MolSpectLLM: A Molecular Foundation Model Bridging Spectroscopy, Molecule Elucidation, and 3D Structure Generation

• URL: http://arxiv.org/abs/2509.21861v2
• Date: Fri, 10 Oct 2025 05:13:53 GMT
• Title: MolSpectLLM: A Molecular Foundation Model Bridging Spectroscopy, Molecule Elucidation, and 3D Structure Generation
• Authors: Shuaike Shen, Jiaqing Xie, Zhuo Yang, Antong Zhang, Shuzhou Sun, Ben Gao, Tianfan Fu, Biqing Qi, Yuqiang Li,
• Abstract summary: MolSpectLLM is a molecular foundation model pretrained on Qwen2.5-7B that unifies experimental spectroscopy with molecular 3D structure.<n>MolSpectLLM achieves state-of-the-art performance on spectrum-related tasks, with an average accuracy of 0.53 across NMR, IR, and MS benchmarks.
• Score: 24.14024904556376
• License: http://creativecommons.org/licenses/by/4.0/
• Abstract: Recent advances in molecular foundation models have shown impressive performance in molecular property prediction and de novo molecular design, with promising applications in areas such as drug discovery and reaction prediction. Nevertheless, most existing approaches rely exclusively on SMILES representations and overlook both experimental spectra and 3D structural information-two indispensable sources for capturing molecular behavior in real-world scenarios. This limitation reduces their effectiveness in tasks where stereochemistry, spatial conformation, and experimental validation are critical. To overcome these challenges, we propose MolSpectLLM, a molecular foundation model pretrained on Qwen2.5-7B that unifies experimental spectroscopy with molecular 3D structure. By explicitly modeling molecular spectra, MolSpectLLM achieves state-of-the-art performance on spectrum-related tasks, with an average accuracy of 0.53 across NMR, IR, and MS benchmarks. MolSpectLLM also shows strong performance on the spectra analysis task, obtaining 15.5% sequence accuracy and 41.7% token accuracy on Spectra-to-SMILES, substantially outperforming large general-purpose LLMs. More importantly, MolSpectLLM not only achieves strong performance on molecular elucidation tasks, but also generates accurate 3D molecular structures directly from SMILES or spectral inputs, bridging spectral analysis, molecular elucidation, and molecular design. Code are available at \href{https://github.com/Eurekashen/MolSpectLLM}{https://github.com/Eurekashen/MolSpectLLM}.

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