基于 QM/MM 的大系统能量分解分析方法

IF 2.8 2区化学 Q3 CHEMISTRY, PHYSICAL

The Journal of Physical Chemistry A Pub Date : 2024-04-30 DOI:10.1021/acs.jpca.4c00183

Xuewei Xiong, Ran Friedman*, Wei Wu and Peifeng Su*,

{"title":"基于 QM/MM 的大系统能量分解分析方法","authors":"Xuewei Xiong, Ran Friedman*, Wei Wu and Peifeng Su*, ","doi":"10.1021/acs.jpca.4c00183","DOIUrl":null,"url":null,"abstract":"<p >In this work, a QM/MM-based EDA method, called GKS-EDA(QM/MM), is proposed. As an extension of GKS-EDA, this scheme divides the total interaction energy into electrostatic, exchange-repulsion, polarization, and correlation/dispersion terms. GKS-EDA(QM/MM) can be applied to describe the interactions of large-scale systems combined with various QM/MM platforms. By using the examples of a hydrated hydronium ion complex in water solution, the barnase–barstar complex, and MMP-13-pyrimidinetrione in a metalloprotein, the capability of GKS-EDA(QM/MM) for various interactions in large systems is validated.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":"128 18","pages":"3529–3538"},"PeriodicalIF":2.8000,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"QM/MM-Based Energy Decomposition Analysis Method for Large Systems\",\"authors\":\"Xuewei Xiong, Ran Friedman*, Wei Wu and Peifeng Su*, \",\"doi\":\"10.1021/acs.jpca.4c00183\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p >In this work, a QM/MM-based EDA method, called GKS-EDA(QM/MM), is proposed. As an extension of GKS-EDA, this scheme divides the total interaction energy into electrostatic, exchange-repulsion, polarization, and correlation/dispersion terms. GKS-EDA(QM/MM) can be applied to describe the interactions of large-scale systems combined with various QM/MM platforms. By using the examples of a hydrated hydronium ion complex in water solution, the barnase–barstar complex, and MMP-13-pyrimidinetrione in a metalloprotein, the capability of GKS-EDA(QM/MM) for various interactions in large systems is validated.</p>\",\"PeriodicalId\":59,\"journal\":{\"name\":\"The Journal of Physical Chemistry A\",\"volume\":\"128 18\",\"pages\":\"3529–3538\"},\"PeriodicalIF\":2.8000,\"publicationDate\":\"2024-04-30\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"The Journal of Physical Chemistry A\",\"FirstCategoryId\":\"1\",\"ListUrlMain\":\"https://pubs.acs.org/doi/10.1021/acs.jpca.4c00183\",\"RegionNum\":2,\"RegionCategory\":\"化学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q3\",\"JCRName\":\"CHEMISTRY, PHYSICAL\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"The Journal of Physical Chemistry A","FirstCategoryId":"1","ListUrlMain":"https://pubs.acs.org/doi/10.1021/acs.jpca.4c00183","RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"CHEMISTRY, PHYSICAL","Score":null,"Total":0}

引用次数: 0

摘要

本文提出了一种基于 QM/MM 的 EDA 方法，称为 GKS-EDA(QM/MM)。作为 GKS-EDA 的扩展，该方案将总相互作用能分为静电、交换-排斥、极化和相关/分散项。GKS-EDA(QM/MM) 可用于描述与各种 QM/MM 平台相结合的大规模系统的相互作用。通过水溶液中的水合氢离子复合物、barnase-barstar 复合物和金属蛋白中的 MMP-13-嘧啶三酮等例子，验证了 GKS-EDA(QM/MM) 在大型系统中的各种相互作用能力。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

QM/MM-Based Energy Decomposition Analysis Method for Large Systems

查看原文本刊更多论文

QM/MM-Based Energy Decomposition Analysis Method for Large Systems

In this work, a QM/MM-based EDA method, called GKS-EDA(QM/MM), is proposed. As an extension of GKS-EDA, this scheme divides the total interaction energy into electrostatic, exchange-repulsion, polarization, and correlation/dispersion terms. GKS-EDA(QM/MM) can be applied to describe the interactions of large-scale systems combined with various QM/MM platforms. By using the examples of a hydrated hydronium ion complex in water solution, the barnase–barstar complex, and MMP-13-pyrimidinetrione in a metalloprotein, the capability of GKS-EDA(QM/MM) for various interactions in large systems is validated.

求助全文

通过发布文献求助，成功后即可免费获取论文全文。去求助

来源期刊

The Journal of Physical Chemistry A 化学-物理：原子、分子和化学物理

CiteScore

5.20

自引率

10.30%

发文量

922

审稿时长

1.3 months

期刊介绍： The Journal of Physical Chemistry A is devoted to reporting new and original experimental and theoretical basic research of interest to physical chemists, biophysical chemists, and chemical physicists.