV forces, originally in the range of 12~33 to ∼2 kcal/mol/Å. Comparisons with the experimental and benchmark AI/MM results, tests of the new method under a variety of simulation protocols, and analyses of the solute-solvent radial distribution functions suggest that RP-FM-CV can be used as an efficient, accurate, and robust method for simulating solution-phase chemical reactions.
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