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Bayesian reaction optimization as a tool for chemical synthesis

Nature volume 590, pages 89–96 (2021)Cite this article

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Abstract

Reaction optimization is fundamental to synthetic chemistry, from optimizing the yield of industrial processes to selecting conditions for the preparation of medicinal candidates1. Likewise, parameter optimization is omnipresent in artificial intelligence, from tuning virtual personal assistants to training social media and product recommendation systems2. Owing to the high cost associated with carrying out experiments, scientists in both areas set numerous (hyper)parameter values by evaluating only a small subset of the possible configurations. Bayesian optimization, an iterative response surface-based global optimization algorithm, has demonstrated exceptional performance in the tuning of machine learning models3. Bayesian optimization has also been recently applied in chemistry4,5,6,7,8,9; however, its application and assessment for reaction optimization in synthetic chemistry has not been investigated. Here we report the development of a framework for Bayesian reaction optimization and an open-source software tool that allows chemists to easily integrate state-of-the-art optimization algorithms into their everyday laboratory practices. We collect a large benchmark dataset for a palladium-catalysed direct arylation reaction, perform a systematic study of Bayesian optimization compared to human decision-making in reaction optimization, and apply Bayesian optimization to two real-world optimization efforts (Mitsunobu and deoxyfluorination reactions). Benchmarking is accomplished via an online game that links the decisions made by expert chemists and engineers to real experiments run in the laboratory. Our findings demonstrate that Bayesian optimization outperforms human decisionmaking in both average optimization efficiency (number of experiments) and consistency (variance of outcome against initially available data). Overall, our studies suggest that adopting Bayesian optimization methods into everyday laboratory practices could facilitate more efficient synthesis of functional chemicals by enabling better-informed, data-driven decisions about which experiments to run.

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Fig. 1: Bayesian reaction optimization.
Fig. 2: Training data used to select Bayesian optimizer parameters.
Fig. 3: Balancing exploration and exploitation in reaction optimization.
Fig. 4: Statistical validation of Bayesian reaction optimization.
Fig. 5: Applications of Bayesian reaction optimization.

Data availability

Quantum mechanical computation data and Gaussian output files used to parameterize reactions 1–5 are available at https://github.com/b-shields/auto-QChem. Processed reaction outcome data for reactions 1–5 are available at https://github.com/b-shields/edbo and in our published Code Ocean capsule at https://doi.org/10.24433/CO.3864629.v1. Tabulated player data for the reaction optimization game are available at https://github.com/b-shields/EvML.

Code availability

Two software packages and one web application were written to support this work. The first, auto-qchem, was written to facilitate high-throughput computational chemistry and reaction featurization. This package is freely available at https://github.com/b-shields/auto-QChem. The second, EDBO, was written as a user-friendly implementation of Bayesian optimization. This package is freely available at https://github.com/b-shields/edbo and in our published Code Ocean capsule at https://doi.org/10.24433/CO.3864629.v1. The web application, EvML, was written to collect user data for comparison of Bayesian optimization with human expert performance. This package is freely available at https://github.com/b-shields/EvML.

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Acknowledgements

Financial support was provided by Bristol-Myers Squibb, the Princeton Catalysis Initiative, the NSF under the CCI Center for Computer Assisted Synthesis (CHE-1925607) and the DataX Program at Princeton University through support from the Schmidt Futures Foundation. We thank A. Żurański and J. Ash for discussions. We thank all the participants in the reaction optimization game for their time and effort in contributing to this study. We thank B. Hao for help with HTE protocols.

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Authors and Affiliations

  1. Department of Chemistry, Princeton University, Princeton, NJ, USA

    Benjamin J. Shields, Marvin Parasram, Jesus I. Martinez Alvarado & Abigail G. Doyle

  2. Chemical Process Development, Bristol-Myers Squibb, New Brunswick, NJ, USA

    Jason Stevens, Jun Li & Jacob M. Janey

  3. Department of Computer Science, Princeton University, Princeton, NJ, USA

    Farhan Damani & Ryan P. Adams

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  1. Benjamin J. Shields
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Contributions

B.J.S. designed the overall research project with A.G.D., R.P.A. and J.J. providing guidance. B.J.S. wrote and ran the software with the assistance of F.D. and input from J.L.; J.J. and J.S. carried out the initial investigation to select the test reaction; J.S. designed and carried out HTE experiments with the assistance of M.P.; J.L. wrote the web application for the reaction optimization game with the assistance of J.S., J.J. and B.J.S.; and B.J.S. carried out data experiments and modelling with input from J.L. and F.D. J.S. and J.M.A. carried out Mitsunobu and deoxyfluorination reaction optimizations. B.J.S. wrote the manuscript with input from all authors.

Corresponding authors

Correspondence to Ryan P. Adams or Abigail G. Doyle.

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The authors declare no competing interests.

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Peer review information Nature thanks Jason Hein and Tiago Rodrigues for their contribution to the peer review of this work. Peer reviewer reports are available.

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Extended data figures and tables

Extended Data Table 1 Simulation outcome summary for reactions 1 and 2a–e
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Extended Data Table 2 Summary of reaction encodings
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Supplementary information

Supplementary Information

This file contains Supplementary Sections 1-12, including Supplementary Tables 1-14 and Supplementary Figs 1-73.

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Shields, B.J., Stevens, J., Li, J. et al. Bayesian reaction optimization as a tool for chemical synthesis. Nature 590, 89–96 (2021). https://doi.org/10.1038/s41586-021-03213-y

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