A Coarse-Grained SPICA Makeover for Solvated and Bare Sodium and Chloride Ions.

IF 5.7 1区 化学 Q2 CHEMISTRY, PHYSICAL
Journal of Chemical Theory and Computation Pub Date : 2024-09-10 Epub Date: 2024-08-19 DOI:10.1021/acs.jctc.4c00529
Janak Prabhu, Matteo Frigerio, Emanuele Petretto, Pablo Campomanes, Stefan Salentinig, Stefano Vanni
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Abstract

Aqueous ionic solutions are pivotal in various scientific domains due to their natural prevalence and vital roles in biological and chemical processes. Molecular dynamics has emerged as an effective methodology for studying the dynamic behavior of these systems. While all-atomistic models have made significant strides in accurately representing and simulating these ions, the challenge persists in achieving precise models for coarse-grained (CG) simulations. Our study introduces two optimized models for sodium and chloride ions within the nonpolarizable surface property fitting coarse-grained force field (SPICA-FF) framework. The two models represent solvated ions, such as the original FF model, and unsolvated or bare ions. The nonbonded Lennard-Jones interactions were reparameterized to faithfully reproduce bulk properties, including density and surface tension, in sodium chloride solutions at varying concentrations. Notably, these optimized models replicate experimental surface tensions at high ionic strengths, a property not well-captured by the ions of the original model in the SPICA-FF. The optimized unsolvated model also proved successful in reproducing experimental osmotic pressure. Additionally, the newly reparameterized ion models capture hydrophobic interactions within sodium chloride solutions and show qualitative agreement when modeling structural changes in phospholipid bilayers, aligning with experimental observations. For aqueous solutions, these optimized models promise a more precise representation of the ion behavior.

Abstract Image

针对溶解和裸露钠离子和氯离子的粗粒 SPICA 改造。
离子水溶液因其在生物和化学过程中的天然普遍性和重要作用,在各个科学领域都举足轻重。分子动力学已成为研究这些系统动态行为的有效方法。虽然全原子模型在精确表示和模拟这些离子方面取得了长足进步,但在实现粗粒度(CG)模拟的精确模型方面仍然存在挑战。我们的研究在非极性表面性质拟合粗粒度力场(SPICA-FF)框架内引入了钠离子和氯离子的两个优化模型。这两个模型分别代表溶解离子(如原始 FF 模型)和非溶解离子或裸离子。对非键合的伦纳德-琼斯相互作用进行了重新参数化,以忠实地再现氯化钠溶液在不同浓度下的体积特性,包括密度和表面张力。值得注意的是,这些优化模型再现了高离子强度下的实验表面张力,而 SPICA-FF 中原始模型的离子并不能很好地捕捉这一特性。事实证明,优化的非溶解模型也成功地再现了实验渗透压。此外,新近重新参数化的离子模型捕捉到了氯化钠溶液中的疏水相互作用,并在模拟磷脂双分子层的结构变化时显示出定性的一致性,与实验观察结果一致。对于水溶液,这些优化模型有望更精确地反映离子行为。
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来源期刊
Journal of Chemical Theory and Computation
Journal of Chemical Theory and Computation 化学-物理:原子、分子和化学物理
CiteScore
9.90
自引率
16.40%
发文量
568
审稿时长
1 months
期刊介绍: The Journal of Chemical Theory and Computation invites new and original contributions with the understanding that, if accepted, they will not be published elsewhere. Papers reporting new theories, methodology, and/or important applications in quantum electronic structure, molecular dynamics, and statistical mechanics are appropriate for submission to this Journal. Specific topics include advances in or applications of ab initio quantum mechanics, density functional theory, design and properties of new materials, surface science, Monte Carlo simulations, solvation models, QM/MM calculations, biomolecular structure prediction, and molecular dynamics in the broadest sense including gas-phase dynamics, ab initio dynamics, biomolecular dynamics, and protein folding. The Journal does not consider papers that are straightforward applications of known methods including DFT and molecular dynamics. The Journal favors submissions that include advances in theory or methodology with applications to compelling problems.
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