# Chemical Chain-of-Thought Functions as a Hallucination-Prone Molecular Scratchpad

arXiv: https://arxiv.org/abs/2607.20935 · HTML: https://mlsanity.com/paper/2607.20935/

## Key facts

- Cited by 3 papers in the map (data through 14 Oct 2026).
- Placed in Clinical and biomedical applications, one of 17 directions in LLM reasoning.
- Builds on 25 of its 33 references that are in the map.
- First posted on arXiv 23 Jul 2026.

## Placed in

- LLM reasoning / [Clinical and biomedical applications](https://mlsanity.com/lr/clinical-and-biomedical-applications/)

## Builds on (most cited first, 25 of 25)

- [Chain-of-Thought Prompting Elicits Reasoning in Large Language Models](https://mlsanity.com/paper/2201.11903/) (2022)
- [Training Verifiers to Solve Math Word Problems](https://mlsanity.com/paper/2110.14168/) (2021)
- [DeepSeekMath: Pushing the Limits of Mathematical Reasoning in Open Language Models](https://mlsanity.com/paper/2402.03300/) (2024)
- [Let's Verify Step by Step](https://mlsanity.com/paper/2305.20050/) (2023)
- [Language Models Don't Always Say What They Think: Unfaithful Explanations in Chain-of-Thought Prompting](https://mlsanity.com/paper/2305.04388/) (2023)
- [Attention is not Explanation](https://mlsanity.com/paper/1902.10186/) (2019)
- [Solving math word problems with process- and outcome-based feedback](https://mlsanity.com/paper/2211.14275/) (2022)
- [Show Your Work: Scratchpads for Intermediate Computation with Language Models](https://mlsanity.com/paper/2112.00114/) (2021)
- [Semantic Uncertainty: Linguistic Invariances for Uncertainty Estimation in Natural Language Generation](https://mlsanity.com/paper/2302.09664/) (2023)
- [Measuring Faithfulness in Chain-of-Thought Reasoning](https://mlsanity.com/paper/2307.13702/) (2023)
- [ChemCrow: Augmenting large-language models with chemistry tools](https://mlsanity.com/paper/2304.05376/) (2023)
- [Towards Faithfully Interpretable NLP Systems: How should we define and evaluate faithfulness?](https://mlsanity.com/paper/2004.03685/) (2020)
- [Reasoning Models Don't Always Say What They Think](https://mlsanity.com/paper/2505.05410/) (2025)
- [Towards Reasoning Era: A Survey of Long Chain-of-Thought for Reasoning Large Language Models](https://mlsanity.com/paper/2503.09567/) (2025)
- [Demystifying Long Chain-of-Thought Reasoning in LLMs](https://mlsanity.com/paper/2502.03373/) (2025)
- [Faithful Chain-of-Thought Reasoning](https://mlsanity.com/paper/2301.13379/) (2023)
- [Translation between Molecules and Natural Language](https://mlsanity.com/paper/2204.11817/) (2022)
- [Chain-of-Thought Reasoning In The Wild Is Not Always Faithful](https://mlsanity.com/paper/2503.08679/) (2025)
- [Retrosynthetic reaction prediction using neural sequence-to-sequence models](https://mlsanity.com/paper/1706.01643/) (2017)
- [Training a Scientific Reasoning Model for Chemistry](https://mlsanity.com/paper/2506.17238/) (2025)
- [Speak-to-Structure: Evaluating LLMs in Open-domain Natural Language-Driven Molecule Generation](https://mlsanity.com/paper/2412.14642/) (2024)
- [ChemDFM-R: A Chemical Reasoning LLM Enhanced with Atomized Chemical Knowledge](https://mlsanity.com/paper/2507.21990/) (2025)
- [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)

## Built on by (most cited first, 3 of 3)

- [Molecular LLM Agents: From Architectural Design to Scientific Autonomy](https://mlsanity.com/paper/2608.23104/) (2026)
- [Hallucination Across the Reasoning Lifecycle: Interface Visibility, Causal Evidence, and Release Control in Large Reasoning Models](https://mlsanity.com/paper/2610.05472/) (2026)
- [MolLean: A Process-Verifiable Language for Chemical Reasoning](https://mlsanity.com/paper/2610.20459/) (2026)

## Abstract (arXiv)

Chemical reasoning language models are expected to derive molecular answers through faithful chain-of-thought (CoT). However, across four reasoning model families and twelve chemistry tasks, hallucination is widespread and largely decoupled from answer correctness: correct answers often coexist with fabricated structural claims absent from the relevant molecules. Yet this does not make the reasoning trace computationally irrelevant. Attribution analyses suggest a shared scratchpad function expressed in model-specific forms: Chem-R and ether-0 rely on fragmented SMILES drafts, whereas ChemDFM-R emphasizes scaffold, positional, and naming cues. Notably, perturbing Chem-R's SMILES sketches degrades generation, showing that structural drafts can be causally load-bearing even when verbal structural claims are largely inert. Together, these results show that chemical CoT is neither a faithful explanation nor merely a post-hoc rationalization, but a hallucination-prone molecular scratchpad. This finding cautions against treating CoT as direct evidence of faithful reasoning and motivates process-level supervision beyond answer-only evaluation.