The paper introduces ChemDiffAgent, a masked diffusion language agent designed for tool‑integrated chemical reasoning. Unlike traditional autoregressive agents, it treats reasoning as iterative denoising over interleaved reasoning and tool‑use trajectories, allowing joint decision making under full‑trajectory context. A two‑stage post‑training framework further refines tool use and reasoning, and the authors benchmark the model on six chemistry tasks, reporting a ~20% performance gain over autoregressive baselines and competitive results against larger models.
arXiv:2512. 13278v2 Announce Type: replace-cross Abstract: Agentic reinforcement learning has advanced large language models (LLMs) to reason through long chain-of-thought trajectories while interleaving external tool use.
arXiv:2602. 07075v5 Announce Type: replace-cross Abstract: Current chemical large language models (LLMs) predominantly rely on explicit Chain-of-Thought (CoT) to solve complex reasoning problems.
arXiv:2606. 03660v1 Announce Type: new Abstract: Large language models are increasingly used as chemistry assistants, yet most chemistry benchmarks still score only final answers.
arXiv:2610.17183v1 Announce Type: new Abstract: Current chemistry benchmarks primarily evaluate outcome prediction or reaction pathway generation, but rarely test whether a model can explain why an o...
oMeBench is a large-scale, expert-curated benchmark designed to evaluate large language models (LLMs) on organic mechanism reasoning. It contains over 10,000 annotated mechanistic steps, including reaction type labels, intermediate structures, and difficulty ratings, and introduces the oMeS scoring framework to assess logical consistency and chemical structural similarity. Evaluation shows that while current LLMs display promising chemical intuition, they often fail to produce correct and consistent multi-step reasoning, though prompting and fine-tuning can bring smaller models up to the level of closed‑source frontier models.
arXiv:2606. 31229v1 Announce Type: new Abstract: Ideation plays a pivotal role in scientific discovery.
The paper introduces a multitask large reasoning model for molecular science that incorporates chemical knowledge via a multispecialist architecture, chain-of-thought supervision, and molecule-informed reinforcement learning. It coordinates prediction and inference specialists across ten molecular tasks—including description, generation, nomenclature translation, property prediction, and reaction prediction—using task-conditioned routing. The model surpasses more than 20 general-purpose and molecular large language models, improving aggregate performance by 50.3% and outperforming leading multitask baselines on most tasks, while maintaining interpretable chemical inference and demonstrating a workflow for CNS candidate generation and retrosynthetic planning.
ChemVTS-Bench is a domain-authentic benchmark that evaluates Visual‑Textual‑Symbolic reasoning in multimodal large language models for chemistry. It presents diverse chemical problems—organic molecules, inorganic materials, and 3D crystal structures—in three input modes: visual-only, visual‑text hybrid, and SMILES-based symbolic. The benchmark includes an automated agent workflow for inference, answer verification, and failure diagnosis, and shows that visual-only inputs and structural chemistry remain challenging for current models.
arXiv:2607. 12771v1 Announce Type: new Abstract: Reaction mechanisms consist of the step-by-step sequences of elementary reactions that explain chemical transformations.
The paper introduces ARCHE, an autonomous system that combines a general-purpose reasoning model, a domain-specialized computational chemistry model, and a structured tool registry to automate chemical mechanism discovery. ARCHE interprets scientific questions, generates and prioritizes mechanistic hypotheses, orchestrates computational workflows, and refines conclusions in a closed loop. The authors validate the system on three challenging scenarios, including reconstructing stereocontrolling transition states, proposing a radical pathway for an unpublished reaction, and identifying a descriptor governing selectivity in nickel-catalyzed cross‑coupling reactions.
The paper introduces ChemCost, a benchmark of 1,427 reactions that tests large language models’ ability to estimate chemical procurement costs by grounding identities, retrieving supplier quotes, selecting purchasable packs, normalizing quantities, and computing costs. It includes a frozen pricing snapshot of 2,261 chemicals and 230,775 supplier quotes, and provides scalar scoring plus stage‑level diagnostics for grounding, retrieval, procurement, and arithmetic errors. Experiments show that even advanced LLM agents achieve only about 50.6% accuracy within 25% relative error on clean inputs, and performance drops sharply with realistic noise, highlighting brittleness in parsing, evidence integration, pack selection, and tool use.
arXiv:2606. 11256v1 Announce Type: cross Abstract: Designing molecules with target properties is most useful when candidate structures are accompanied by feasible synthetic routes.