首页> 外文期刊>Journal of chemical theory and computation: JCTC >Systematic Parametrization of Divalent Metal Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models
【24h】

Systematic Parametrization of Divalent Metal Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models

机译:用于OPC3,OPC,Tip3P-FB和Tip4P-FB水模型的二价金属离子的系统参数化

获取原文
获取原文并翻译 | 示例
           

摘要

Divalent metal ions play important roles in biological and materials systems. Molecular dynamics simulation is an efficient tool to investigate these systems at the microscopic level. Recently, four new water models (OPC3, OPC, TIP3P-FB, and TIP4P-FB) have been developed and better represent the physical properties of water than previous models. Metal ion parameters are dependent on the water model employed, making it necessary to develop metal ion parameters for select new water models. In the present work, we performed parameter scanning for the 12-6 Lennard-Jones nonbonded model of divalent metal ions in conjunction with the four new water models as well as four previous water models (TIP3P, SPC/E, TIP4P, and TIP4P-Ew). We found that these new three-point and four-point water models provide comparable or significantly improved performance for the simulation of divalent metal ions when compared to previous water models in the same category. Among all eight water models, the OPC3 water model yields the best performance for the simulation of divalent metal ions in the aqueous phase when using the 12-6 model. On the basis of the scanning results, we independently parametrized the 12-6 model for 24 divalent metal ions with each of the four new water models. As noted previously, the 12-6 model still fails to simultaneously reproduce the experimental hydration free energy (HFE) and ion-oxygen distance (IOD) values even with these new water models. To solve this problem, we parametrized the 12-6-4 model for the 16 divalent metal ions for which we have both experimental HFE and IOD values for each of the four new water models. The final parameters are able to reproduce both the experimental HFE and IOD values accurately. To validate the transferability of our parameters, we carried out benchmark calculations to predict the energies and geometries of ion–water clusters as well as the ion diffusivity coefficient of Mg~(2+). By comparison to quantum chemical calculations and experimental data, these results show that our parameters are well designed and have excellent transferability. The metal ion parameters for the 12-6 and 12-6-4 models reported herein can be employed in simulations of various biological and materials systems when using the OPC3, OPC, TIP3P-FB, or TIP4P-FB water model.
机译:二价金属离子在生物和材料系统中起重要作用。分子动力学仿真是一种有效的工具,可以在微观水平处研究这些系统。最近,已经开发出了四种新的水模型(OPC3,OPC,Tip3P-FB和Tip4P-FB),并且更好地代表了水的物理性质而多的模型。金属离子参数取决于所采用的水模型,使得有必要开发用于选择新水模型的金属离子参数。在本作工作中,我们与四个新的水模型以及四个新的水模型以及四个新的水模型(Tip3P,SPC / E,Tip4P和Tip4P - ew)。我们发现,与以前的不同类别中的水模型相比,这些新的三点和四点水模型提供了类似的或显着提高了二价金属离子的模拟性能。在所有八种水模型中,OPC3水模型在使用12-6型模型时产生了水相中二价金属离子的最佳性能。在扫描结果的基础上,我们独立地参数化了24种二价金属离子的12-6型,其中四种新的水模型中的每一种。如前所述,即使使用这些新的水模型,12-6型型号仍然不能同时再现实验性水合的可自由能(HFE)和离子氧距离(IOD)值。为了解决这个问题,我们参数化了12-6-4模型,用于16个二价金属离子,我们为四种新的水模型中的每一个具有实验HFE和IOD值。最终参数能够精确地再现实验HFE和IOD值。为了验证我们参数的可转换性,我们进行了基准计算,以预测离子水簇的能量和几何形状以及Mg〜(2+)的离子扩散系数。通过与量子化学计算和实验数据的比较,这些结果表明我们的参数设计良好并具有优异的可转移性。当使用OPC3,OPC,Tip3P-FB或Tip4P-FB水模型时,可以在各种生物和材料系统的模拟中使用本文的12-6和12-6-4模型的金属离子参数。

著录项

相似文献

  • 外文文献
  • 中文文献
  • 专利
获取原文

客服邮箱:kefu@zhangqiaokeyan.com

京公网安备:11010802029741号 ICP备案号:京ICP备15016152号-6 六维联合信息科技 (北京) 有限公司©版权所有
  • 客服微信

  • 服务号