# MolQuest: A Benchmark for Agentic Evaluation of Abductive Reasoning in Chemical Structure Elucidation

arXiv: https://arxiv.org/abs/2603.25253 · HTML: https://mlsanity.com/paper/2603.25253/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Placed in Clinical and biomedical applications, one of 17 directions in LLM reasoning.
- Builds on 12 of its 38 references that are in the map.
- First posted on arXiv 26 Mar 2026.

## Placed in

- LLM reasoning / [Clinical and biomedical applications](https://mlsanity.com/lr/clinical-and-biomedical-applications/)
- LLM agents and tool use / [Medical and scientific domain agents](https://mlsanity.com/agents/medical-and-scientific-domain-agents/)

## Builds on (most cited first, 12 of 12)

- [Qwen3 Technical Report](https://mlsanity.com/paper/2505.09388/) (2025)
- [GPQA: A Graduate-Level Google-Proof Q&A Benchmark](https://mlsanity.com/paper/2311.12022/) (2023)
- [DeepSeek-V3.2: Pushing the Frontier of Open Large Language Models](https://mlsanity.com/paper/2512.02556/) (2025)
- [Humanity's Last Exam](https://mlsanity.com/paper/2501.14249/) (2025)
- [ARC-AGI-2: A New Challenge for Frontier AI Reasoning Systems](https://mlsanity.com/paper/2505.11831/) (2025)
- [From Automation to Autonomy: A Survey on Large Language Models in Scientific Discovery](https://mlsanity.com/paper/2505.13259/) (2025)
- [Beyond Chemical QA: Evaluating LLM's Chemical Reasoning with Modular Chemical Operations](https://mlsanity.com/paper/2505.21318/) (2025)
- [Evaluating Large Language Models in Scientific Discovery](https://mlsanity.com/paper/2512.15567/) (2025)
- [ChemAgent: Self-updating Library in Large Language Models Improves Chemical Reasoning](https://mlsanity.com/paper/2501.06590/) (2025)
- [Are large language models superhuman chemists?](https://mlsanity.com/paper/2404.01475/) (2024)
- [ChemEval: A Comprehensive Multi-Level Chemical Evaluation for Large Language Models](https://mlsanity.com/paper/2409.13989/) (2024)
- [FGBench: A Dataset and Benchmark for Molecular Property Reasoning at Functional Group-Level in Large Language Models](https://mlsanity.com/paper/2508.01055/) (2025)

## Built on by (most cited first, 2 of 2)

- [Reasoning Depth and Environment Complexity: A Controlled Study of RLVR Data Allocation across Logical Reasoning Tasks](https://mlsanity.com/paper/2605.26934/) (2026)
- [MolP2SBench: Do LLMs Really Reason from Molecular Properties to Structure?](https://mlsanity.com/paper/2610.12522/) (2026)

## Abstract (arXiv)

Large language models (LLMs) hold considerable potential for advancing scientific discovery, yet systematic assessment of their dynamic reasoning in real-world research remains limited. Current scientific evaluation benchmarks predominantly rely on static, single-turn Question Answering (QA) formats, which are inadequate for measuring model performance in complex scientific tasks that require multi-step iteration and experimental interaction. To address this gap, we introduce MolQuest, a novel agent-based evaluation framework for molecular structure elucidation built upon authentic chemical experimental data. Unlike existing datasets, MolQuest formalizes molecular structure elucidation as a multi-turn interactive task, requiring models to proactively plan experimental steps, integrate heterogeneous spectral sources (e.g., NMR, MS), and iteratively refine structural hypotheses. This framework systematically evaluates LLMs' abductive reasoning and strategic decision-making abilities within a vast and complex chemical space. Empirical results reveal that contemporary frontier models exhibit significant limitations in authentic scientific scenarios: notably, even state-of-the-art (SOTA) models achieve an accuracy of only approximately 50%, while the performance of most other models remains below the 30% threshold. This work provides a reproducible and extensible framework for science-oriented LLM evaluation, our findings highlight the critical gap in current LLMs' strategic scientific reasoning, setting a clear direction for future research toward AI that can actively participate in the scientific process.