Roca Maite, Moliner Vicente, Ruiz-Pernía J Javier, Silla Estanislao, Tuñón Iñaki
Departamento de Ciencias Experimentales, Universitat Jaume I, 12080 Castellón, Spain.
J Phys Chem A. 2006 Jan 19;110(2):503-9. doi: 10.1021/jp0520953.
We use quantum mechanics/molecular mechanics (QM/MM) calculations to estimate the activation free energy for the chemical reaction catalyzed by catechol O-methyltransferase. While in many cases the activation free energy of a chemical process is directly determined by the potential of mean force associated with a particular reaction coordinate, here we have included several corrections that have been proposed in the literature. These include the free energy change associated with release of the reaction coordinate motion in the reactant state, consideration of the curvilinear nature of the reaction coordinate, and correction due to the classical treatment of molecular vibrations. In addition, since potentials of mean force are usually obtained from low levels of QM theory to describe the quantum subsystem, we have included an interpolated correction term to improve this description at small additional cost. This last correction term has a dramatic effect, improving the agreement between the theoretical predictions and the experimental value, while the other terms considered make only small contributions to this particular reaction.
我们使用量子力学/分子力学（QM/MM）计算来估算由儿茶酚O-甲基转移酶催化的化学反应的活化自由能。虽然在许多情况下，化学过程的活化自由能直接由与特定反应坐标相关的平均力势决定，但在此我们纳入了文献中提出的几种校正。这些校正包括与反应物状态下反应坐标运动释放相关的自由能变化、对反应坐标曲线性质的考虑以及由于分子振动的经典处理而产生的校正。此外，由于平均力势通常从低水平的量子力学理论获得以描述量子子系统，我们纳入了一个插值校正项，以在增加少量成本的情况下改善这种描述。最后这个校正项具有显著效果，改善了理论预测与实验值之间的一致性，而所考虑的其他项对这个特定反应仅做出很小的贡献。
