Kroutil Ondřej, Předota Milan, Kabeláč Martin
Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, České Budějovice, Czech Republic.
Faculty of Chemistry, Materials Research Centre, Brno University of Technology, Purkyňova 118, 612 00, Brno, Czech Republic.
J Mol Model. 2017 Oct 28;23(11):327. doi: 10.1007/s00894-017-3490-x.
Models of the hydrogenoxalate (bioxalate, charge -1) and oxalate (charge -2) anions were developed for classical molecular dynamics (CMD) simulations and parametrized against ab initio molecular dynamics (AIMD) data from our previous study (Kroutil et al. (2016) J Mol Model 22:210). The interactions of the anions with water were described using charges scaled according to the electronic continuum correction approach with rescaling of nonbonded parameters (ECCR), and those descriptions of anion interactions were found to agree well with relevant AIMD and experimental results. The models with full RESP charges showed excessively strong electrostatic interactions between the solute and water molecules, leading to an overstructured solvation shell around the anions and thus to a diffusion coefficient that was much too low. The effect of charge scaling was more evident for the oxalate dianion than for the hydrogenoxalate anion. Our work provides CMD models for ions of oxalic acid and extends previous studies that showed the importance of ECCR for modeling divalent ions and ions of organic compounds. Graphical abstract The radial distribution function between a water oxygen (Ow) and an oxygen of the oxalate dianion (Ox) significantly improved when scaled charges were applied to the anion.
为经典分子动力学(CMD)模拟开发了草酸氢根(草酸氢盐,电荷为 -1)和草酸根(电荷为 -2)阴离子的模型,并根据我们之前研究(Kroutil等人,(2016) J Mol Model 22:210)中的从头算分子动力学(AIMD)数据进行了参数化。使用根据电子连续介质校正方法(ECCR)缩放电荷并重新缩放非键参数来描述阴离子与水的相互作用,发现这些阴离子相互作用的描述与相关的AIMD和实验结果非常吻合。具有完整RESP电荷的模型显示溶质与水分子之间的静电相互作用过强,导致阴离子周围的溶剂化壳过度结构化,从而导致扩散系数过低。电荷缩放对草酸二价阴离子的影响比对草酸氢根阴离子更明显。我们的工作提供了草酸离子的CMD模型,并扩展了先前的研究,这些研究表明ECCR对于模拟二价离子和有机化合物离子的重要性。图形摘要当对阴离子应用缩放电荷时,水氧(Ow)与草酸二价阴离子氧(Ox)之间的径向分布函数显著改善。