Reaction-network reasoning with frontier models for experimentally confirmed catalyst-selectivity hypotheses

The discovery of catalysts for electrochemical applications such as the oxygen reduction reaction (ORR), nitrogen reduction reaction (NRR), and CO2 reduction reaction (CO2RR) remains a central challenge in chemistry and materials science. Machine-learning interatomic potentials (MLIPs) and graph neural network models now accelerate individual adsorption-energy calculations by orders of magnitude relative to density functional theory. However, true large-scale screening is still blocked by human decisions: selecting candidates, constructing slabs, enumerating adsorption sites, interpreting descriptor failures, and choosing follow-up modifications. Here, we introduce Catalyst-Agent, a Model Context Protocol (MCP) server-based, LLM-powered agent that autonomously coordinates closed-loop catalyst screening. Catalyst-Agent searches materials databases through OPTIMADE, constructs slabs, computes adsorption energies using Meta FAIRchem's UMA MLIP within AdsorbML, evaluates reaction-specific descriptors, and applies structural modifications to refine near-miss candidates. In ORR, NRR, and CO2RR campaigns, Catalyst-Agent demonstrates high performance and converges in 1.40-3.41 trials per successful material on average. It identified Sn3Sc, Sn3Y, Tl3La, Pb3Y and In3Y as CO2RR candidates for further validation that were not previously reported in the literature. DFT single-point checks confirmed screening outcomes for representative NRR and CO2RR candidates. Ablations show these gains arise from chemically informed candidate selection and feedback-directed modification rather than brute-force evaluation: fully randomized screening dropped to 13.3%, 16.7%, and 0% success for ORR, NRR, and CO2RR, respectively. These results show that tool-grounded LLM agents can shift catalyst screening from manual trial-and-error toward more autonomous, reproducible and adaptive workflows.

Unraveling reaction mechanisms is central to modern chemistry, yet automating these investigations remains challenging because computational workflows still rely heavily on expert intervention. Here we introduce ARCHE, an autonomous agentic system that integrates a general-purpose reasoning model, a domain-specialized computational chemistry model, and a structured tool registry to transform mechanistic inquiry into a scalable, self-validating process. ARCHE interprets scientific questions, generates and prioritizes mechanistic hypotheses, orchestrates computational workflows, and iteratively refines conclusions based on computed evidence within a closed loop. We validate its capabilities across three increasingly demanding scenarios: reconstructing stereocontrolling transition states and validating the corresponding reaction mechanism in a previously reported asymmetric catalytic reaction; proposing and validating a plausible radical pathway through iterative hypothesis refinement for a recently discovered but unpublished $\alpha$-iodoboronate C-I cleavage reaction; and identifying a chemically interpretable descriptor that governs selectivity in nickel-catalysed migratory cross-coupling reactions. By coupling agentic reasoning with rigorous computational validation, ARCHE advances autonomous mechanistic discovery and establishes a foundation for broader machine-assisted chemical research. The code for ARCHE is publicly available at https://github.com/JetAstra/Arche-Harness.

Reaction mechanisms consist of the step-by-step sequences of elementary reactions that explain chemical transformations. Learning the mechanism logic is therefore essential for enhancing the fundamental chemical intelligence of large language models (LLMs). The stepwise deduction of reaction mechanism aligns naturally with the reasoning paradigms of reasoning LLMs. However, current chemical LLMs primarily emphasize coarse-grained name reactions for product prediction and retrosynthesis, often leading to physical inconsistencies and hallucinations. In contrast, specialized small-scale generative models for mechanism inference typically suffer from restricted generalization capacity across diverse chemical spaces. To overcome these limitations, we built a novel, large-scale reasoning dataset of reaction mechanisms. Furthermore, we established the FukuyamaBench, a difficult benchmark derived from Fukuyama's Advanced Organic Reaction Mechanism book, to rigorously evaluate model performance on hierarchical mechanism reasoning. Our fine-tuned Qwen3-30B-A3B achieves 8.3% exact pathway match on FukuyamaBench Set~A, surpassing the specialized FlowER model (5.1%), demonstrating that mechanism-aware training substantially enhances chemical reasoning in language models.