# MolLean: A Process-Verifiable Language for Chemical Reasoning

arXiv: https://arxiv.org/abs/2610.20459 · HTML: https://mlsanity.com/paper/2610.20459/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 21 of its 35 references that are in the map.
- First posted on arXiv 14 Oct 2026.

## Placed in

- LLM reasoning

## Builds on (most cited first, 21 of 21)

- [Chain-of-Thought Prompting Elicits Reasoning in Large Language Models](https://mlsanity.com/paper/2201.11903/) (2022)
- [ReAct: Synergizing Reasoning and Acting in Language Models](https://mlsanity.com/paper/2210.03629/) (2022)
- [Let's Verify Step by Step](https://mlsanity.com/paper/2305.20050/) (2023)
- [Self-Refine: Iterative Refinement with Self-Feedback](https://mlsanity.com/paper/2303.17651/) (2023)
- [Language Models Don't Always Say What They Think: Unfaithful Explanations in Chain-of-Thought Prompting](https://mlsanity.com/paper/2305.04388/) (2023)
- [Program of Thoughts Prompting: Disentangling Computation from Reasoning for Numerical Reasoning Tasks](https://mlsanity.com/paper/2211.12588/) (2022)
- [Large Language Models Cannot Self-Correct Reasoning Yet](https://mlsanity.com/paper/2310.01798/) (2023)
- [CRITIC: Large Language Models Can Self-Correct with Tool-Interactive Critiquing](https://mlsanity.com/paper/2305.11738/) (2023)
- [PAL: Program-aided Language Models](https://mlsanity.com/paper/2211.10435/) (2022)
- [ChemCrow: Augmenting large-language models with chemistry tools](https://mlsanity.com/paper/2304.05376/) (2023)
- [LeanDojo: Theorem Proving with Retrieval-Augmented Language Models](https://mlsanity.com/paper/2306.15626/) (2023)
- [Draft, Sketch, and Prove: Guiding Formal Theorem Provers with Informal Proofs](https://mlsanity.com/paper/2210.12283/) (2022)
- [Translation between Molecules and Natural Language](https://mlsanity.com/paper/2204.11817/) (2022)
- [Training a Scientific Reasoning Model for Chemistry](https://mlsanity.com/paper/2506.17238/) (2025)
- [ChemReasoner: Heuristic Search over a Large Language Model's Knowledge Space using Quantum-Chemical Feedback](https://mlsanity.com/paper/2402.10980/) (2024)
- [Speak-to-Structure: Evaluating LLMs in Open-domain Natural Language-Driven Molecule Generation](https://mlsanity.com/paper/2412.14642/) (2024)
- [Chem-R: Learning to Reason as a Chemist](https://mlsanity.com/paper/2510.16880/) (2025)
- [MolReasoner: Toward Effective and Interpretable Reasoning for Molecular LLMs](https://mlsanity.com/paper/2508.02066/) (2025)
- [Mol-R1: Towards Explicit Long-CoT Reasoning in Molecule Discovery](https://mlsanity.com/paper/2508.08401/) (2025)
- [Structural Reasoning Improves Molecular Understanding of LLM](https://mlsanity.com/paper/2410.05610/) (2024)
- [Chemical Chain-of-Thought Functions as a Hallucination-Prone Molecular Scratchpad](https://mlsanity.com/paper/2607.20935/) (2026)

## Abstract (arXiv)

Chemical chain-of-thought can contain hallucinated structural and property claims. We thereby introduce MolLean, a process-verifiable language that grounds chemical reasoning in an explicit molecular state. A layered Lean-based kernel checks state transitions and assertions over molecular readouts, from primitive graph edits to compound transformations. Meanwhile, a typed witness protocol separates native structural checks from externally supplied measurements. We further introduce MolLean-MCP, a stateful tool interface that exposes these transitions, checks, and readouts during generation: the model receives feedback to decide its next action, and rejected actions leave the state unchanged. MolLean supports one-pass trace execution, whole-trace refinement, and interactive reasoning through MolLean-MCP. We evaluate these three modes with direct chain-of-thought on 8,800 matched examples across 12 tasks spanning molecular generation, editing, optimization, and reactions. With Qwen3.6-27B, whole-trace refinement outperforms direct chain-of-thought on all 12 tasks. MolLean-MCP complements whole-trace refinement with stepwise verification feedback, reaching better performance in reaction tasks. Together, these results highlight an executable foundation for chemical reasoning, in which explicit chemical commitments can be checked and revised rather than remaining solely in free-form explanations.