Towards Generalizable and Evidential Nuclear Magnetic Resonance-Based Molecular Structure Elucidation via Large Language Model Agent

Zheng Fang; Chen Yang; Yusen Tan; Yunpeng Zhao; Fanjie Xu; Hongxin Xiang; Hanyu Sun; Hanyu Gao; Xiaojian Wang; Wenjie Du; Yuqiang Li; Jun Xia

arXiv · 2606.29776

Towards Generalizable and Evidential Nuclear Magnetic Resonance-Based Molecular Structure Elucidation via Large Language Model Agent

Zheng Fang·Chen Yang·Yusen Tan·Yunpeng Zhao·Fanjie Xu·Hongxin Xiang·Hanyu Sun·Hanyu Gao·Xiaojian Wang·Wenjie Du·Yuqiang Li·Jun Xia

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Abstract

Nuclear Magnetic Resonance (NMR) spectroscopy is the gold standard for molecular structure elucidation, yet interpreting complex spectra for unknown molecules remains a bottleneck reliant on human expertise. While artificial intelligence has advanced this field, current methods face a critical trade-off: database retrieval cannot identify novel scaffolds, while de novo molecular structure elucidation models operate as black boxes, lacking the atom-level interpretability required for rigorous scientific validation. Here, we present NMRAgent, an evidential reasoning agent powered by large language models (LLMs) that bridges this gap by integrating specialized spectral analysis tools with chemical knowledge graphs. Unlike previous approaches, NMRAgent mimics the deductive reasoning of human experts: it takes experimental NMR spectra and molecular formula as input, plans the elucidation process, proposes candidate structures, verifies peak-atom consistency, and refines misaligned substructure through formula-aware fragment optimization. Enabled by its evidential reasoning, NMRAgent outperforms state-of-the-art methods, improving top-1 accuracy by 46.5% and Tanimoto similarity by 0.502 on a scaffold-split benchmark with novel scaffolds in the test set. Besides, we demonstrate the agent's practical utility by elucidating the structures of two previously unknown natural products isolated from Hydrangea davidii and Vitex trifolia, and by correcting structural misassignments in established literature. By combining high-accuracy prediction with transparent and evidence-based reasoning, NMRAgent establishes a new paradigm for interpretable AI in analytical chemistry.

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Zheng Fang, Chen Yang, Yusen Tan, Yunpeng Zhao, Fanjie Xu, Hongxin Xiang, Hanyu Sun, Hanyu Gao, Xiaojian Wang, Wenjie Du, Yuqiang Li, Jun Xia. 2026-06-29. Towards Generalizable and Evidential Nuclear Magnetic Resonance-Based Molecular Structure Elucidation via Large Language Model Agent. https://arxiv.org/abs/2606.29776

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