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采用精确力场的分子动力学模拟研究氰根离子和氢氧根离子的溶剂化自由能。

Hydration free energies of cyanide and hydroxide ions from molecular dynamics simulations with accurate force fields.

机构信息

Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland.

出版信息

Phys Chem Chem Phys. 2013 Dec 14;15(46):20303-12. doi: 10.1039/c3cp52713a.

DOI:10.1039/c3cp52713a
PMID:24170171
Abstract

The evaluation of hydration free energies is a sensitive test to assess force fields used in atomistic simulations. We showed recently that the vibrational relaxation times, 1D- and 2D-infrared spectroscopies for CN(-) in water can be quantitatively described from molecular dynamics (MD) simulations with multipolar force fields and slightly enlarged van der Waals radii for the C- and N-atoms. To validate such an approach, the present work investigates the solvation free energy of cyanide in water using MD simulations with accurate multipolar electrostatics. It is found that larger van der Waals radii are indeed necessary to obtain results close to the experimental values when a multipolar force field is used. For CN(-), the van der Waals ranges refined in our previous work yield hydration free energy between -72.0 and -77.2 kcal mol(-1), which is in excellent agreement with the experimental data. In addition to the cyanide ion, we also study the hydroxide ion to show that the method used here is readily applicable to similar systems. Hydration free energies are found to sensitively depend on the intermolecular interactions, while bonded interactions are less important, as expected. We also investigate in the present work the possibility of applying the multipolar force field in scoring trajectories generated using computationally inexpensive methods, which should be useful in broader parametrization studies with reduced computational resources, as scoring is much faster than the generation of the trajectories.

摘要

评估水合自由能是评估原子模拟中使用的力场的敏感测试。我们最近表明,通过使用多极力场和略微增大 C 和 N 原子的范德华半径,可以从分子动力学 (MD) 模拟中定量描述 CN(-)在水中的振动弛豫时间、1D 和 2D 红外光谱。为了验证这种方法,本工作使用精确的多极静电的 MD 模拟研究了氰化物在水中的溶剂化自由能。结果发现,当使用多极力场时,确实需要更大的范德华半径才能获得接近实验值的结果。对于 CN(-),我们在前一项工作中精细调整的范德华半径得出的水合自由能在-72.0 到-77.2 kcal mol(-1)之间,与实验数据非常吻合。除了氰离子,我们还研究了氢氧根离子,以表明这里使用的方法很容易适用于类似的系统。水合自由能被发现强烈依赖于分子间相互作用,而键相互作用则不那么重要,这是预期的。我们还在本工作中研究了在使用计算成本较低的方法生成的轨迹中应用多极力场的可能性,这对于使用减少的计算资源进行更广泛的参数化研究应该是有用的,因为评分比生成轨迹快得多。

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