Li Pengfei, Song Lin Frank, Merz Kenneth M
Department of Chemistry, Department of Biochemistry and Molecular Biology, Michigan State University , 578 S. Shaw Lane, East Lansing, Michigan 48824-1322, United States.
J Phys Chem B. 2015 Jan 22;119(3):883-95. doi: 10.1021/jp505875v. Epub 2014 Sep 12.
Highly charged metal ions act as catalytic centers and structural elements in a broad range of chemical complexes. The nonbonded model for metal ions is extensively used in molecular simulations due to its simple form, computational speed, and transferability. We have proposed and parametrized a 12-6-4 LJ (Lennard-Jones)-type nonbonded model for divalent metal ions in previous work, which showed a marked improvement over the 12-6 LJ nonbonded model. In the present study, by treating the experimental hydration free energies and ion-oxygen distances of the first solvation shell as targets for our parametrization, we evaluated 12-6 LJ parameters for 18 M(III) and 6 M(IV) metal ions for three widely used water models (TIP3P, SPC/E, and TIP4PEW). As expected, the interaction energy underestimation of the 12-6 LJ nonbonded model increases dramatically for the highly charged metal ions. We then parametrized the 12-6-4 LJ-type nonbonded model for these metal ions with the three water models. The final parameters reproduced the target values with good accuracy, which is consistent with our previous experience using this potential. Finally, tests were performed on a protein system, and the obtained results validate the transferability of these nonbonded model parameters.
高电荷金属离子在广泛的化学络合物中充当催化中心和结构元素。金属离子的非键合模型由于其形式简单、计算速度快和可转移性，在分子模拟中被广泛使用。我们在之前的工作中提出并参数化了一种用于二价金属离子的12 - 6 - 4 Lennard - Jones（LJ）型非键合模型，该模型相对于12 - 6 LJ非键合模型有显著改进。在本研究中，通过将第一溶剂化层的实验水化自由能和离子 - 氧距离作为参数化的目标，我们针对三种广泛使用的水模型（TIP3P、SPC/E和TIP4PEW）评估了18种M(III)和6种M(IV)金属离子的12 - 6 LJ参数。正如预期的那样，对于高电荷金属离子，12 - 6 LJ非键合模型的相互作用能低估显著增加。然后，我们用这三种水模型对这些金属离子的12 - 6 - 4 LJ型非键合模型进行了参数化。最终参数以良好的精度再现了目标值，这与我们之前使用该势的经验一致。最后，在一个蛋白质系统上进行了测试，所得结果验证了这些非键合模型参数的可转移性。
