Accelerated end-to-end chemical synthesis development with large language models
Open accessAbstract
The rapid emergence of large language model (LLM) technology presents significant opportunities to facilitate the development of synthetic reactions. In this work, we leveraged the power of GPT-4 to build a multi-agent system to handle fundamental tasks involved throughout the chemical synthesis development process. The multi-agent system comprises six specialized LLM-based agents, including Literature Scouter, Experiment Designer, Hardware Executor, Spectrum Analyzer, Separation Instructor, and Result Interpreter, which are pre-prompted to accomplish the designated tasks. A web application was built with the multi-agent system as the backend to allow chemist users to interact with experimental platforms and analyze results via natural language, thus, requiring zero-coding skills to allow easy access for all chemists. We demonstrated this multi-agent system on the development of a recently developed copper/TEMPO catalyzed aerobic alcohol oxidation to aldehyde reaction, and this LLM multi-agent copiloted end-to-end reaction development process includes: literature search and information extraction, substrate scope and condition screening, reaction kinetics study, reaction condition optimization, reaction scale-up and product purification. This work showcases the trilogy among chemist users, LLM-based agents, and automated experimental platforms to reform the traditional expert-centric and labor-intensive reaction development workflow.
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LLM-RDF, tested on copper/TEMPO catalyzed aerobic alcohol oxidation, demonstrates end-to-end synthesis automation.
“Tested on copper/TEMPO catalyzed aerobic alcohol oxidation, it demonstrates end-to-end synthesis automation.”
From Agentic AI for Scientific Discovery: A Survey of Progress, Challenges, and Future Directions (2025) · cites this paper as Ruan et al., 2024
Cites
Bayesian reaction optimization as a tool for chemical synthesis
Shields, B. J., Stevens, J., Li, J., Parasram, M., Damani, F., Alvarado, J. I. M., Janey, J. M., Adams, R. P., & Doyle, A. G. (2021) · Nature · doi:10.1038/s41586-021-03213-y · Cited by 1,063 · see citing works
Autonomous chemical research with large language models
Boiko, D. A., MacKnight, R., Kline, B., & Gomes, G. (2023) · Nature · doi:10.1038/s41586-023-06792-0 · Cited by 1,050 · see citing works
Prediction of higher-selectivity catalysts by computer-driven workflow and machine learning
Zahrt, A. F., Henle, J. J., Rose, B. T., Wang, Y., Darrow, W. T., & Denmark, S. E. (2019) · Science · doi:10.1126/science.aau5631 · Cited by 683 · see citing works
Large Language Models as Optimizers
Yang, C., Wang, X., Lu, Y., Liu, H., Le, Q. V., Zhou, D., & Chen, X. (2023) · arXiv · doi:10.48550/arxiv.2309.03409 · Cited by 151 · see citing works
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A review of large language models and autonomous agents in chemistry
Ramos, M. C., Collison, C. J., & White, A. D. (2025) · Chemical Science · doi:10.1039/d4sc03921a · Cited by 274 · see citing works
Large language models for reticular chemistry
Zheng, Z., Rampal, N., Inizan, T. J., Borgs, C., Chayes, J. T., & Yaghi, O. M. (2025) · Nature Reviews Materials · doi:10.1038/s41578-025-00772-8 · Cited by 134 · see citing works
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Gridach, M., Nanavati, J., Abidine, K. Z. E., Mendes, L., & Mack, C. (2025) · arXiv · doi:10.48550/arxiv.2503.08979 · Cited by 18 · see citing works
- Authors
- Ruan, Y., Lu, C., Xu, N., Zhang, J., Xuan, J., Pan, J., Fang, Q., Gao, H., Shen, X., Ye, N., Zhang, Q., & Mo, Y.
- Affiliations
- Zhejiang University (CN)
- Zhejiang University
- Hong Kong University of Science and Technology (HK)
- Novartis (China) (CN)
- Rezubio Pharmaceuticals Co. Ltd.
- Corresponding author
- Mo, Yiming
- Venue
- Nature Communications
- Publisher
- American Chemical Society (ACS)
- Published
- 2024-05-07
- Volume
- 15
- Issue
- 1
- Pages
- 10160-10160
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC11585555
- OpenAlex
- W4404641323
- Cited by
- 140
- References
- 4
- Citations by year
- 2026: 84 · 2025: 50 · 2024: 6
- FWCI
- 13.19
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nature Communications (publishedVersion, cc-by-nc-nd)
- ChemRxiv (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- The Novartis Repository (Novartis) (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Rare & Special e-Zone (The Hong Kong University of Science and Technology) (submittedVersion)
- Funders
- National Natural Science Foundation of China (22478335, 22108242, 22227812)
- Topics
- Physical Sciences › Materials Science › Materials Chemistry › Machine Learning in Materials Science
- Physical Sciences › Computer Science › Artificial Intelligence › Artificial Intelligence Applications
- Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Various Chemistry Research Topics
- Keywords
- large language models, GPT-4, LLM agents, aerobic oxidation of alcohols, reaction condition optimization, reaction kinetics, product purification, nucleophilic aromatic substitution, web application
- MeSH terms
- Alcohols, Aldehydes, Catalysis, Copper, Cyclic N-Oxides, Kinetics, Oxidation-Reduction, Software, Chemistry Techniques, Synthetic
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