MolLean: A Process-Verifiable Language for Chemical Reasoning

Jiatong Li, Yatao Bian

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…