oMeBench: Towards Robust Benchmarking of LLMs in Organic Mechanism Elucidation and Reasoning

arXiv:2510.07731v4 Announce Type: replace Abstract: Organic reaction mechanisms describe the step-wise elementary processes by which reactants transform into intermediates and products, and are fundamental to understanding chemical reactivity and guiding molecular and reaction de-sign. While large language models (LLMs) have shown promise on chemical tasks such as synthesis design, it remains unclear to what extent this reflects genuine chemical reasoning capabilities: the ability to generate chemically valid intermediates, maintain consistency across reaction steps, and follow logically coherent multi-step pathways. To investigate this, we introduce oMeBench, the first large-scale, expert-curated benchmark for organic mechanism reasoning, comprising over 10,000 annotated mechanistic steps with reaction type labels, intermediate structures, and difficulty ratings. To enable fine-grained evaluation, we further propose oMeS, a dynamic scoring framework that jointly assesses step-level logical consistency and chemical structural similarity. Systematic evaluation of state-of-the-art LLMs reveals that while current models exhibit promising chemical intuition, they struggle to produce correct and consistent reasoning across multi-step mechanisms. Notably, combining prompting strategies with fine-tuning enables smaller-scale models to achieve performance comparable to closed-source frontier models. We hope oMeBench will serve as a rigorous foundation for advancing AI systems toward genuine chemical reasoning.

Abstract:Organic reaction mechanisms describe the step-wise elementary processes by which reactants transform into intermediates and products, and are fundamental to understanding chemical reactivity and guiding molecular and reaction de-sign. While large language models (LLMs) have shown promise on chemical tasks such as synthesis design, it remains unclear to what extent this reflects genuine chemical reasoning capabilities: the ability to generate chemically valid intermediates, maintain consistency across reaction steps, and follow logically coherent multi-step pathways. To investigate this, we introduce oMeBench, the first large-scale, expert-curated benchmark for organic mechanism reasoning, comprising over 10,000 annotated mechanistic steps with reaction type labels, intermediate structures, and difficulty ratings. To enable fine-grained evaluation, we further propose oMeS, a dynamic scoring framework that jointly assesses step-level logical consistency and chemical structural similarity. Systematic evaluation of state-of-the-art LLMs reveals that while current models exhibit promising chemical intuition, they struggle to produce correct and consistent reasoning across multi-step mechanisms. Notably, combining prompting strategies with fine-tuning enables smaller-scale models to achieve performance comparable to closed-source frontier models. We hope oMeBench will serve as a rigorous foundation for advancing AI systems toward genuine chemical reasoning.

Artificial Intelligence (cs.AI); Computation and Language (cs.CL)

arXiv:2510.07731 [cs.AI]

(or arXiv:2510.07731v4 [cs.AI] for this version)

https://doi.org/10.48550/arXiv.2510.07731 Focus to learn more arXiv-issued DOI via DataCite

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oMeBench: Towards Robust Benchmarking of LLMs in Organic Mechanism Elucidation and Reasoning

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