Parameterization of highly charged metal ions using the 12-6-4 LJ-type nonbonded model in explicit water.
Parameterization of highly charged metal ions using the 12-6-4 LJ-type nonbonded model in explicit water.
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DOI：
10.1021/jp505875v
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发表时间：
2015-01-22
期刊：
影响因子：
--
通讯作者：
Merz KM Jr
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文献类型：
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作者：
Li P;Song LF;Merz KM Jr
高电荷态金属离子在一系列化学络合物中起催化中心和结构元素的作用。金属离子的非键模型因其形式简单、计算速度快和可转换性而在分子模拟中得到广泛应用。我们在前人的工作中提出并参数化了一个二价金属离子的12-6-4LJ(Lennard-Jones)型非键模型，该模型比12-6LJ非键模型有了显著的改进。在本研究中，通过将实验的第一溶剂化壳层的水合自由能和离子-氧距离作为我们的参数化目标，我们计算了三个广泛使用的水模型(TIP3P、SPC/E和TIP4PEW)中18M(III)和6M(IV)金属离子的12-6LJ参数。正如预期的那样，对于高电荷态金属离子，12-6LJ非键模型的相互作用能低估显著增加。然后，我们用这三个水模型对这些金属离子进行了12-6-4LJ型非键模型的参数化。最终的参数准确地再现了目标值，这与我们以前使用该潜力的经验是一致的。最后，对一个蛋白质系统进行了测试，得到的结果验证了这些非键合模型参数的可传递性。
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.