Diffusion-based generative AI for exploring transition states from 2D molecular graphs

Seonghwan Kim, Jeheon Woo and Woo Youn Kim ()
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Seonghwan Kim: KAIST
Jeheon Woo: KAIST
Woo Youn Kim: KAIST

Nature Communications, 2024, vol. 15, issue 1, 1-12

Abstract: Abstract The exploration of transition state (TS) geometries is crucial for elucidating chemical reaction mechanisms and modeling their kinetics. Recently, machine learning (ML) models have shown remarkable performance for prediction of TS geometries. However, they require 3D conformations of reactants and products often with their appropriate orientations as input, which demands substantial efforts and computational cost. Here, we propose a generative approach based on the stochastic diffusion method, namely TSDiff, for prediction of TS geometries just from 2D molecular graphs. TSDiff outperforms the existing ML models with 3D geometries in terms of both accuracy and efficiency. Moreover, it enables to sample various TS conformations, because it learns the distribution of TS geometries for diverse reactions in training. Thus, TSDiff finds more favorable reaction pathways with lower barrier heights than those in the reference database. These results demonstrate that TSDiff shows promising potential for an efficient and reliable TS exploration.

Date: 2024
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DOI: 10.1038/s41467-023-44629-6

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