• 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

通过微调有效两体相互作用提高从头算分子动力学的准确性:以乙腈为例

Enhancing the Accuracy of Ab Initio Molecular Dynamics by Fine Tuning of Effective Two-Body Interactions: Acetonitrile as a Test Case.

作者信息

Barbosa Nuno, Pagliai Marco, Sinha Sourab, Barone Vincenzo, Alfè Dario, Brancato Giuseppe

机构信息

Scuola Normale Superiore and CSGI, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.

Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.

出版信息

J Phys Chem A. 2021 Dec 9;125(48):10475-10484. doi: 10.1021/acs.jpca.1c07576. Epub 2021 Nov 29.

DOI:10.1021/acs.jpca.1c07576
PMID:34843249
Abstract

Grimme's dispersion-corrected density functional theory (DFT-D) methods have emerged among the most practical approaches to perform accurate quantum mechanical calculations on molecular systems ranging from small clusters to microscopic and mesoscopic samples, i.e., including hundreds or thousands of molecules. Moreover, DFT-D functionals can be easily integrated into popular molecular dynamics (MD) software packages to carry out first-principles condensed-phase simulations at an affordable computational cost. Here, starting from the well-established D3 version of the dispersion-correction term, we present a simple protocol to improve the accurate description of the intermolecular interactions of molecular clusters of growing size, considering acetonitrile as a test case. Optimization of the interaction energy was performed with reference to diffusion quantum Monte Carlo calculations, successfully reaching the same inherent accuracy of the latter (statistical error of ∼0.1 kcal/mol per molecule). The refined DFT-D3 model was then used to perform MD simulations of liquid acetonitrile, again showing significant improvements toward available experimental data with respect to the default correction.

摘要

格林的色散校正密度泛函理论(DFT-D)方法已成为对从小团簇到微观和介观样品(即包含数百或数千个分子)的分子系统进行精确量子力学计算的最实用方法之一。此外,DFT-D泛函可以很容易地集成到流行的分子动力学(MD)软件包中,以合理的计算成本进行第一性原理凝聚相模拟。在此,从成熟的色散校正项D3版本出发,我们提出了一个简单的方案,以改进对不断增大尺寸的分子团簇分子间相互作用的精确描述,以乙腈作为测试案例。参考扩散量子蒙特卡罗计算对相互作用能进行了优化,成功达到了后者相同的固有精度(每个分子的统计误差约为0.1 kcal/mol)。然后,使用改进后的DFT-D3模型对液态乙腈进行MD模拟,相对于默认校正,再次显示出在可用实验数据方面的显著改进。

相似文献

1
Enhancing the Accuracy of Ab Initio Molecular Dynamics by Fine Tuning of Effective Two-Body Interactions: Acetonitrile as a Test Case.通过微调有效两体相互作用提高从头算分子动力学的准确性:以乙腈为例
J Phys Chem A. 2021 Dec 9;125(48):10475-10484. doi: 10.1021/acs.jpca.1c07576. Epub 2021 Nov 29.
2
Fine Tuning the Intermolecular Interactions of Water Clusters Using the Dispersion-Corrected Density Functional Theory.利用色散校正密度泛函理论精细调整水分子簇的分子间相互作用。
Molecules. 2023 Apr 30;28(9):3834. doi: 10.3390/molecules28093834.
3
Proceedings of the Second Workshop on Theory meets Industry (Erwin-Schrödinger-Institute (ESI), Vienna, Austria, 12-14 June 2007).第二届理论与产业研讨会会议录(2007年6月12日至14日,奥地利维也纳埃尔温·薛定谔研究所)
J Phys Condens Matter. 2008 Feb 13;20(6):060301. doi: 10.1088/0953-8984/20/06/060301. Epub 2008 Jan 24.
4
Empirical D3 Dispersion as a Replacement for ab Initio Dispersion Terms in Density Functional Theory-Based Symmetry-Adapted Perturbation Theory.基于密度泛函理论的对称适应微扰理论中,经验性D3色散作为从头算色散项的替代方法
J Chem Theory Comput. 2017 Apr 11;13(4):1638-1646. doi: 10.1021/acs.jctc.6b01198. Epub 2017 Mar 22.
5
Enabling Large-Scale Condensed-Phase Hybrid Density Functional Theory Based Molecular Dynamics. 1. Theory, Algorithm, and Performance.实现基于大规模凝聚相杂化密度泛函理论的分子动力学。1. 理论、算法和性能。
J Chem Theory Comput. 2020 Jun 9;16(6):3757-3785. doi: 10.1021/acs.jctc.9b01167. Epub 2020 May 14.
6
Appropriate description of intermolecular interactions in the methane hydrates: an assessment of DFT methods.甲烷水合物中分子间相互作用的恰当描述:DFT 方法的评估。
J Comput Chem. 2013 Jan 15;34(2):121-31. doi: 10.1002/jcc.23112. Epub 2012 Sep 5.
7
Ab Initio Calculations for Molecule-Surface Interactions with Chemical Accuracy.具有化学精度的分子-表面相互作用的从头算计算。
Acc Chem Res. 2019 Dec 17;52(12):3502-3510. doi: 10.1021/acs.accounts.9b00506. Epub 2019 Nov 25.
8
Calculations on noncovalent interactions and databases of benchmark interaction energies.非共价相互作用的计算和基准相互作用能数据库。
Acc Chem Res. 2012 Apr 17;45(4):663-72. doi: 10.1021/ar200255p. Epub 2012 Jan 6.
9
Liquid Methanol from DFT and DFT/MM Molecular Dynamics Simulations.基于密度泛函理论(DFT)和DFT/分子力学(MM)分子动力学模拟的液态甲醇
J Chem Theory Comput. 2013 Jan 8;9(1):106-18. doi: 10.1021/ct300784x. Epub 2012 Oct 30.
10
A machine learning correction for DFT non-covalent interactions based on the S22, S66 and X40 benchmark databases.基于S22、S66和X40基准数据库的用于密度泛函理论非共价相互作用的机器学习校正。
J Cheminform. 2016 May 3;8:24. doi: 10.1186/s13321-016-0133-7. eCollection 2016.

引用本文的文献

1
Structural and Dynamical Insights into Acetonitrile-Water Mixtures: A Molecular Dynamics Study of Self-Diffusion, Reorientational Correlation Times, and Temperature-Dependent Behavior.乙腈 - 水混合物的结构与动力学见解:自扩散、重取向相关时间及温度依赖性行为的分子动力学研究
ACS Omega. 2025 Aug 15;10(33):38092-38102. doi: 10.1021/acsomega.5c05444. eCollection 2025 Aug 26.
2
Adsorption Behaviors and Mechanism of Phenol and Catechol in Wastewater by Magnetic Graphene Oxides: A Comprehensive Study Based on Adsorption Experiments, Mathematical Models, and Molecular Simulations.磁性氧化石墨烯对废水中苯酚和邻苯二酚的吸附行为及机理:基于吸附实验、数学模型和分子模拟的综合研究
ACS Omega. 2024 Mar 23;9(13):15101-15113. doi: 10.1021/acsomega.3c09346. eCollection 2024 Apr 2.
3
Fine Tuning the Intermolecular Interactions of Water Clusters Using the Dispersion-Corrected Density Functional Theory.利用色散校正密度泛函理论精细调整水分子簇的分子间相互作用。
Molecules. 2023 Apr 30;28(9):3834. doi: 10.3390/molecules28093834.