Giese Timothy J, Panteva Maria T, Chen Haoyuan, York Darrin M
Center for Integrative Proteomics Research, BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854-8087, United States
J Chem Theory Comput. 2015 Feb 10;11(2):451-61. doi: 10.1021/ct500799g.
A fully quantum mechanical force field (QMFF) based on a modified “divide-and-conquer” (mDC) framework is applied to a series of molecular simulation applications, using a generalized Particle Mesh Ewald method extended to multipolar charge densities. Simulation results are presented for three example applications: liquid water, p-nitrophenylphosphate reactivity in solution, and crystalline N,N-dimethylglycine. Simulations of liquid water using a parametrized mDC model are compared to TIP3P and TIP4P/Ew water models and experiment. The mDC model is shown to be superior for cluster binding energies and generally comparable for bulk properties. Examination of the dissociative pathway for dephosphorylation of p-nitrophenylphosphate shows that the mDC method evaluated with the DFTB3/3OB and DFTB3/OPhyd semiempirical models bracket the experimental barrier, whereas DFTB2 and AM1/d-PhoT QM/MM simulations exhibit deficiencies in the barriers, the latter for which is related, in part, to the anomalous underestimation of the p-nitrophenylate leaving group pKa. Simulations of crystalline N,N-dimethylglycine are performed and the overall structure and atomic fluctuations are compared with the experiment and the general AMBER force field (GAFF). The QMFF, which was not parametrized for this application, was shown to be in better agreement with crystallographic data than GAFF. Our simulations highlight some of the application areas that may benefit from using new QMFFs, and they demonstrate progress toward the development of accurate QMFFs using the recently developed mDC framework.
一种基于改进的“分而治之”(mDC)框架的全量子力学力场(QMFF)被应用于一系列分子模拟应用中,使用了扩展到多极电荷密度的广义粒子网格埃瓦尔德方法。给出了三个示例应用的模拟结果:液态水、溶液中对硝基苯磷酸酯的反应性以及结晶态的N,N - 二甲基甘氨酸。使用参数化的mDC模型对液态水的模拟结果与TIP3P和TIP4P/Ew水模型以及实验进行了比较。结果表明,mDC模型在团簇结合能方面表现更优,在整体性质方面通常与其他模型相当。对对硝基苯磷酸酯去磷酸化的解离途径的研究表明,使用DFTB3/3OB和DFTB3/OPhyd半经验模型评估的mDC方法给出的势垒与实验值相符,而DFTB2和AM1/d - PhoT QM/MM模拟在势垒方面存在不足,后者部分原因与对硝基苯酚离去基团pKa的异常低估有关。对结晶态N,N - 二甲基甘氨酸进行了模拟,并将其整体结构和原子涨落与实验以及通用琥珀色力场(GAFF)进行了比较。该QMFF并非针对此应用进行参数化,但结果表明它比GAFF与晶体学数据的吻合度更高。我们的模拟突出了一些可能受益于使用新QMFF的应用领域,并且展示了使用最近开发的mDC框架在开发精确QMFF方面取得的进展。