• 文献检索
  • 文档翻译
  • 深度研究
  • 学术资讯
  • Suppr Zotero 插件Zotero 插件
  • 邀请有礼
  • 套餐&价格
  • 历史记录
应用&插件
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
定价
高级版会员购买积分包购买API积分包
服务
文献检索文档翻译深度研究API 文档MCP 服务
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利:CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2026

文献检索

告别复杂PubMed语法,用中文像聊天一样搜索,搜遍4000万医学文献。AI智能推荐,让科研检索更轻松。

立即免费搜索

文件翻译

保留排版,准确专业,支持PDF/Word/PPT等文件格式,支持 12+语言互译。

免费翻译文档

深度研究

AI帮你快速写综述,25分钟生成高质量综述,智能提取关键信息,辅助科研写作。

立即免费体验

组合规则、理论水平和势函数对稀有气体气相和凝聚相性质建模的影响。

Impact of Combination Rules, Level of Theory, and Potential Function on the Modeling of Gas- and Condensed-Phase Properties of Noble Gases.

作者信息

Kříž Kristian, van Maaren Paul J, van der Spoel David

机构信息

Department of Cell and Molecular Biology, Uppsala University, Box 596, Uppsala SE-75124, Sweden.

出版信息

J Chem Theory Comput. 2024 Mar 26;20(6):2362-2376. doi: 10.1021/acs.jctc.3c01257. Epub 2024 Mar 13.

DOI:10.1021/acs.jctc.3c01257
PMID:38477573
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10976648/
Abstract

The systems of noble gases are particularly instructive for molecular modeling due to the elemental nature of their interactions. They do not normally form bonds nor possess a (permanent) dipole moment, and the only forces determining their bonding/clustering stems from van der Waals forces─dispersion and Pauli repulsion, which can be modeled by empirical potential functions. Combination rules, that is, formulas to derive parameters for pair potentials of heterodimers from parameters of corresponding homodimers, have been studied at length for the Lennard-Jones 12-6 potentials but not in great detail for other, more accurate, potentials. In this work, we examine the usefulness of nine empirical potentials in their ability to reproduce quantum mechanical (QM) benchmark dissociation curves of noble gas dimers (He, Ne, Ar, Kr, and Xe homo- and heterodimers), and we systematically study the efficacy of different permutations of combination relations for each parameter of the potentials. Our QM benchmark comprises dissociation curves computed by several different coupled cluster implementations as well as symmetry-adapted perturbation theory. The two-parameter Lennard-Jones potentials were decisively outperformed by more elaborate potentials that sport a 25-30 times lower root-mean-square error (RMSE) when fitted to QM dissociation curves. Very good fits to the QM dissociation curves can be achieved with relatively inexpensive four- or even three-parameter potentials, for instance, the damped 14-7 potential (Halgren, 7827-7843), a four-parameter Buckingham potential (Werhahn et al., 133-138), or the three-parameter Morse potential (Morse, 57-64). Potentials for heterodimers that are generated from combination rules have an RMSE that is up to 20 times higher than potentials that are directly fitted to the QM dissociation curves. This means that the RMSE, in particular, for light atoms, is comparable in magnitude to the well-depth of the potential. Based on a systematic permutation of combination rules, we present one or more combination rules for each potential tested that yield a relatively low RMSE. Two new combination rules are introduced that perform well, one for the van der Waals radius σ as and one for the well-depth ϵ as . The QM data and the fitted potentials were evaluated in the gas phase against experimental second virial coefficients for homo- and heterodimers, the latter of which allowed evaluation of the combination rules. The fitted models were used to perform condensed phase molecular dynamics simulations to verify the melting points, liquid densities at the melting point, and the enthalpies of vaporization produced by the models for pure substances. Subtle differences in the benchmark potentials, in particular, the well-depth, due to the level of theory used were found here to have a profound effect on the macroscopic properties of noble gases: second virial coefficients or the bulk properties in simulations. By explicitly including three-body dispersion in molecular simulations employing the best pair potential, we were able to obtain accurate melting points as well as satisfactory densities and enthalpies of vaporization.

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f57/10976648/7f55066d577b/ct3c01257_0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f57/10976648/1053d7dcf76c/ct3c01257_0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f57/10976648/8015c210d8e4/ct3c01257_0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f57/10976648/3136280f5f0e/ct3c01257_0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f57/10976648/7f55066d577b/ct3c01257_0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f57/10976648/1053d7dcf76c/ct3c01257_0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f57/10976648/8015c210d8e4/ct3c01257_0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f57/10976648/3136280f5f0e/ct3c01257_0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f57/10976648/7f55066d577b/ct3c01257_0004.jpg
摘要

由于稀有气体相互作用的基本性质,其体系对于分子建模具有特别的指导意义。它们通常不形成化学键,也不具有(永久)偶极矩,决定其键合/聚集的唯一作用力来自范德华力——色散力和泡利排斥力,这可以通过经验势函数进行建模。对于 Lennard-Jones 12 - 6 势,组合规则(即从相应同二聚体的参数推导异二聚体对势参数的公式)已被深入研究,但对于其他更精确的势则研究得不够详细。在这项工作中,我们研究了九种经验势在重现稀有气体二聚体(He、Ne、Ar、Kr 和 Xe 的同二聚体和异二聚体)量子力学(QM)基准解离曲线方面的有效性,并系统地研究了势的每个参数的不同组合关系排列的功效。我们的 QM 基准包括由几种不同的耦合簇实现以及对称适配微扰理论计算得到的解离曲线。当拟合 QM 解离曲线时,更精细的势明显优于两参数 Lennard-Jones 势,前者的均方根误差(RMSE)低 25 - 30 倍。使用相对简单的四参数甚至三参数势,例如阻尼 14 - 7 势(哈尔格伦,7827 - 7843)、四参数白金汉势(韦尔哈恩等人,133 - 138)或三参数莫尔斯势(莫尔斯,57 - 64),可以很好地拟合 QM 解离曲线。由组合规则生成的异二聚体势的 RMSE 比直接拟合 QM 解离曲线的势高出多达 20 倍。这意味着特别是对于轻原子,RMSE 的大小与势的阱深相当。基于组合规则的系统排列,我们为每个测试的势提出了一个或多个组合规则,这些规则产生相对较低的 RMSE。引入了两个表现良好的新组合规则,一个用于范德华半径 σ,另一个用于阱深 ϵ。在气相中,针对同二聚体和异二聚体的实验第二维里系数评估了 QM 数据和拟合势,后者用于评估组合规则。使用拟合模型进行凝聚相分子动力学模拟,以验证模型预测的纯物质的熔点、熔点时的液体密度和汽化焓。在此发现,由于所使用的理论水平,基准势中的细微差异,特别是阱深,对稀有气体的宏观性质(第二维里系数或模拟中的体相性质)有深远影响。通过在采用最佳对势的分子模拟中明确包含三体色散,我们能够获得准确的熔点以及令人满意的密度和汽化焓。

相似文献

1
Impact of Combination Rules, Level of Theory, and Potential Function on the Modeling of Gas- and Condensed-Phase Properties of Noble Gases.组合规则、理论水平和势函数对稀有气体气相和凝聚相性质建模的影响。
J Chem Theory Comput. 2024 Mar 26;20(6):2362-2376. doi: 10.1021/acs.jctc.3c01257. Epub 2024 Mar 13.
2
Combination Rules for Morse-Based van der Waals Force Fields.基于莫尔斯函数的范德华力场的组合规则
J Phys Chem A. 2018 Feb 15;122(6):1672-1677. doi: 10.1021/acs.jpca.7b11252. Epub 2018 Feb 2.
3
Solubility Equilibrium Isotope Effects of Noble Gases in Water: Theory and Observations.稀有气体在水中的溶解度平衡同位素效应:理论与观测
J Phys Chem B. 2023 Nov 16;127(45):9802-9812. doi: 10.1021/acs.jpcb.3c05651. Epub 2023 Nov 8.
4
Transferability and accuracy by combining dispersionless density functional and incremental post-Hartree-Fock theories: Noble gases adsorption on coronene/graphene/graphite surfaces.通过结合无弥散密度泛函和增量后哈特里-福克理论实现的可转移性与准确性:稀有气体在并五苯/石墨烯/石墨表面的吸附
J Chem Phys. 2015 Nov 21;143(19):194701. doi: 10.1063/1.4935511.
5
Pseudopotential analysis on hyperfine splitting frequency shift of alkali-metal atoms in noble gases, revisited.碱金属原子在稀有气体中的超精细分裂频率位移的赝势分析,再探。
J Chem Phys. 2023 Feb 28;158(8):084306. doi: 10.1063/5.0138434.
6
The ground state van der Waals potentials of the calcium dimer and calcium rare-gas complexes.钙二聚体和钙稀有气体配合物的基态范德华势能。
J Chem Phys. 2009 Oct 21;131(15):154301. doi: 10.1063/1.3246351.
7
Dynamics and spectroscopy of van der Waals complexes composed of ammonia and noble gases.由氨和稀有气体组成的范德华复合物的动力学与光谱学
J Mol Model. 2019 Apr 24;25(5):126. doi: 10.1007/s00894-019-4023-6.
8
Universal Pairwise Interatomic van der Waals Potentials Based on Quantum Drude Oscillators.基于量子德鲁德振荡器的通用成对原子间范德华势
J Chem Theory Comput. 2023 Nov 14;19(21):7895-7907. doi: 10.1021/acs.jctc.3c00797. Epub 2023 Oct 24.
9
The potential energy curves of atom pairs and transport properties of high-temperature vapors of Cu and Si and their mixtures with He, Ar, and Xe gases.铜和硅及其与氦气、氩气和氙气混合物的高温蒸汽中原子对的势能曲线和输运性质。
Phys Chem Chem Phys. 2023 Feb 8;25(6):4872-4898. doi: 10.1039/d2cp04981c.
10
Accurate non-bonded potentials based on periodic quantum mechanics calculations for use in molecular simulations of materials and systems.基于周期性量子力学计算的精确非键相互作用势在材料和体系的分子模拟中的应用。
J Chem Phys. 2019 Oct 21;151(15):154111. doi: 10.1063/1.5113811.

引用本文的文献

1
Quantification of Anisotropy in Exchange and Dispersion Interactions: A Simple Model for Physics-Based Force Fields.交换与色散相互作用中各向异性的量化:基于物理的力场的简单模型
J Phys Chem Lett. 2024 Oct 3;15(39):9974-9978. doi: 10.1021/acs.jpclett.4c02034. Epub 2024 Sep 24.

本文引用的文献

1
Universal Pairwise Interatomic van der Waals Potentials Based on Quantum Drude Oscillators.基于量子德鲁德振荡器的通用成对原子间范德华势
J Chem Theory Comput. 2023 Nov 14;19(21):7895-7907. doi: 10.1021/acs.jctc.3c00797. Epub 2023 Oct 24.
2
The Challenge of ab Initio Calculations in Small Neon Clusters.小氖团簇从头算计算的挑战
Chemphyschem. 2023 Dec 14;24(24):e202300485. doi: 10.1002/cphc.202300485. Epub 2023 Oct 26.
3
Influence of the Lennard-Jones Combination Rules on the Simulated Properties of Organic Liquids at Optimal Force-Field Parametrization.
最优化力场参数化条件下 Lennard-Jones 组合规则对有机液体模拟性质的影响。
J Chem Theory Comput. 2023 Apr 11;19(7):2048-2063. doi: 10.1021/acs.jctc.2c01170. Epub 2023 Mar 15.
4
Microscopic origins of conductivity in molten salts unraveled by computer simulations.计算机模拟揭示熔盐导电性的微观起源
Commun Chem. 2021 Jan 27;4(1):9. doi: 10.1038/s42004-020-00446-2.
5
Thermodynamic properties of argon from Monte Carlo simulations using ab initio potentials.基于从头算势的蒙特卡罗模拟得到的氩的热力学性质
Phys Rev E. 2022 Jun;105(6-1):064129. doi: 10.1103/PhysRevE.105.064129.
6
Where Lennard-Jones Potentials Fail: Iterative Optimization of Ion-Water Pair Potentials Based on Ab Initio Molecular Dynamics Data.伦纳德-琼斯势失效的地方:基于从头算分子动力学数据的离子-水对势的迭代优化
J Phys Chem Lett. 2022 Apr 28;13(16):3712-3717. doi: 10.1021/acs.jpclett.2c00121. Epub 2022 Apr 19.
7
Non-bonded force field model with advanced restrained electrostatic potential charges (RESP2).具有先进受限静电势电荷(RESP2)的非键合作用力场模型。
Commun Chem. 2020;3. doi: 10.1038/s42004-020-0291-4. Epub 2020 Apr 3.
8
Benchmarking of Molecular Dynamics Force Fields for Solid-Liquid and Solid-Solid Phase Transitions in Alkanes.烷烃固-液和固-固相转变的分子动力学力场基准测试。
J Phys Chem B. 2021 May 20;125(19):5145-5159. doi: 10.1021/acs.jpcb.0c07587. Epub 2021 Mar 16.
9
Conformal Analytical Potential for All the Rare Gas Dimers over the Full Range of Internuclear Distances.全核间距范围内所有稀有气体二聚体的共形分析势
Phys Rev Lett. 2020 Dec 18;125(25):253402. doi: 10.1103/PhysRevLett.125.253402.
10
Systematic design of biomolecular force fields.生物分子力场的系统设计。
Curr Opin Struct Biol. 2021 Apr;67:18-24. doi: 10.1016/j.sbi.2020.08.006. Epub 2020 Sep 24.