Multistructural microiteration combined with QM/MM-ONIOM electrostatic embedding
Multistructural microiteration combined with QM/MM-ONIOM electrostatic embedding
复制标题
多结构微迭代结合 QM/MM-ONIOM 静电嵌入
DOI：
10.1039/d2cp02270b
复制
发表时间：
2022
影响因子：
3.3
通讯作者：
Maeda Satoshi
中科院分区：
文献类型：
--
作者：
Suzuki Kimichi;Maeda Satoshi
多结构微迭代（MSM）是一种在使用量子力学/分子力学（QM/MM）ONIOM方法进行几何优化或反应路径计算时考虑多个周围结构贡献的方法。在这项研究中，我们结合MSM与QM/MM-ONIOM方法的静电嵌入（EE）计划，通过扩展其原始配方的机械嵌入（ME）。MSM-EE考虑了由分配给多个周围结构中的原子的点电荷引起的QM区域中的极化，其中点电荷由通过MSM确定的每个周围结构的权重因子缩放。将MSM-EE的性能与其他方法的性能进行了比较，即，ONIOM-ME、ONIOM-EE和MSM-ME，通过将它们应用于三种化学过程：（1）在水溶液中分支酸盐至预苯酸盐的转化，（2）与（1）在酶中相同的转化，和（3）在对羟基苯甲酸羟化酶中的羟基化。这些数值试验的MSM-EE产生的障碍和反应能量接近实验值的计算成本相比，其他三种方法。
Multistructural microiteration (MSM) is a method to take account of contributions of multiple surrounding structures in a geometrical optimization or reaction path calculation using the quantum mechanics/molecular mechanics (QM/MM) ONIOM method. In this study, we combined MSM with the electrostatic embedding (EE) scheme of the QM/MM-ONIOM method by extending its original formulation for mechanical embedding (ME). MSM–EE takes account of the polarization in the QM region induced by point charges assigned to atoms in the multiple surrounding structures, where the point charges are scaled by the weight factor of each surrounding structure determined through MSM. The performance of MSM–EE was compared with that of the other methods, i.e., ONIOM–ME, ONIOM–EE, and MSM–ME, by applying them to three chemical processes: (1) chorismate-to-prephenate transformation in aqueous solution, (2) the same transformation as (1) in an enzyme, and (3) hydroxylation in p-hydroxybenzoate hydroxylase. These numerical tests of MSM–EE yielded barriers and reaction energies close to experimental values with computational costs comparable to those of the other three methods.