DeepMech: A Machine Learning Framework for Chemical Reaction Mechanism Prediction

2025-09-19 · Manajit Das, Ajnabiul Hoque, Mayank Baranwal, Raghavan B. Sunoj arxiv

Prediction of complete step-by-step chemical reaction mechanisms (CRMs) remains a major challenge. Whereas the traditional approaches in CRM tasks rely on expert-driven experiments or costly quantum chemical computations, contemporary deep learning (DL) alternatives ignore key intermediates and mechanistic steps and often suffer from hallucinations. We present DeepMech, an interpretable graph-based DL framework employing atom- and bond-level attention, guided by generalized templates of mechanistic operations (TMOps), to generate CRMs. Trained on our curated ReactMech dataset (~30K CRMs with 100K atom-mapped and mass-balanced elementary steps), DeepMech achieves 98.98+/-0.12% accuracy in predicting elementary steps and 95.94+/-0.21% in complete CRM tasks, besides maintaining high fidelity even in out-of-distribution scenarios as well as in predicting side and/or byproducts. Extension to multistep CRMs relevant to prebiotic chemistry, demonstrates the ability of DeepMech in effectively reconstructing 2 pathways from simple primordial substrates to complex biomolecules such as serine and aldopentose. Attention analysis identifies reactive atoms/bonds in line with chemical intuition, rendering our model interpretable and suitable for reaction design.

📄 PDF Abstract BibTeX arXiv:2509.15872

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