用机器学习势能模拟金属复合物中的配体交换

IF 3.3 3区 化学 Q2 CHEMISTRY, PHYSICAL
Veronika Jurásková, Gers Tusha, Hanwen Zhang, Lars V Schäfer, Fernanda Duarte
{"title":"用机器学习势能模拟金属复合物中的配体交换","authors":"Veronika Jurásková, Gers Tusha, Hanwen Zhang, Lars V Schäfer, Fernanda Duarte","doi":"10.1039/d4fd00140k","DOIUrl":null,"url":null,"abstract":"Metal ions are irreplaceable in many areas of chemistry, including (bio)catalysis, self-assembly and charge transfer processes. Yet, modelling their structural and dynamic properties in diverse chemical environments remains challenging for both force fields and ab initio methods. Here, we introduce a strategy to train machine learning potentials (MLPs) using MACE, an equivariant message-passing neural network, for metal-ligand complexes in explicit solvents. We explore the structure and ligand exchange dynamics of Mg<small><sup>2+</sup></small> in water and Pd<small><sup>2+</sup></small> in acetonitrile as two illustrative model systems. The trained potentials accurately reproduce equilibrium structures of the complexes in solution, including different coordination numbers and geometries. Furthermore, the MLPs can model structural changes between metal ions and ligands in the first coordination shell, and reproduce the free energy barriers for the corresponding ligand exchange. The strategy presented here provides a computationally efficient approach to model metal ions in solution, paving the way for modelling larger and more diverse metal complexes relevant to biomolecules and supramolecular assemblies.","PeriodicalId":76,"journal":{"name":"Faraday Discussions","volume":null,"pages":null},"PeriodicalIF":3.3000,"publicationDate":"2024-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Modelling ligand exchange in metal complexes with machine learning potentials\",\"authors\":\"Veronika Jurásková, Gers Tusha, Hanwen Zhang, Lars V Schäfer, Fernanda Duarte\",\"doi\":\"10.1039/d4fd00140k\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"Metal ions are irreplaceable in many areas of chemistry, including (bio)catalysis, self-assembly and charge transfer processes. Yet, modelling their structural and dynamic properties in diverse chemical environments remains challenging for both force fields and ab initio methods. Here, we introduce a strategy to train machine learning potentials (MLPs) using MACE, an equivariant message-passing neural network, for metal-ligand complexes in explicit solvents. We explore the structure and ligand exchange dynamics of Mg<small><sup>2+</sup></small> in water and Pd<small><sup>2+</sup></small> in acetonitrile as two illustrative model systems. The trained potentials accurately reproduce equilibrium structures of the complexes in solution, including different coordination numbers and geometries. Furthermore, the MLPs can model structural changes between metal ions and ligands in the first coordination shell, and reproduce the free energy barriers for the corresponding ligand exchange. The strategy presented here provides a computationally efficient approach to model metal ions in solution, paving the way for modelling larger and more diverse metal complexes relevant to biomolecules and supramolecular assemblies.\",\"PeriodicalId\":76,\"journal\":{\"name\":\"Faraday Discussions\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":3.3000,\"publicationDate\":\"2024-08-03\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Faraday Discussions\",\"FirstCategoryId\":\"92\",\"ListUrlMain\":\"https://doi.org/10.1039/d4fd00140k\",\"RegionNum\":3,\"RegionCategory\":\"化学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"CHEMISTRY, PHYSICAL\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Faraday Discussions","FirstCategoryId":"92","ListUrlMain":"https://doi.org/10.1039/d4fd00140k","RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"CHEMISTRY, PHYSICAL","Score":null,"Total":0}
引用次数: 0

摘要

金属离子在(生物)催化、自组装和电荷转移过程等许多化学领域都具有不可替代的作用。然而,在不同的化学环境中模拟金属离子的结构和动态特性,对于力场和自洽方法来说仍然具有挑战性。在此,我们介绍了一种利用等变信息传递神经网络 MACE 训练显式溶剂中金属配体复合物的机器学习势(MLP)的策略。我们探索了 Mg2+ 在水中和 Pd2+ 在乙腈中的结构和配体交换动力学,以此作为两个示例模型系统。经过训练的电位能准确再现复合物在溶液中的平衡结构,包括不同的配位数和几何形状。此外,MLP 还能模拟金属离子和配体在第一配位层中的结构变化,并再现相应配体交换的自由能障。本文介绍的策略提供了一种计算高效的方法来模拟溶液中的金属离子,为模拟与生物大分子和超分子组装体相关的更大型、更多样化的金属配合物铺平了道路。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Modelling ligand exchange in metal complexes with machine learning potentials
Metal ions are irreplaceable in many areas of chemistry, including (bio)catalysis, self-assembly and charge transfer processes. Yet, modelling their structural and dynamic properties in diverse chemical environments remains challenging for both force fields and ab initio methods. Here, we introduce a strategy to train machine learning potentials (MLPs) using MACE, an equivariant message-passing neural network, for metal-ligand complexes in explicit solvents. We explore the structure and ligand exchange dynamics of Mg2+ in water and Pd2+ in acetonitrile as two illustrative model systems. The trained potentials accurately reproduce equilibrium structures of the complexes in solution, including different coordination numbers and geometries. Furthermore, the MLPs can model structural changes between metal ions and ligands in the first coordination shell, and reproduce the free energy barriers for the corresponding ligand exchange. The strategy presented here provides a computationally efficient approach to model metal ions in solution, paving the way for modelling larger and more diverse metal complexes relevant to biomolecules and supramolecular assemblies.
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
Faraday Discussions
Faraday Discussions 化学-物理化学
自引率
0.00%
发文量
259
期刊介绍: Discussion summary and research papers from discussion meetings that focus on rapidly developing areas of physical chemistry and its interfaces
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信