Systematic Parameterization of Monovalent Ions Employing the Nonbonded Model
Systematic Parameterization of Monovalent Ions Employing the Nonbonded Model
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DOI：
10.1021/ct500918t
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发表时间：
2015-04-01
影响因子：
5.5
通讯作者：
Merz, Kenneth M., Jr.
中科院分区：
文献类型：
--
作者：
Li, Pengfei;Song, Lin Frank;Merz, Kenneth M., Jr.
一价离子在生物体的许多生物过程中起着重要作用。在分子模拟中对这些离子进行建模仍然是一个具有挑战性的问题。12-6 Lennard-Jones（LJ）非键模型是经典分子动力学模拟中常用的一价离子模型。许多参数化的努力已经报道了这些离子与一些实验终点。然而，一些报道的参数集没有在两个Lennard-Jones参数（货车范德华（VDW）半径和势阱深度）之间具有良好的平衡，这影响了它们的可转移性。在目前的工作中，通过使用惰性气体曲线，我们拟合在以前的工作（J.化学理论计算。2013，9，2733），我们重新优化了三种广泛使用的水模型（TIP 3 P、SPC/E和TIP 4P（EW））的15种单价离子（11种正离子和4种负离子）的12-6 LJ参数。由于12-6 LJ非键模型在某些情况下对这些离子表现不佳，我们还将12-6-4 LJ型非键模型参数化（J. Chem. Theory Comput. 2014，10，289）使用相同的三种水模型。使用12-6 LJ非键合模型和12-6-4 LJ型非键合模型（12-6-4集），三个导出的参数集集中于再现水合自由能（HFE集）和离子-氧距离（IOD集），总体上给出了改进的结果。特别是，最终的参数集显示出更好的协议与量子力学计算的VDW半径和改进的转移到离子对的解决方案相比，以前的参数集。
Monovalent ions play fundamental roles in many biological processes in organisms. Modeling these ions in molecular simulations continues to be a challenging problem. The 12-6 Lennard-Jones (LJ) nonbonded model is widely used to model monovalent ions in classical molecular dynamics simulations. A lot of parameterization efforts have been reported for these ions with a number of experimental end points. However, some reported parameter sets do not have a good balance between the two Lennard-Jones parameters (the van der Waals (VDW) radius and potential well depth), which affects their transferability. In the present work, via the use of a noble gas curve we fitted in former work ( J. Chem. Theory Comput. 2013, 9, 2733), we reoptimized the 12-6 LJ parameters for 15 monovalent ions (11 positive and 4 negative ions) for three extensively used water models (TIP3P, SPC/E, and TIP4P(EW)). Since the 12-6 LJ nonbonded model performs poorly in some instances for these ions, we have also parameterized the 12-6-4 LJ-type nonbonded model ( J. Chem. Theory Comput. 2014, 10, 289) using the same three water models. The three derived parameter sets focused on reproducing the hydration free energies (the HFE set) and the ion-oxygen distance (the IOD set) using the 12-6 LJ nonbonded model and the 12-6-4 LJ-type nonbonded model (the 12-6-4 set) overall give improved results. In particular, the final parameter sets showed better agreement with quantum mechanically calculated VDW radii and improved transferability to ion-pair solutions when compared to previous parameter sets.