• 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

使用含杂化泛函和平面波的从头算分子动力学高效计算化学反应的自由能面

Efficient computation of free energy surfaces of chemical reactions using ab initio molecular dynamics with hybrid functionals and plane waves.

作者信息

Mandal Sagarmoy, Nair Nisanth N

机构信息

Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India.

出版信息

J Comput Chem. 2020 Jul 15;41(19):1790-1797. doi: 10.1002/jcc.26222. Epub 2020 May 14.

DOI:10.1002/jcc.26222
PMID:32407582
Abstract

Ab initio molecular dynamics (AIMD) simulations employing density functional theory (DFT) and plane waves are routinely carried out using density functionals at the level of generalized gradient approximation (GGA). AIMD simulations employing hybrid density functionals are of great interest as it offers a more accurate description of structural and dynamic properties than the GGA functionals. However, the computational cost for carrying out calculations using hybrid functionals and plane wave basis set is at least two orders of magnitude higher than that using GGA functionals. Recently, we proposed a strategy that combined the adaptively compressed exchange operator formulation and the multiple time step integration scheme to reduce the computational cost by an order of magnitude [J. Chem. Phys. 151, 151102 (2019)]. In this work, we demonstrate the application of this method to study chemical reactions, in particular, formamide hydrolysis in an alkaline aqueous medium. By actuating our implementation with the well-sliced metadynamics scheme, we can compute the two-dimensional free energy surface of this reaction at the level of hybrid-DFT. This work also investigates the accuracy of the PBE0 (hybrid) and the PBE (GGA) functionals in predicting the free energetics of this chemical reaction.

摘要

采用密度泛函理论(DFT)和平面波的从头算分子动力学(AIMD)模拟通常使用广义梯度近似(GGA)水平的密度泛函来进行。采用杂化密度泛函的AIMD模拟备受关注,因为它比GGA泛函能更准确地描述结构和动力学性质。然而,使用杂化泛函和平面波基组进行计算的成本比使用GGA泛函至少高两个数量级。最近,我们提出了一种策略,该策略结合了自适应压缩交换算符公式和多时间步积分方案,将计算成本降低了一个数量级[《化学物理杂志》151, 151102 (2019)]。在这项工作中,我们展示了该方法在研究化学反应中的应用,特别是在碱性水介质中的甲酰胺水解反应。通过用精心切片的元动力学方案启动我们的实现,我们可以在杂化DFT水平上计算该反应的二维自由能表面。这项工作还研究了PBE0(杂化)和PBE(GGA)泛函在预测该化学反应自由能方面的准确性。

相似文献

1
Efficient computation of free energy surfaces of chemical reactions using ab initio molecular dynamics with hybrid functionals and plane waves.使用含杂化泛函和平面波的从头算分子动力学高效计算化学反应的自由能面
J Comput Chem. 2020 Jul 15;41(19):1790-1797. doi: 10.1002/jcc.26222. Epub 2020 May 14.
2
Improving the scaling and performance of multiple time stepping-based molecular dynamics with hybrid density functionals.利用混合密度泛函提高基于多时间步长的分子动力学的规模和性能。
J Comput Chem. 2022 Apr 5;43(9):588-597. doi: 10.1002/jcc.26816. Epub 2022 Feb 11.
3
Speeding-up Hybrid Functional-Based Molecular Dynamics Using Multiple Time-stepping and Resonance-Free Thermostat.使用多时间步长和无共振恒温器加速基于混合泛函的分子动力学
J Chem Theory Comput. 2023 Nov 28;19(22):8351-8364. doi: 10.1021/acs.jctc.3c00964. Epub 2023 Nov 6.
4
Speeding-up ab initio molecular dynamics with hybrid functionals using adaptively compressed exchange operator based multiple timestepping.基于自适应压缩交换算子的多时间步长混合泛函加速从头分子动力学。
J Chem Phys. 2019 Oct 21;151(15):151102. doi: 10.1063/1.5125422.
5
Hybrid Functional and Plane Waves based Ab Initio Molecular Dynamics Study of the Aqueous Fe /Fe Redox Reaction.基于杂化泛函和平面波的水溶液中Fe²⁺/Fe³⁺氧化还原反应的从头算分子动力学研究
Chemphyschem. 2023 Feb 1;24(3):e202200617. doi: 10.1002/cphc.202200617. Epub 2022 Nov 2.
6
Achieving an Order of Magnitude Speedup in Hybrid-Functional- and Plane-Wave-Based Molecular Dynamics: Applications to Proton-Transfer Reactions in Enzymes and in Solution.实现杂化泛函和平面波基分子动力学的数量级加速:在酶和溶液中的质子转移反应中的应用。
J Chem Theory Comput. 2021 Apr 13;17(4):2244-2255. doi: 10.1021/acs.jctc.1c00009. Epub 2021 Mar 19.
7
Enhanced sampling and free energy calculations with hybrid functionals and plane waves for chemical reactions.利用杂化泛函和平面波进行化学反应的增强采样和自由能计算。
J Chem Phys. 2018 Oct 14;149(14):144113. doi: 10.1063/1.5049700.
8
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.
9
Comparison of density functionals for energy and structural differences between the high- [5T2g:(t2g)4(eg)2] and low- [1A1g:(t2g)6(eg)0] spin states of iron(II) coordination compounds. II. More functionals and the hexaminoferrous cation, [Fe(NH3)6]2+.铁(II)配位化合物的高自旋态[5T2g:(t2g)4(eg)2]和低自旋态[1A1g:(t2g)6(eg)0]之间能量和结构差异的密度泛函比较。II. 更多泛函与六氨合亚铁阳离子[Fe(NH3)6]2+
J Chem Phys. 2005 Jan 22;122(4):44110. doi: 10.1063/1.1839854.
10
Do Models beyond Hybrid Density Functionals Increase the Agreement with Experiment for Predicted NMR Chemical Shifts or Electric Field Gradient Tensors in Organic Solids?除杂化密度泛函之外的模型能否提高与有机固体中预测的核磁共振化学位移或电场梯度张量实验结果的一致性?
J Phys Chem A. 2023 Mar 30;127(12):2846-2858. doi: 10.1021/acs.jpca.2c07657. Epub 2023 Mar 20.

引用本文的文献

1
Born-Oppenheimer Molecular Dynamics with a Linear Combination of Atomic Orbitals and Hybrid Functionals for Condensed Matter Simulations Made Possible. Theory and Performance for the Microcanonical and Canonical Ensembles.借助原子轨道线性组合和杂化泛函实现凝聚态模拟的玻恩-奥本海默分子动力学。微正则系综和正则系综的理论与性能。
J Chem Theory Comput. 2024 May 14;20(9):3954-3975. doi: 10.1021/acs.jctc.3c01231. Epub 2024 Apr 22.