Machine Learning Transition State Geometries and Applications in Reaction Property Prediction

Research output: Contribution to journalArticlepeer-review

Abstract

The calculation of transition state (TS) geometries is essential for understanding reaction mechanisms and rational synthetic methodology design. However, traditional methods like density functional theory are often too computationally expensive for large-scale TS identification and are significantly slower than high-throughput experimental screening methods. Recent advancements in machine learning (ML) offer promising alternatives, enabling the direct prediction of TS geometries, reducing the reliance on expensive quantum mechanical (QM) calculations, and affording predictions ahead of experiments. The works explored here include the broader application of ML in reaction property prediction, emphasizing how accurate TS geometries can serve as vital input data to improve model accuracy. A comprehensive review of ML methods developed to explicitly predict TS geometries is then presented, with attention to their application in downstream tasks, such as energy barrier calculations, and their use as initial structures for further optimization via QM methods. Finally, a critical evaluation of the accuracy and limitations of existing TS prediction methods is discussed, highlighting challenges that impede wider adoption and areas where further research is needed.
Original languageEnglish
Article numbere70025
JournalWIREs Computational Molecular Science
Volume15
Issue number3
Early online date2 Jun 2025
DOIs
Publication statusPublished - 30 Jun 2025

Data Availability Statement

The data that supports the findings of this study are available in the Supporting Information of this article.

Funding

EHEF is an employee of AstraZeneca and may hold share options and shares in AstraZeneca. MNG has received PhD funding from AstraZeneca which includes funding for MJP's PhD. This work was supported by the Engineering and Physical Sciences Research Council, EP/W003724/1; AstraZeneca UK; UK Research and Innovation (EP/S023437/1). Funding: Funding: This work was supported by the Engineering and Physical Sciences Research Council, EP/W003724/1; AstraZeneca UK; UK Research and Innovation (EP/S023437/1). The authors thank ART-AI CDT, University of Bath, and AstraZeneca for supporting this work. The authors gratefully acknowledge the University of Bath's Research Computing Group (https://doi.org/10.15125/b6cd-s854) for their support in this work; this work made use of the Anatra High-Performance Computing (HPC) service at the University of Bath. Molecules displayed in the Graphical Abstract and Figures\u00A02, 3, 5\u20137, 9, 10, and 12 were generated with CYLView [190].

FundersFunder number
AstraZeneca
AstraZeneca UK Ltd
AstraZeneca
Engineering and Physical Sciences Research CouncilEP/W003724/1
UK Research and InnovationEP/S023437/1

Keywords

  • geometry prediction
  • machine learning
  • property prediction
  • reaction mechanisms
  • transition state

ASJC Scopus subject areas

  • Biochemistry
  • Computer Science Applications
  • Physical and Theoretical Chemistry
  • Computational Mathematics
  • Materials Chemistry

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