Graph neural networks for predicting metal-ligand coordination of transition metal complexes

• 成果类型: Article
• 署名作者: Toney, Jacob W.; St Michel, Roland G.; Garrison, Aaron G.; Kevlishvili, Ilia; Kulik, Heather J.; Schatz, George
• 署名单位: Massachusetts Institute of Technology (MIT); Massachusetts Institute of Technology (MIT); Massachusetts Institute of Technology (MIT)
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.2415658122
• 发表日期: 2025-10-14
• 页码: e2415658122
• 关键词: Machine learning; transition metal chemistry; graph neural networks; KNOWLEDGE-BASE; COMPUTATIONAL DESCRIPTORS; electronic-structure; CHELATING P; P-DONOR; DISCOVERY; catalysis; SMILES; polymerization; expansion; nickel

摘要

High-throughput virtual screening campaigns are invaluable for surveying the combinatorial space of possible transition metal complexes (TMCs), but they rely on accurate metal-ligand connectivity for meaningful results. Here, we curate a dataset of 70,069 unique ligands of known coordination from experimental structures of TMCs deposited in the Cambridge Structural Database. Using this dataset, we train separate graph neural network models to predict the total number and individual identities of ligand coordinating atoms with high accuracy and precision. Interpreting each model in terms of the learned molecular representations uncovers trends aligned with our understanding of coordination chemistry as well as chemical insights. Next, we integrate the trained models with the high-throughput screening software molSimplify and illustrate their utility by generating 1,175 TMCs and validating their geometries with density functional theory calculations. We anticipate these models will accelerate computational screening of TMCs with de novo combinations of metals and ligands in physically realistic coordination.