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利用机器学习势对金属配合物中的配体交换进行建模。

Modelling ligand exchange in metal complexes with machine learning potentials.

作者信息

Juraskova Veronika, Tusha Gers, Zhang Hanwen, Schäfer Lars V, Duarte Fernanda

机构信息

Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK.

Center for Theoretical Chemistry, Ruhr University Bochum, D-44780 Bochum, Germany.

出版信息

Faraday Discuss. 2025 Jan 14;256(0):156-176. doi: 10.1039/d4fd00140k.

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 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 in water and Pd 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.

摘要

金属离子在化学的许多领域中都是不可替代的,包括(生物)催化、自组装和电荷转移过程。然而,对于力场和方法而言,在不同化学环境中对其结构和动力学性质进行建模仍然具有挑战性。在这里,我们介绍一种使用MACE(一种等变消息传递神经网络)来训练机器学习势(MLP)的策略,用于明确溶剂中的金属-配体配合物。我们以水中的镁和乙腈中的钯作为两个示例模型系统,探索它们的结构和配体交换动力学。训练后的势能够准确再现溶液中配合物的平衡结构,包括不同的配位数和几何形状。此外,MLP可以对第一配位层中金属离子和配体之间的结构变化进行建模,并再现相应配体交换的自由能垒。这里提出的策略提供了一种计算效率高的方法来对溶液中的金属离子进行建模,为对与生物分子和超分子组装相关的更大、更多样化的金属配合物进行建模铺平了道路。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5a97/11417676/8e1725481160/d4fd00140k-f1.jpg

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