journal article·2024-07Open access

Universal descriptors of quasi transition states for small-data-driven asymmetric catalysis prediction in machine learning model

Guan-Ming Chen, Zi-Hao Ye, Zhi-Ming Li, Jun-Liang Zhang

Cell Reports Physical Science· Volume 5· Issue 7

Abstract

In enantioselectivity prediction models, the demand for numerous descriptors and extensive datasets poses a substantial challenge. Descriptor selection, fraught with uncertainty, compounds the issue, while amassing requisite data remains a daunting task. The introduction of descriptors derived from quasi transition states offers a promising avenue to alleviate this burden. However, the challenge of descriptor selection persists. Here, we report a small-data-driven model based on universal descriptors. Key differentiating properties between diastereomeric quasi transition states, encompassing single-point energies, frontier orbital energies, Cartesian forces, and charges of core atoms, are proposed as universal descriptors. The model's efficacy is validated through its application to the asymmetric aldol and Negishi reactions, utilizing 3 experimental variables, merely less than 9 universal descriptors, and fewer than 150 training samples. Moreover, a method is presented using Cartesian forces to rectify discrepancies between quasi transition states and true transition states. This strategy circumvents tedious large-scale descriptor exploration and screening, offering an efficient choice for small-data-driven enantioselectivity prediction.
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Research context

OpenAlex topics: Machine Learning in Materials Science · Advanced Chemical Physics Studies · Surface Chemistry and Catalysis

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References (39)

Show source-provided references
1. Proline-catalyzed direct asymmetric aldol reactions10.1021/ja994280y ↗
2. Asymmetric enamine catalysis10.1021/cr0684016 ↗
3. The advent and development of organocatalysis10.1038/nature07367 ↗
4. Aminocatalytic Asymmetric Diels-Alder Reactions via HOMO Activation10.1021/ar3000822 ↗
5. Hydrogen-Bonding in Aminocatalysis: From Proline and Beyond10.1002/chem.201303982 ↗
6. Quantitative Structure-Selectivity Relationships in Enantioselective Catalysis: Past, Present, and Future10.1021/acs.chemrev.9b00425 ↗
7. Holistic prediction of enantioselectivity in asymmetric catalysis10.1038/s41586-019-1384-z ↗
8. Steric influences on the selectivity in palladium-catalyzed allylation10.1021/om9700371 ↗
9. Prediction of higher-selectivity catalysts by computer-driven workflow and machine learning10.1126/science.aau5631 ↗
10. A unified machine-learning protocol for asymmetric catalysis as a proof of concept demonstration using asymmetric hydrogenation10.1073/pnas.1916392117 ↗
11. Reaction-based machine learning representations for predicting the enantioselectivity of organocatalysts10.1039/D1SC00482D ↗
12. Scaffold-Directed Face Selectivity Machine-Learned from Vectors of Non-covalent Interactions10.1002/anie.202101986 ↗
13. A Multi-Objective Active Learning Platform and Web App for Reaction Optimization10.1021/jacs.2c08592 ↗
14. Reoptimization of MDL keys for use in drug discovery10.1021/ci010132r ↗
15. The Generation of a Unique Machine Description for Chemical Structures-A Technique Developed at Chemical Abstracts Service10.1021/c160017a018 ↗
16. Extended-connectivity fingerprints10.1021/ci100050t ↗
17. Smiles, a Chemical Language and Information-System .1. Introduction to Methodology and Encoding Rules10.1021/ci00057a005 ↗
18. InChI - the worldwide chemical structure identifier standard10.1186/1758-2946-5-7 ↗
19. Computational prediction of small-molecule catalysts10.1038/nature07368 ↗
20. Comparing quantitative prediction methods for the discovery of small-molecule chiral catalysts10.1038/s41570-018-0040-8 ↗
21. Design and Optimization of Catalysts Based on Mechanistic Insights Derived from Quantum Chemical Reaction Modeling10.1021/acs.chemrev.9b00073 ↗
22. Machine learning meets mechanistic modelling for accurate prediction of experimental activation energies10.1039/D0SC04896H ↗
23. Organic reactivity from mechanism to machine learning10.1038/s41570-021-00260-x ↗
24. A Holy Grail in Chemistry: Computational Catalyst Design: Feasible or Fiction?10.1021/acs.accounts.6b00606 ↗
25. Prediction of Stereochemistry using Q2MM10.1021/acs.accounts.6b00037 ↗
26. Enantioselectivity prediction of palladaelectrocatalysed C–H activation using transition state knowledge in machine learning10.1038/s44160-022-00233-y ↗
27. Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements10.1007/s00894-007-0233-4 ↗
28. Extended tight-binding quantum chemistry methods10.1002/wcms.1493 ↗
29. AARON: An Automated Reaction Optimizer for New Catalysts10.1021/acs.jctc.8b00578 ↗
30. Quantum mechanical predictions of the stereoselectivities of proline-catalyzed asymmetric intermolecular aldol reactions10.1021/ja028812d ↗
31. LASP: Fast global potential energy surface exploration10.1002/wcms.1415 ↗
32. Learning Representations by Back-Propagating Errors10.1038/323533a0 ↗
33. Variable selection using neural-network models10.1016/S0925-2312(99)00146-0 ↗
34. Selective Carbon-Carbon Bond Formation via Transition Metal catalysis. 3. A Highly Selective Synthesis of Unsymmetrical Biaryls and Diarylmethanes by the Nickel or Palladium-Catalyzed Reaction of Aryl- and Benzylzinc Derivatives with Aryl Halides10.1021/jo00430a041 ↗
35. Aryl-Aryl Bond Formation One Century after the Discovery of the Ullmann Reaction10.1021/cr000664r ↗
36. Palladium-Catalyzed Cross-Coupling Reactions of Organoboron Compounds10.1021/cr00039a007 ↗
37. Feed-Forward Neural Network for Predicting Enantioselectivity of the Asymmetric Negishi Reaction10.1021/acscentsci.3c00512 ↗
38. Computationally Assisted Mechanistic Investigation and Development of Pd-Catalyzed Asymmetric Suzuki-Miyaura and Negishi Cross-Coupling Reactions for Tetra- Ortho-Substituted Biaryl Synthesis10.1021/acscatal.8b02509 ↗
39. Ligand-Based Principal Component Analysis Followed by Ridge Regression: Application to an Asymmetric Negishi Reaction10.1021/acscatal.3c06230 ↗