Department of Drug Discovery and Development, Italian Institute of Technology, Via Morego 30, I-16163 Genoa, Italy.
Dipartimento di Chimica, Università "Federico II", Complesso Universitario di Monte S.Angelo, via Cintia, I-80126 Napoli, Italy.
J Chem Theory Comput. 2011 Mar 8;7(3):539-43. doi: 10.1021/ct100547a. Epub 2011 Jan 5.
Herein, we propose a conceptually innovative approach to investigating reaction mechanisms. This study demonstrates the importance of considering explicitly the effects of large amplitude motions, aside from the intrinsic reaction coordinate, when tuning the free energy landscape of reaction pathways. We couple the path collective variables method with DFT-based enhanced sampling simulations to characterize the associative mechanism of the hydrolysis of the methyl phosphate dianion in solution. Importantly, energetics and mechanistic differences are observed when passing from the potential to the free energy surface.
在此,我们提出了一种概念创新的方法来研究反应机制。本研究表明,在调整反应途径的自由能景观时,除了固有反应坐标外,还需要明确考虑大振幅运动的影响。我们将路径集体变量方法与基于密度泛函理论的增强采样模拟相结合,以描述在溶液中磷酸二甲酸二阴离子的水解的缔合机制。重要的是,当从势能面转变到自由能面时,会观察到能量学和机制上的差异。