1
|
Handjaya JP, Patankar N, Reid JP. The Diversity and Evolution of Chiral Brønsted Acid Structures. Chemistry 2024; 30:e202400921. [PMID: 38706381 DOI: 10.1002/chem.202400921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/22/2024] [Accepted: 05/06/2024] [Indexed: 05/07/2024]
Abstract
The chemical space of chiral Brønsted acid catalysts is defined by quantity and complexity, reflecting the diverse synthetic challenges confronted and the innovative molecular designs introduced. Here, we detail how this successful outcome is a powerful demonstration of the benefits of utilizing both local structure searches and a comprehensive understanding of catalyst performance for effective and efficient exploration of Brønsted acid properties. In this concept article we provide an evolutionary overview of this field by summarizing the approaches to catalyst optimization, the resulting structures, and functions.
Collapse
Affiliation(s)
- Jasemine P Handjaya
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z1, Canada
| | - Niraja Patankar
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z1, Canada
| | - Jolene P Reid
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z1, Canada
| |
Collapse
|
2
|
Su Y, Wang X, Ye Y, Xie Y, Xu Y, Jiang Y, Wang C. Automation and machine learning augmented by large language models in a catalysis study. Chem Sci 2024; 15:12200-12233. [PMID: 39118602 PMCID: PMC11304797 DOI: 10.1039/d3sc07012c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 06/21/2024] [Indexed: 08/10/2024] Open
Abstract
Recent advancements in artificial intelligence and automation are transforming catalyst discovery and design from traditional trial-and-error manual mode into intelligent, high-throughput digital methodologies. This transformation is driven by four key components, including high-throughput information extraction, automated robotic experimentation, real-time feedback for iterative optimization, and interpretable machine learning for generating new knowledge. These innovations have given rise to the development of self-driving labs and significantly accelerated materials research. Over the past two years, the emergence of large language models (LLMs) has added a new dimension to this field, providing unprecedented flexibility in information integration, decision-making, and interacting with human researchers. This review explores how LLMs are reshaping catalyst design, heralding a revolutionary change in the fields.
Collapse
Affiliation(s)
- Yuming Su
- iChem, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University Xiamen 361005 P. R. China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM) Xiamen 361005 P. R. China
| | - Xue Wang
- iChem, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University Xiamen 361005 P. R. China
| | - Yuanxiang Ye
- Institute of Artificial Intelligence, Xiamen University Xiamen 361005 P. R. China
| | - Yibo Xie
- Institute of Artificial Intelligence, Xiamen University Xiamen 361005 P. R. China
| | - Yujing Xu
- iChem, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University Xiamen 361005 P. R. China
| | - Yibin Jiang
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM) Xiamen 361005 P. R. China
| | - Cheng Wang
- iChem, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University Xiamen 361005 P. R. China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM) Xiamen 361005 P. R. China
| |
Collapse
|
3
|
Gayraud O, Courbière B, Guégan F. Automated exploration of the conformational degrees of freedom along reaction profiles - driving a FASTCAR. Phys Chem Chem Phys 2024. [PMID: 39101325 DOI: 10.1039/d4cp01721h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/06/2024]
Abstract
This publication aims at presenting a Python-based workflow designed to enable a fully automatised and exhaustive exploration of the conformational degrees of freedom within the calculation of reaction paths in molecular systems. The proposed strategy focuses on effectively representing the lowest energy conformers for intricate, highly rotatable, and non-intuitive transition states, reagents and products, using existing computational tools. The article presents a workflow that is demonstrated through the application of five chemical reactions, chosen to be representative of the diversity and complexity of actual experimental studies, and which often prove to be challenging to study "by hand". The proposed methodology is expected to be of a great help in the modelling of state-of-the art organic chemistry reactions, whose complexity is ever increasing.
Collapse
Affiliation(s)
- Oscar Gayraud
- Applied Quantum Chemistry Group, E4 Team, IC2MP UMR 7285, Université de Poitiers - CNRS, Poitiers 86073, France.
- Spectrometry, Interaction and Theoretical Chemistry team, DCM UMR 5250, Université Grenoble Alpes - CNRS, Grenoble 38058, France.
| | - Bastien Courbière
- Applied Quantum Chemistry Group, E4 Team, IC2MP UMR 7285, Université de Poitiers - CNRS, Poitiers 86073, France.
- Sorbonne Université, CNRS, Laboratoire de Chimie Théorique CC 137, Paris Cedex 05 75252, France
| | - Frédéric Guégan
- Applied Quantum Chemistry Group, E4 Team, IC2MP UMR 7285, Université de Poitiers - CNRS, Poitiers 86073, France.
| |
Collapse
|
4
|
Mészáros BB, Kubicskó K, Németh DD, Daru J. Emerging Conformational-Analysis Protocols from the RTCONF55-16K Reaction Thermochemistry Conformational Benchmark Set. J Chem Theory Comput 2024. [PMID: 38899777 DOI: 10.1021/acs.jctc.4c00565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
RTCONF55-16K is a new, reactive conformational data set based on cost-efficient methods to assess different conformational analysis protocols. Our reference calculations underpinned the accuracy of the CENSO (Grimme et al. J. Phys. Chem. A, 2021, 125, 4039) procedure and resulted in alternative recipes with different cost-accuracy compromises. Our general-purpose and economical protocols (CENSO-light and zero, respectively) were found to be 10-30 times faster than the original algorithm, adding only 0.4-0.7 kcal/mol absolute error to the relative free energy estimates.
Collapse
Affiliation(s)
- Bence Balázs Mészáros
- Hevesy György PhD School of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
- Department of Organic Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
| | - Károly Kubicskó
- Hevesy György PhD School of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
- Department of Organic Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
| | - Dávid Dorián Németh
- Department of Organic Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
| | - János Daru
- Department of Organic Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
| |
Collapse
|
5
|
Chen F, Chen Y, Chang XY, He D, Yang Q, Wang DZ, Xu C, Yu P, Xing X. Polarizability matters in enantio-selection. Nat Commun 2024; 15:3394. [PMID: 38649371 PMCID: PMC11035643 DOI: 10.1038/s41467-024-47813-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 03/22/2024] [Indexed: 04/25/2024] Open
Abstract
The prevalence of chirality, or, handedness in biological world is a fundamental phenomenon and a characteristic hallmark of life. Thus, understanding the origin of enantio-selection, i.e., the sense and magnitude of asymmetric induction, has been a long-pursued goal in asymmetric catalysis. Herein, we demonstrated a polarizability-derived electronic effect that was shown to be capable of rationalizing a broad range of stereochemical observations made in the field of asymmetric catalysis. This effect provided a consistent enantio-control model for the prediction of major enantiomers formed in a ruthenium-catalyzed asymmetric transfer hydrogenations of ketones. Direct and quantitative linear free energy relationships between substrates' local polarizabilities and observed enantio-selectivity were also revealed in three widely known asymmetric catalytic systems covering both reductions and oxidations. This broadly applicable polarizability-based electronic effect, in conjunction with conventional wisdom mainly leveraging on steric effect considerations, should aid rational design of enantio-selective processes for better production of chiral substances.
Collapse
Affiliation(s)
- Fumin Chen
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
- Shenzhen Grubbs Institute and Department of Chemistry, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yu Chen
- Shenzhen Grubbs Institute and Department of Chemistry, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xiao-Yong Chang
- Shenzhen Grubbs Institute and Department of Chemistry, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Dongxu He
- Shenzhen Grubbs Institute and Department of Chemistry, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Qingjing Yang
- Shenzhen Grubbs Institute and Department of Chemistry, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen, 518055, China
| | | | - Chen Xu
- Shenzhen Grubbs Institute and Department of Chemistry, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Peiyuan Yu
- Shenzhen Grubbs Institute and Department of Chemistry, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Xiangyou Xing
- Shenzhen Grubbs Institute and Department of Chemistry, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen, 518055, China.
| |
Collapse
|
6
|
Calderón JC, Herrera A, Heinemann FW, Langer J, Linden A, Chelouan A, Grasruck A, Añez R, Clark T, Dorta R. Stereochemical Stability of Planar-Chiral Benzazepine Tricyclics: Inversion Energies of P- and S-Alkene Ligands. J Org Chem 2023; 88:16144-16154. [PMID: 37944159 DOI: 10.1021/acs.joc.3c01447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Inversion barriers ΔG‡ for planar chiral phosphine-alkene and sulfonamide-alkene hybrid ligands based on phenyl-dibenz[b,f]azepine have been determined by density-functional theory calculations. Analysis of the structural and electronic characteristics of the minima and transition states explains the magnitudes of ΔG‡ and the geometrical changes during the inversion process. The steric repulsion caused by bulky substituents attached to the azepine nitrogen atom has a pronounced effect on the ΔG‡ value, explaining, inter alia, the stereochemical stability of the P- and S-alkene ligands when compared to the fluxional parent compound where X = H.
Collapse
Affiliation(s)
- Jacqueline C Calderón
- Laboratorio de Química Física y Catálisis Computacional, Centro de Química, Instituto Venezolano de Investigaciones Científicas, Apartado 21827, Caracas, Venezuela
- Computer-Chemie-Centrum, Department Chemie und Pharmazie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstraße. 25, 91052 Erlangen, Germany
| | - Alberto Herrera
- Anorganische und Allgemeine Chemie, Department Chemie und Pharmazie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Egerlandstraße 1, 91058 Erlangen, Germany
| | - Frank W Heinemann
- Anorganische und Allgemeine Chemie, Department Chemie und Pharmazie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Egerlandstraße 1, 91058 Erlangen, Germany
| | - Jens Langer
- Anorganische und Metallorganische Chemie, Department Chemie und Pharmazie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Egerlandstraße 1, 91058 Erlangen, Germany
| | - Anthony Linden
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Ahmed Chelouan
- Anorganische und Allgemeine Chemie, Department Chemie und Pharmazie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Egerlandstraße 1, 91058 Erlangen, Germany
| | - Alexander Grasruck
- Anorganische und Allgemeine Chemie, Department Chemie und Pharmazie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Egerlandstraße 1, 91058 Erlangen, Germany
| | - Rafael Añez
- Laboratorio de Química Física y Catálisis Computacional, Centro de Química, Instituto Venezolano de Investigaciones Científicas, Apartado 21827, Caracas, Venezuela
| | - Timothy Clark
- Computer-Chemie-Centrum, Department Chemie und Pharmazie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstraße. 25, 91052 Erlangen, Germany
| | - Romano Dorta
- Anorganische und Allgemeine Chemie, Department Chemie und Pharmazie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Egerlandstraße 1, 91058 Erlangen, Germany
| |
Collapse
|
7
|
Rajapaksha R, Samanta P, Quadrelli EA, Canivet J. Heterogenization of molecular catalysts within porous solids: the case of Ni-catalyzed ethylene oligomerization from zeolites to metal-organic frameworks. Chem Soc Rev 2023; 52:8059-8076. [PMID: 37902965 DOI: 10.1039/d3cs00188a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
The last decade has seen a tremendous expansion of the field of heterogenized molecular catalysis, especially with the growing interest in metal-organic frameworks and related porous hybrid solids. With successful achievements in the transfer from molecular homogeneous catalysis to heterogenized processes come the necessary discussions on methodologies used and a critical assessment on the advantages of heterogenizing molecular catalysis. Here we use the example of nickel-catalyzed ethylene oligomerization, a reaction of both fundamental and applied interest, to review heterogenization methodologies of well-defined molecular catalysts within porous solids while addressing the biases in the comparison between original molecular systems and heterogenized counterparts.
Collapse
Affiliation(s)
- Rémy Rajapaksha
- Univ. Lyon, Université Claude Bernard Lyon 1, CNRS, IRCELYON - UMR 5256, 2 Av. Albert Einstein, 69626 Villeurbanne, France.
| | - Partha Samanta
- Univ. Lyon, Université Claude Bernard Lyon 1, CNRS, IRCELYON - UMR 5256, 2 Av. Albert Einstein, 69626 Villeurbanne, France.
| | - Elsje Alessandra Quadrelli
- Univ. Lyon, Université Claude Bernard Lyon 1, CNRS, IRCELYON - UMR 5256, 2 Av. Albert Einstein, 69626 Villeurbanne, France.
| | - Jérôme Canivet
- Univ. Lyon, Université Claude Bernard Lyon 1, CNRS, IRCELYON - UMR 5256, 2 Av. Albert Einstein, 69626 Villeurbanne, France.
| |
Collapse
|
8
|
Hayashi H, Maeda S, Mita T. Quantum chemical calculations for reaction prediction in the development of synthetic methodologies. Chem Sci 2023; 14:11601-11616. [PMID: 37920348 PMCID: PMC10619630 DOI: 10.1039/d3sc03319h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/29/2023] [Indexed: 11/04/2023] Open
Abstract
Quantum chemical calculations have been used in the development of synthetic methodologies to analyze the reaction mechanisms of the developed reactions. Their ability to estimate chemical reaction pathways, including transition state energies and connected equilibria, has led researchers to embrace their use in predicting unknown reactions. This perspective highlights strategies that leverage quantum chemical calculations for the prediction of reactions in the discovery of new methodologies. Selected examples demonstrate how computation has driven the development of unknown reactions, catalyst design, and the exploration of synthetic routes to complex molecules prior to often laborious, costly, and time-consuming experimental investigations.
Collapse
Affiliation(s)
- Hiroki Hayashi
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University Kita 21, Nishi 10, Kita-ku Sapporo Hokkaido 001-0021 Japan
- JST-ERATO, Maeda Artificial Intelligence in Chemical Reaction Design and Discovery Project Kita 10, Nishi 8, Kita-ku Sapporo Hokkaido 060-0810 Japan
| | - Satoshi Maeda
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University Kita 21, Nishi 10, Kita-ku Sapporo Hokkaido 001-0021 Japan
- JST-ERATO, Maeda Artificial Intelligence in Chemical Reaction Design and Discovery Project Kita 10, Nishi 8, Kita-ku Sapporo Hokkaido 060-0810 Japan
- Department of Chemistry, Faculty of Science, Hokkaido University Kita 10, Nishi 8, Kita-ku Sapporo Hokkaido 060-0810 Japan
| | - Tsuyoshi Mita
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University Kita 21, Nishi 10, Kita-ku Sapporo Hokkaido 001-0021 Japan
- JST-ERATO, Maeda Artificial Intelligence in Chemical Reaction Design and Discovery Project Kita 10, Nishi 8, Kita-ku Sapporo Hokkaido 060-0810 Japan
| |
Collapse
|
9
|
Jabbour R, Ashling CW, Robinson TC, Khan AH, Wisser D, Berruyer P, Ghosh AC, Ranscht A, Keen DA, Brunner E, Canivet J, Bennett TD, Mellot-Draznieks C, Lesage A, Wisser FM. Unravelling the Molecular Structure and Confining Environment of an Organometallic Catalyst Heterogenized within Amorphous Porous Polymers. Angew Chem Int Ed Engl 2023; 62:e202310878. [PMID: 37647152 DOI: 10.1002/anie.202310878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/30/2023] [Accepted: 08/30/2023] [Indexed: 09/01/2023]
Abstract
The catalytic activity of multifunctional, microporous materials is directly linked to the spatial arrangement of their structural building blocks. Despite great achievements in the design and incorporation of isolated catalytically active metal complexes within such materials, a detailed understanding of their atomic-level structure and the local environment of the active species remains a fundamental challenge, especially when these latter are hosted in non-crystalline organic polymers. Here, we show that by combining computational chemistry with pair distribution function analysis, 129 Xe NMR, and Dynamic Nuclear Polarization enhanced NMR spectroscopy, a very accurate description of the molecular structure and confining surroundings of a catalytically active Rh-based organometallic complex incorporated inside the cavity of amorphous bipyridine-based porous polymers is obtained. Small, but significant, differences in the structural properties of the polymers are highlighted depending on their backbone motifs.
Collapse
Affiliation(s)
- Ribal Jabbour
- Centre de RMN à Très Hauts Champs, Université de Lyon (CNRS/ENS Lyon/UCB Lyon 1), 69100, Villeurbanne, France
| | - Christopher W Ashling
- Department of Materials Science and Metallurgy, University of Cambridge, 27 Charles Babbage Road, Cambridge, CB3 0FS, UK
| | - Thomas C Robinson
- Centre de RMN à Très Hauts Champs, Université de Lyon (CNRS/ENS Lyon/UCB Lyon 1), 69100, Villeurbanne, France
| | - Arafat Hossain Khan
- Chair of Bioanalytical Chemistry, TU Dresden, Bergstraße 66, 01069, Dresden, Germany
| | - Dorothea Wisser
- Erlangen Center for Interface Research and Catalysis (ECRC), Friedrich-Alexander-Universität Erlangen-Nürnberg, Egerlandstraße 3, 91058, Erlangen, Germany
| | - Pierrick Berruyer
- Centre de RMN à Très Hauts Champs, Université de Lyon (CNRS/ENS Lyon/UCB Lyon 1), 69100, Villeurbanne, France
| | - Ashta C Ghosh
- Univ. Lyon, Université Claude Bernard Lyon 1, CNRS, IRCELYON - UMR 5256, 2 Avenue Albert Einstein, 69626, Villeurbanne Cedex, France
| | - Alisa Ranscht
- Univ. Lyon, Université Claude Bernard Lyon 1, CNRS, IRCELYON - UMR 5256, 2 Avenue Albert Einstein, 69626, Villeurbanne Cedex, France
| | - David A Keen
- ISIS Facility, Rutherford Appleton Laboratory, Harwell Campus, Didcot, Oxfordshire, OX11 0QX, UK
| | - Eike Brunner
- Chair of Bioanalytical Chemistry, TU Dresden, Bergstraße 66, 01069, Dresden, Germany
| | - Jérôme Canivet
- Univ. Lyon, Université Claude Bernard Lyon 1, CNRS, IRCELYON - UMR 5256, 2 Avenue Albert Einstein, 69626, Villeurbanne Cedex, France
| | - Thomas D Bennett
- Department of Materials Science and Metallurgy, University of Cambridge, 27 Charles Babbage Road, Cambridge, CB3 0FS, UK
| | - Caroline Mellot-Draznieks
- Laboratoire de Chimie des Processus Biologiques (LCPB), Collège de France, PSL Research University, CNRS Sorbonne Université, 11 Place Marcelin Berthelot, 75231, Paris Cedex 05, France
| | - Anne Lesage
- Centre de RMN à Très Hauts Champs, Université de Lyon (CNRS/ENS Lyon/UCB Lyon 1), 69100, Villeurbanne, France
| | - Florian M Wisser
- Erlangen Center for Interface Research and Catalysis (ECRC), Friedrich-Alexander-Universität Erlangen-Nürnberg, Egerlandstraße 3, 91058, Erlangen, Germany
| |
Collapse
|
10
|
Cuomo A, Ibarraran S, Sreekumar S, Li H, Eun J, Menzel JP, Zhang P, Buono F, Song JJ, Crabtree RH, Batista VS, Newhouse TR. Feed-Forward Neural Network for Predicting Enantioselectivity of the Asymmetric Negishi Reaction. ACS CENTRAL SCIENCE 2023; 9:1768-1774. [PMID: 37780365 PMCID: PMC10540279 DOI: 10.1021/acscentsci.3c00512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Indexed: 10/03/2023]
Abstract
Density functional theory (DFT) is a powerful tool to model transition state (TS) energies to predict selectivity in chemical synthesis. However, a successful multistep synthesis campaign must navigate energetically narrow differences in pathways that create some limits to rapid and unambiguous application of DFT to these problems. While powerful data science techniques may provide a complementary approach to overcome this problem, doing so with the relatively small data sets that are widespread in organic synthesis presents a significant challenge. Herein, we show that a small data set can be labeled with features from DFT TS calculations to train a feed-forward neural network for predicting enantioselectivity of a Negishi cross-coupling reaction with P-chiral hindered phosphines. This approach to modeling enantioselectivity is compared with conventional approaches, including exclusive use of DFT energies and data science approaches, using features from ligands or ground states with neural network architectures.
Collapse
Affiliation(s)
- Abbigayle
E. Cuomo
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Sebastian Ibarraran
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Sanil Sreekumar
- Chemical
Development, Boehringer Ingelheim Pharmaceuticals
Inc, 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Haote Li
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Jungmin Eun
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Jan Paul Menzel
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Pengpeng Zhang
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Frederic Buono
- Chemical
Development, Boehringer Ingelheim Pharmaceuticals
Inc, 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Jinhua J. Song
- Chemical
Development, Boehringer Ingelheim Pharmaceuticals
Inc, 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Robert H. Crabtree
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Victor S. Batista
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Timothy R. Newhouse
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| |
Collapse
|
11
|
Nakanishi T, Terada M. Computational molecular refinement to enhance enantioselectivity by reinforcing hydrogen bonding interactions in major reaction pathway. Chem Sci 2023; 14:5712-5721. [PMID: 37265716 PMCID: PMC10231322 DOI: 10.1039/d3sc01637d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 04/29/2023] [Indexed: 06/03/2023] Open
Abstract
Computational analyses have revealed that the distortion of a catalyst and the substrates and their interactions are key to determining the stability of the transition state. Hence, two strategies "distortion strategy" and "interaction strategy" can be proposed for improving enantiomeric excess in enantioselective reactions. The "distortion strategy" is used as a conventional approach that destabilizes the TS (transition state) of the minor pathway. On the other hand, the "interaction strategy" focuses on the stabilization of the TS of the major pathway in which an enhancement of the reaction rate is expected. To realize this strategy, we envisioned the TS stabilization of the major reaction pathway by reinforcing hydrogen bonding and adopted the chiral phosphoric acid-catalysed enantioselective Diels-Alder reaction of 2-vinylquinolines with dienylcarbamates. The intended "interaction strategy" led to remarkable improvements in the enantioselectivity and reaction rate.
Collapse
Affiliation(s)
- Taishi Nakanishi
- Department of Chemistry, Graduate School of Science, Tohoku University 6-3 Aramaki Aza Aoba, Aoba-ku Sendai Miyagi 980-8578 Japan
| | - Masahiro Terada
- Department of Chemistry, Graduate School of Science, Tohoku University 6-3 Aramaki Aza Aoba, Aoba-ku Sendai Miyagi 980-8578 Japan
| |
Collapse
|
12
|
Han J, Liu S, Wang H, Wang J, Qian H, Li Z, Ma S, Zhang J. Pd/Xu-Phos-catalyzed asymmetric elimination of fully substituted enol triflates into axially chiral trisubstituted allenes. SCIENCE ADVANCES 2023; 9:eadg1002. [PMID: 36930705 PMCID: PMC10022902 DOI: 10.1126/sciadv.adg1002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
The β-H elimination, as one of the most important elementary reactions in transition metal chemistry, is a key step in quenching the carbon-palladium bond for the Heck reaction. However, the β-H elimination of the alkenyl palladium species leading to allene is an energetically unfavored process, and therefore, it has been a long-standing challenge in control of this process via enantioselective manner. We developed a concise and efficient methodology to construct trisubstituted chiral allenes from stereodefined fully substituted enol triflates by the enantioselective β-H elimination of the alkenyl palladium species under mild conditions. The identified Xu-Phos play a crucial role in the chemoselectivity and enantioselectivity. Multiple linear regression analysis shows the important steric effect on enantioselectivity. DFT computation results allow us to propose an intramolecular base (-OAc)-assisted deprotonation mechanism for this progress. Distortion-interaction and energy decomposition analysis indicate that the difference in electrostatic energy (Eelec) of the two intramolecular base-assisted deprotonation transition states dominates the stereoselectivity.
Collapse
Affiliation(s)
- Jie Han
- Department of Chemistry, Fudan University, Shanghai 200438, China
- Zhuhai Fudan Innovation Institute, Zhuhai 519000, China
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Department of Chemistry, East China Normal University, 3663 N. Zhongshan Road, Shanghai 200062, China
| | - Siyuan Liu
- Department of Chemistry, Fudan University, Shanghai 200438, China
| | - Huanan Wang
- Department of Chemistry, Fudan University, Shanghai 200438, China
| | - Jie Wang
- Department of Chemistry, Fudan University, Shanghai 200438, China
| | - Hui Qian
- Department of Chemistry, Fudan University, Shanghai 200438, China
| | - Zhiming Li
- Department of Chemistry, Fudan University, Shanghai 200438, China
| | - Shengming Ma
- Department of Chemistry, Fudan University, Shanghai 200438, China
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, CAS, Shanghai, China
| | - Junliang Zhang
- Department of Chemistry, Fudan University, Shanghai 200438, China
- Zhuhai Fudan Innovation Institute, Zhuhai 519000, China
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Department of Chemistry, East China Normal University, 3663 N. Zhongshan Road, Shanghai 200062, China
| |
Collapse
|
13
|
Chen Y, Ou Y, Zheng P, Huang Y, Ge F, Dral PO. Benchmark of general-purpose machine learning-based quantum mechanical method AIQM1 on reaction barrier heights. J Chem Phys 2023; 158:074103. [PMID: 36813722 DOI: 10.1063/5.0137101] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Artificial intelligence-enhanced quantum mechanical method 1 (AIQM1) is a general-purpose method that was shown to achieve high accuracy for many applications with a speed close to its baseline semiempirical quantum mechanical (SQM) method ODM2*. Here, we evaluate the hitherto unknown performance of out-of-the-box AIQM1 without any refitting for reaction barrier heights on eight datasets, including a total of ∼24 thousand reactions. This evaluation shows that AIQM1's accuracy strongly depends on the type of transition state and ranges from excellent for rotation barriers to poor for, e.g., pericyclic reactions. AIQM1 clearly outperforms its baseline ODM2* method and, even more so, a popular universal potential, ANI-1ccx. Overall, however, AIQM1 accuracy largely remains similar to SQM methods (and B3LYP/6-31G* for most reaction types) suggesting that it is desirable to focus on improving AIQM1 performance for barrier heights in the future. We also show that the built-in uncertainty quantification helps in identifying confident predictions. The accuracy of confident AIQM1 predictions is approaching the level of popular density functional theory methods for most reaction types. Encouragingly, AIQM1 is rather robust for transition state optimizations, even for the type of reactions it struggles with the most. Single-point calculations with high-level methods on AIQM1-optimized geometries can be used to significantly improve barrier heights, which cannot be said for its baseline ODM2* method.
Collapse
Affiliation(s)
- Yuxinxin Chen
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yanchi Ou
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Peikun Zheng
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yaohuang Huang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Fuchun Ge
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Pavlo O Dral
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| |
Collapse
|
14
|
Flaget A, Zhang C, Mazet C. Ni-Catalyzed Enantioselective Hydrofunctionalizations of 1,3-Dienes. ACS Catal 2022; 12:15638-15647. [PMID: 36570078 PMCID: PMC9765749 DOI: 10.1021/acscatal.2c05251] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/15/2022] [Indexed: 12/12/2022]
Abstract
Ni-catalyzed enantioselective hydrofunctionalizations of conjugated dienes are particularly demanding reactions to devise because they require not only addressing the inherent challenges associated with the development of an enantioselective transformation but also overcoming all other aspects of selective catalysis (chemoselectivity, regioselectivity, diastereoselectivity, etc.). However, the value-added nature of the chiral allylic and homoallylic derivatives obtained by these methods, the lack of efficient alternatives, and the use of an earth-abundant first-row transition metal have led to renewed interest over the past decade. In this Perspective, we give an overview of the developments in this field, from the original findings (often dating back to the last century) to the most recent contributions. Emphasis is placed on the nature of the hydrofunctionalization agent (C(sp), C(sp2), C(sp3), N, P, or O).
Collapse
Affiliation(s)
| | | | - Clément Mazet
- Department of Organic Chemistry, University of Geneva, 30 quai Ernest Ansermet, 1211 Geneva, Switzerland
| |
Collapse
|
15
|
Rose BT, Timmerman JC, Bawel SA, Chin S, Zhang H, Denmark SE. High-Level Data Fusion Enables the Chemoinformatically Guided Discovery of Chiral Disulfonimide Catalysts for Atropselective Iodination of 2-Amino-6-arylpyridines. J Am Chem Soc 2022; 144:22950-22964. [DOI: 10.1021/jacs.2c08820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Brennan T. Rose
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IIllinois 61801, United States
| | - Jacob C. Timmerman
- Department of Small Molecule Process Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Seth A. Bawel
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IIllinois 61801, United States
| | - Steven Chin
- Department of Small Molecule Process Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Haiming Zhang
- Department of Small Molecule Process Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Scott E. Denmark
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IIllinois 61801, United States
| |
Collapse
|
16
|
Lai J, Reid JP. Interrogating the thionium hydrogen bond as a noncovalent stereocontrolling interaction in chiral phosphate catalysis. Chem Sci 2022; 13:11065-11073. [PMID: 36320465 PMCID: PMC9516887 DOI: 10.1039/d2sc02171d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/15/2022] [Indexed: 12/04/2022] Open
Abstract
CH⋯O bonds are a privileged noncovalent interaction determining the energies and geometries of a large number of structures. In catalytic settings, these are invoked as a decisive feature controlling many asymmetric transformations involving aldehydes. However, little is known about their stereochemical role when the interaction involves other substrate types. We report the results of computations that show for the first time thionium hydrogen bonds to be an important noncovalent interaction in asymmetric catalysis. As a validating case study, we explored an asymmetric Pummerer rearrangement involving thionium intermediates to yield enantioenriched N,S-acetals under BINOL-derived chiral phosphate catalysis. DFT and QM/MM hybrid calculations showed that the lowest energy pathway corresponded to a transition state involving two hydrogen bonding interactions from the thionium intermediate to the catalyst. However, the enantiomer resulting from this process differed from the originally published absolute configuration. Experimental determination of the absolute configuration resolved this conflict in favor of our calculations. The reaction features required for enantioselectivity were further interrogated by statistical modeling analysis that utilized bespoke featurization techniques to enable the translation of enantioselectivity trends from intermolecular reactions to those proceeding intramolecularly. Through this suite of computational modeling techniques, a new model is revealed that provides a different explanation for the product outcome and enabled reassignment of the absolute product configuration.
Collapse
Affiliation(s)
- Junshan Lai
- Department of Chemistry, University of British Columbia 2036 Main Mall Vancouver British Columbia V6T 1Z1 Canada
| | - Jolene P Reid
- Department of Chemistry, University of British Columbia 2036 Main Mall Vancouver British Columbia V6T 1Z1 Canada
| |
Collapse
|
17
|
Wahlers J, Rosales AR, Berkel N, Forbes A, Helquist P, Norrby PO, Wiest O. A Quantum-Guided Molecular Mechanics Force Field for the Ferrocene Scaffold. J Org Chem 2022; 87:12334-12341. [PMID: 36066498 DOI: 10.1021/acs.joc.2c01553] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ferrocene derivatives have a wide range of applications, including as ligands in asymmetric catalysis, due to their chemical stability, rigid backbone, steric bulk, and ability to encode stereochemical information via planar chirality. Unfortunately, few of the available molecular mechanics force fields incorporate parameters for the accurate study of this important building block. Here, we present a MM3* force field for ferrocenyl ligands, which was generated using the quantum-guided molecular mechanics (Q2MM) method. Detailed validation by comparison to DFT calculations and crystal structures demonstrates the accuracy of the parameters and uncovers the physical origin of deviations through excess energy analysis. Combining the ferrocene force field with a force field for Pd-allyl complexes and comparing the crystal structures shows the compatibility with previously developed MM3* force fields. Finally, the ferrocene force field was combined with a previously published transition-state force field to predict the stereochemical outcomes of the aminations of Pd-allyl complexes with different amines and different chiral ferrocenyl ligands, with an R2 of ∼0.91 over 10 examples.
Collapse
Affiliation(s)
- Jessica Wahlers
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Anthony R Rosales
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Neil Berkel
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Aaron Forbes
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Paul Helquist
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Per-Ola Norrby
- Data Science and Modelling, Pharmaceutical Sciences, R&D, AstraZeneca Gothenburg, Pepparedsleden 1, Mölndal SE-431 83, Sweden
| | - Olaf Wiest
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| |
Collapse
|
18
|
When machine learning meets molecular synthesis. TRENDS IN CHEMISTRY 2022. [DOI: 10.1016/j.trechm.2022.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
19
|
Yang L, Zhu L, Zhang S, Hong X. Machine Learning Prediction of
Structure‐Performance
Relationship in Organic Synthesis. CHINESE J CHEM 2022. [DOI: 10.1002/cjoc.202200039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Li‐Cheng Yang
- Center of Chemistry for Frontier Technologies, Department of Chemistry, State Key Laboratory of Clean Energy Utilization, Zhejiang University Hangzhou Zhejiang 310027 China
| | - Lu‐Jing Zhu
- Center of Chemistry for Frontier Technologies, Department of Chemistry, State Key Laboratory of Clean Energy Utilization, Zhejiang University Hangzhou Zhejiang 310027 China
| | - Shuo‐Qing Zhang
- Center of Chemistry for Frontier Technologies, Department of Chemistry, State Key Laboratory of Clean Energy Utilization, Zhejiang University Hangzhou Zhejiang 310027 China
| | - Xin Hong
- Center of Chemistry for Frontier Technologies, Department of Chemistry, State Key Laboratory of Clean Energy Utilization, Zhejiang University Hangzhou Zhejiang 310027 China
- Beijing National Laboratory for Molecular Sciences, Zhongguancun North First Street NO. 2 Beijing 100190 China
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, 18 Shilongshan Road Hangzhou Zhejiang 310024 China
| |
Collapse
|
20
|
Wei J, Li M, Ding J, Dai W, Yang Q, Feng Y, Yang C, Yang W, Zheng Y, Wang MY, Ma X. Parameterization of Phosphine Ligands Modified Rh Complexes to Unravel Quantitative Structure‐Activity Relationship and Mechanistic Pathways in Hydroformylation. ChemCatChem 2022. [DOI: 10.1002/cctc.202200423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Jie Wei
- Tianjin University School of Chemical Engineering and Technology Tianjin UniversitySchool of Chemical Engineering and Technology Tianjin CHINA
| | - Maoshuai Li
- Tianjin Chemical Engineering and Technology Weijin RoadNankai District 300072 Tianjin CHINA
| | - Jie Ding
- Tianjin University School of Chemical Engineering and Technology CHINA
| | - Weikang Dai
- Tianjin University School of Chemical Engineering and Technology CHINA
| | - Qi Yang
- Tianjin University School of Chemical Engineering and Technology CHINA
| | - Yi Feng
- Tianjin University School of Chemical Engineering and Technology CHINA
| | - Cheng Yang
- Tianjin University School of Chemical Engineering and Technology CHINA
| | - Wanxin Yang
- Tianjin University School of Chemical Engineering and Technology CHINA
| | - Ying Zheng
- Joint School of Tianjin University and National University of Singapore International Campus of Tianjin University CHINA
| | - Mei-Yan Wang
- Tianjin University School of Chemical Engineering and Technology CHINA
| | - Xinbin Ma
- Tianjin University School of Chemical Engineering and Technology CHINA
| |
Collapse
|
21
|
Yuan M, Gutierrez O. Mechanisms, Challenges, and Opportunities of Dual Ni/Photoredox-Catalyzed C(sp 2)-C(sp 3) Cross-Couplings. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2022; 12:e1573. [PMID: 35664524 PMCID: PMC9162266 DOI: 10.1002/wcms.1573] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/09/2021] [Indexed: 12/28/2022]
Abstract
The merging of photoredox and nickel catalysis has revolutionized the field of C-C cross-coupling. However, in comparison to the development of synthetic methods, detailed mechanistic investigations of these catalytic systems are lagging. To improve the mechanistic understanding, computational tools have emerged as powerful tools to elucidate the factors controlling reactivity and selectivity in these complex catalytic transformations. Based on the reported computational studies, it appears that the mechanistic picture of catalytic systems is not generally applicable, but is rather dependent on the specific choice of substrate, ligands, photocatalysts, etc. Given the complexity of these systems, the need for more accurate computational methods, readily available and user-friendly dynamics simulation tools, and data-driven approaches is clear in order to understand at the molecular level the mechanisms of these transformations. In particular, we anticipate that such improvement of theoretical methods will become crucial to advance the understanding of excited-state properties and dynamics of key species, as well as to enable faster and unbiased exploration of reaction pathways. Further, with greater collaboration between computational, experimental, and spectroscopic communities, the mechanistic investigation of photoredox/Ni dual-catalytic reactions is expected to thrive quickly, facilitating the design of novel catalytic systems and promoting our understanding of the reaction selectivity.
Collapse
|
22
|
Betinol IO, Reid JP. A predictive and mechanistic statistical modelling workflow for improving decision making in organic synthesis and catalysis. Org Biomol Chem 2022; 20:6012-6018. [PMID: 35389396 DOI: 10.1039/d2ob00272h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The application of multivariate linear regression models has been widely utilized as a strategy to streamline the reaction optimization process. While these tools likely provide relatively safe predictions, embedding a method for forecasting the probability of achieving the desired reaction outcome would be valuable for streamlining the identification of promising structures with the best chance of success. Herein, we present a workflow that predicts the probability that a reaction will be successful and is easy and quick to apply. We show that this probabilistic framework can effectively differentiate between predictions often indistinguishable by multivariate linear regression analysis. Moreover, these techniques can enhance the development of mechanistically informative correlations by producing more direct pathways for molecular development and design. Overall, we anticipate this protocol will be generally applicable and useful for accelerating successful chemical discovery.
Collapse
Affiliation(s)
- Isaiah O Betinol
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada.
| | - Jolene P Reid
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada.
| |
Collapse
|
23
|
Tang T, Friede NC, Minteer SD, Sigman MS. Comparing Halogen Atom Abstraction Kinetics for Mn(I), Fe(I), Co(I), and Ni(I) Complexes by Combining Electroanalytical and Statistical Modeling. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | | | - Shelley D. Minteer
- The University of Utah Department of Chemistry 315 S 1400 E Room 2020 84112 Salt Lake City UNITED STATES
| | | |
Collapse
|
24
|
Crawford JM, Gensch T, Sigman MS, Elward JM, Steves JE. Impact of Phosphine Featurization Methods in Process Development. Org Process Res Dev 2022. [DOI: 10.1021/acs.oprd.1c00357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jennifer M. Crawford
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Tobias Gensch
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Matthew S. Sigman
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Jennifer M. Elward
- Molecular Design, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Janelle E. Steves
- Chemical Development, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| |
Collapse
|
25
|
Maley SM, Steagall R, Lief GR, Buck RM, Yang Q, Sydora OL, Bischof SM, Ess DH. Computational Evaluation and Design of Polyethylene Zirconocene Catalysts with Noncovalent Dispersion Interactions. Organometallics 2022. [DOI: 10.1021/acs.organomet.1c00670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Steven M. Maley
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Robert Steagall
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Graham R. Lief
- Research and Technology, Chevron Phillips Chemical Company LP, Highways 60 & 123, Bartlesville, Oklahoma 74003, United States
| | - Richard M. Buck
- Research and Technology, Chevron Phillips Chemical Company LP, Highways 60 & 123, Bartlesville, Oklahoma 74003, United States
| | - Qing Yang
- Research and Technology, Chevron Phillips Chemical Company LP, Highways 60 & 123, Bartlesville, Oklahoma 74003, United States
| | - Orson L. Sydora
- Research and Technology, Chevron Phillips Chemical Company LP, 1862, Kingwood Drive, Kingwood, Texas 77339, United States
| | - Steven M. Bischof
- Research and Technology, Chevron Phillips Chemical Company LP, 1862, Kingwood Drive, Kingwood, Texas 77339, United States
| | - Daniel H. Ess
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| |
Collapse
|
26
|
Betinol IO, Kuang Y, Reid JP. Guiding Target Synthesis with Statistical Modeling Tools: A Case Study in Organocatalysis. Org Lett 2022; 24:1429-1433. [PMID: 35030005 DOI: 10.1021/acs.orglett.1c04134] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Practitioners are generally not willing to explore modern reactions where considerable synthetic effort is required to generate materials and the results are not certain. Organocatalysis exemplifies this, in which a broad set of enantioselective reactions have been successfully developed but further applications to include additional substrates are often not performed. Herein we demonstrate how statistical models can be utilized to accurately distinguish between different catalysts and reactions to guide the selection of efficient synthetic routes to obtain a target molecule.
Collapse
Affiliation(s)
- Isaiah O Betinol
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Yutao Kuang
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Jolene P Reid
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| |
Collapse
|
27
|
Gallarati S, Laplaza R, Corminboeuf C. Harvesting the fragment-based nature of bifunctional organocatalysts to enhance their activity. Org Chem Front 2022. [DOI: 10.1039/d2qo00550f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Enhancing the activity of bifunctional organocatalysts: a fragment-based approach coupled with activity maps helps identifying better-performing catalytic motifs.
Collapse
Affiliation(s)
- Simone Gallarati
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Ruben Laplaza
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- National Center for Competence in Research – Catalysis (NCCR-Catalysis), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Clemence Corminboeuf
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- National Center for Competence in Research – Catalysis (NCCR-Catalysis), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- National Center for Computational Design and Discovery of Novel Materials (MARVEL), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| |
Collapse
|
28
|
Lee W, Kim J, Kim H, Back S. Catalytic Activity Trends of Pyrite Transition Metal Dichalcogenides for Oxygen Reduction and Evolution. Phys Chem Chem Phys 2022; 24:19911-19918. [DOI: 10.1039/d2cp01518h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Transition metal dichalcogenides (TMDs) have been considered as promising materials for oxygen reduction reaction (ORR) and oxygen evolution reaction (OER) electrocatalysis. While there have been numerous studies focusing on layered...
Collapse
|
29
|
Escofet I, Zuccarello G, Echavarren AM. Gold-catalyzed enantioselective cyclizations and cycloadditions. ADVANCES IN ORGANOMETALLIC CHEMISTRY 2022. [DOI: 10.1016/bs.adomc.2022.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
30
|
|
31
|
Proofreading experimentally assigned stereochemistry through Q2MM predictions in Pd-catalyzed allylic aminations. Nat Commun 2021; 12:6719. [PMID: 34795274 PMCID: PMC8602308 DOI: 10.1038/s41467-021-27065-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 11/03/2021] [Indexed: 11/26/2022] Open
Abstract
The palladium-catalyzed enantioselective allylic substitution by carbon or nitrogen nucleophiles is a key transformation that is particularly useful for the synthesis of bioactive compounds. Unfortunately, the selection of a suitable ligand/substrate combination often requires significant screening effort. Here, we show that a transition state force field (TSFF) derived by the quantum-guided molecular mechanics (Q2MM) method can be used to rapidly screen ligand/substrate combinations. Testing of this method on 77 literature reactions revealed several cases where the computationally predicted major enantiomer differed from the one reported. Interestingly, experimental follow-up led to a reassignment of the experimentally observed configuration. This result demonstrates the power of mechanistically based methods to predict and, where necessary, correct the stereochemical outcome.
Collapse
|
32
|
Zell D, Kingston C, Jermaks J, Smith SR, Seeger N, Wassmer J, Sirois LE, Han C, Zhang H, Sigman MS, Gosselin F. Stereoconvergent and -divergent Synthesis of Tetrasubstituted Alkenes by Nickel-Catalyzed Cross-Couplings. J Am Chem Soc 2021; 143:19078-19090. [PMID: 34735129 DOI: 10.1021/jacs.1c08399] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We report the development of a method to diastereoselectively access tetrasubstituted alkenes via nickel-catalyzed Suzuki-Miyaura cross-couplings of enol tosylates and boronic acid esters. Either diastereomeric product was selectively accessed from a mixture of enol tosylate starting material diastereomers in a convergent reaction by judicious choice of the ligand and reaction conditions. A similar protocol also enabled a divergent synthesis of each product isomer from diastereomerically pure enol tosylates. Notably, high-throughput optimization of the monophosphine ligands was guided by chemical space analysis of the kraken library to ensure a diverse selection of ligands was examined. Stereoelectronic analysis of the results provided insight into the requirements for reactive and selective ligands in this transformation. The synthetic utility of the optimized catalytic system was then probed in the stereoselective synthesis of various tetrasubstituted alkenes, with yields up to 94% and diastereomeric ratios up to 99:1 Z/E and 93:7 E/Z observed. Moreover, a detailed computational analysis and experimental mechanistic studies provided key insights into the nature of the underlying isomerization process impacting selectivity in the cross-coupling.
Collapse
Affiliation(s)
- Daniel Zell
- Department of Small Molecule Process Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Cian Kingston
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Janis Jermaks
- Department of Small Molecule Process Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Sleight R Smith
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Natalie Seeger
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Jana Wassmer
- Department of Small Molecule Process Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Lauren E Sirois
- Department of Small Molecule Process Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Chong Han
- Department of Small Molecule Process Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Haiming Zhang
- Department of Small Molecule Process Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Matthew S Sigman
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Francis Gosselin
- Department of Small Molecule Process Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| |
Collapse
|
33
|
Sunoj RB. Coming of Age of Computational Chemistry from a Resilient Past to a Promising Future. Isr J Chem 2021. [DOI: 10.1002/ijch.202100106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Raghavan B. Sunoj
- Department of Chemistry Indian Institute of Technology Bombay, Powai Mumbai 400076 India
| |
Collapse
|
34
|
De Jesus Silva J, Bartalucci N, Jelier B, Grosslight S, Gensch T, Schünemann C, Müller B, Kamer PCJ, Copéret C, Sigman MS, Togni A. Development and Molecular Understanding of a Pd‐Catalyzed Cyanation of Aryl Boronic Acids Enabled by High‐Throughput Experimentation and Data Analysis. Helv Chim Acta 2021. [DOI: 10.1002/hlca.202100200] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Jordan De Jesus Silva
- Department of Chemistry and Applied Biosciences ETH Zürich Vladimir-Prelog-Weg 1–5 CH-8093 Zürich Switzerland
| | - Niccolò Bartalucci
- Department of Chemistry and Applied Biosciences ETH Zürich Vladimir-Prelog-Weg 1–5 CH-8093 Zürich Switzerland
| | - Benson Jelier
- Department of Chemistry and Applied Biosciences ETH Zürich Vladimir-Prelog-Weg 1–5 CH-8093 Zürich Switzerland
| | - Samantha Grosslight
- Department of Chemistry University of Utah 315 South 1400 East Salt Lake City Utah 84112 United States
| | - Tobias Gensch
- Department of Chemistry University of Utah 315 South 1400 East Salt Lake City Utah 84112 United States
- Department of Chemistry TU Berlin Straße des 17. Juni 135 DE-10623 Berlin Germany
| | - Claas Schünemann
- Leibniz-Institute for Catalysis e. V. Albert-Einstein-Straße 29a DE-18059 Rostock Germany
| | - Bernd Müller
- Leibniz-Institute for Catalysis e. V. Albert-Einstein-Straße 29a DE-18059 Rostock Germany
| | - Paul C. J. Kamer
- Leibniz-Institute for Catalysis e. V. Albert-Einstein-Straße 29a DE-18059 Rostock Germany
| | - Christophe Copéret
- Department of Chemistry and Applied Biosciences ETH Zürich Vladimir-Prelog-Weg 1–5 CH-8093 Zürich Switzerland
| | - Matthew S. Sigman
- Department of Chemistry University of Utah 315 South 1400 East Salt Lake City Utah 84112 United States
| | - Antonio Togni
- Department of Chemistry and Applied Biosciences ETH Zürich Vladimir-Prelog-Weg 1–5 CH-8093 Zürich Switzerland
| |
Collapse
|
35
|
Towards Data‐Driven Design of Asymmetric Hydrogenation of Olefins: Database and Hierarchical Learning. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106880] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
36
|
Affiliation(s)
- Hidetoshi Noda
- Institute of Microbial Chemistry 3-14-23 Kamiosaki, Shinagaku-ku Tokyo 141-0021 Japan
| | - Xinxin Tang
- Institute of Microbial Chemistry 3-14-23 Kamiosaki, Shinagaku-ku Tokyo 141-0021 Japan
| | - Masakatsu Shibasaki
- Institute of Microbial Chemistry 3-14-23 Kamiosaki, Shinagaku-ku Tokyo 141-0021 Japan
| |
Collapse
|
37
|
Shoja A, Zhai J, Reid JP. Comprehensive Stereochemical Models for Selectivity Prediction in Diverse Chiral Phosphate-Catalyzed Reaction Space. ACS Catal 2021. [DOI: 10.1021/acscatal.1c03520] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Ali Shoja
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Jianyu Zhai
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Jolene P. Reid
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| |
Collapse
|
38
|
Xu LC, Zhang SQ, Li X, Tang MJ, Xie PP, Hong X. Towards Data-driven Design of Asymmetric Hydrogenation of Olefins: Database and Hierarchical Learning. Angew Chem Int Ed Engl 2021; 60:22804-22811. [PMID: 34370892 DOI: 10.1002/anie.202106880] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 07/14/2021] [Indexed: 11/09/2022]
Abstract
Asymmetric hydrogenation of olefins is one of the most powerful asymmetric transformations in molecular synthesis. Although several privileged catalyst scaffolds are available, the catalyst development for asymmetric hydrogenation is still a time- and resource-consuming process due to the lack of predictive catalyst design strategy. Targeting the data-driven design of asymmetric catalysis, we herein report the development of a standardized database that contains the detailed information of over 12000 literature asymmetric hydrogenations of olefins. This database provides a valuable platform for the machine learning applications in asymmetric catalysis. Based on this database, we developed a hierarchical learning approach to achieve predictive machine leaning model using only dozens of enantioselectivity data with the target olefin, which offers a useful solution for the few-shot learning problem and will facilitate the reaction optimization with new olefin substrate in catalysis screening.
Collapse
Affiliation(s)
- Li-Cheng Xu
- Zhejiang University, Department of Chemistry, CHINA
| | | | - Xin Li
- Zhejiang University, Department of Chemistry, CHINA
| | | | - Pei-Pei Xie
- Zhejiang University, Department of Chemistry, CHINA
| | - Xin Hong
- Zhejiang University, Department of Chemistry, 38 Zheda Road, 310028, Hangzhou, CHINA
| |
Collapse
|
39
|
Krieger AM, Pidko EA. The Impact of Computational Uncertainties on the Enantioselectivity Predictions: A Microkinetic Modeling of Ketone Transfer Hydrogenation with a Noyori-type Mn-diamine Catalyst. ChemCatChem 2021; 13:3517-3524. [PMID: 34589158 PMCID: PMC8453751 DOI: 10.1002/cctc.202100341] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/23/2021] [Indexed: 12/26/2022]
Abstract
Selectivity control is one of the most important functions of a catalyst. In asymmetric catalysis the enantiomeric excess (e.e.) is a property of major interest, with a lot of effort dedicated to developing the most enantioselective catalyst, understanding the origin of selectivity, and predicting stereoselectivity. Herein, we investigate the relationship between predicted selectivity and the uncertainties in the computed energetics of the catalytic reaction mechanism obtained by DFT calculations in a case study of catalytic asymmetric transfer hydrogenation (ATH) of ketones with an Mn-diamine catalyst. Data obtained from our analysis of DFT data by microkinetic modeling is compared to results from experiment. We discuss the limitations of the conventional reductionist approach of e.e. estimation from assessing the enantiodetermining steps only. Our analysis shows that the energetics of other reaction steps in the reaction mechanism have a substantial impact on the predicted reaction selectivity. The uncertainty of DFT calculations within the commonly accepted energy ranges of chemical accuracy may reverse the predicted e.e. with the non-enantiodetermining steps contributing to e.e. deviations of up to 25 %.
Collapse
Affiliation(s)
- Annika M. Krieger
- Inorganic Systems EngineeringDepartment of Chemical EngineeringFaculty of Applied SciencesDelft University of TechnologyVan der Maasweg 92629 HZDelftThe Netherlands
| | - Evgeny A. Pidko
- Inorganic Systems EngineeringDepartment of Chemical EngineeringFaculty of Applied SciencesDelft University of TechnologyVan der Maasweg 92629 HZDelftThe Netherlands
| |
Collapse
|
40
|
Crawford JM, Kingston C, Toste FD, Sigman MS. Data Science Meets Physical Organic Chemistry. Acc Chem Res 2021; 54:10.1021/acs.accounts.1c00285. [PMID: 34351757 PMCID: PMC9078128 DOI: 10.1021/acs.accounts.1c00285] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
ConspectusAt the heart of synthetic chemistry is the holy grail of predictable catalyst design. In particular, researchers involved in reaction development in asymmetric catalysis have pursued a variety of strategies toward this goal. This is driven by both the pragmatic need to achieve high selectivities and the inability to readily identify why a certain catalyst is effective for a given reaction. While empiricism and intuition have dominated the field of asymmetric catalysis since its inception, enantioselectivity offers a mechanistically rich platform to interrogate catalyst-structure response patterns that explain the performance of a particular catalyst or substrate.In the early stages of an asymmetric reaction development campaign, the overarching mechanism of the reaction, catalyst speciation, the turnover limiting step, and many other details are unknown or posited based on related reactions. Considering the unclear details leading to a successful reaction, initial enantioselectivity data are often used to intuitively guide the ultimate direction of optimization. However, if the conditions of the Curtin-Hammett principle are satisfied, then measured enantioselectivity can be directly connected to the ensemble of diastereomeric transition states (TSs) that lead to the enantiomeric products, and the associated free energy difference between competing TSs (ΔΔG⧧ = -RT ln[(S)/(R)], where (S) and (R) represent the concentrations of the enantiomeric products). We, and others, speculated that this important piece of information can be leveraged to guide reaction optimization in a quantitative way.Although traditional linear free energy relationships (LFERs), such as Hammett plots, have been used to illuminate important mechanistic features, we sought to develop data science derived tools to expand the power of LFERs in order to describe complex reactions frequently encountered in modern asymmetric catalysis. Specifically, we investigated whether enantioselectivity data from a reaction can be quantitatively connected to the attributes of reaction components, such as catalyst and substrate structural features, to harness data for asymmetric catalyst design.In this context, we developed a workflow to relate computationally derived features of reaction components to enantioselectivity using data science tools. The mathematical representation of molecules can incorporate many aspects of a transformation, such as molecular features from substrate, product, catalyst, and proposed transition states. Statistical models relating these features to reaction outputs can be used for various tasks, such as performance prediction of untested molecules. Perhaps most importantly, statistical models can guide the generation of mechanistic hypotheses that are embedded within complex patterns of reaction responses. Overall, merging traditional physical organic experiments with statistical modeling techniques creates a feedback loop that enables both evaluation of multiple mechanistic hypotheses and future catalyst design. In this Account, we highlight the evolution and application of this approach in the context of a collaborative program based on chiral phosphoric acid catalysts (CPAs) in asymmetric catalysis.
Collapse
Affiliation(s)
- Jennifer M Crawford
- Department of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, Utah 84112, United States
| | - Cian Kingston
- Department of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, Utah 84112, United States
| | - F Dean Toste
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Matthew S Sigman
- Department of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, Utah 84112, United States
| |
Collapse
|
41
|
Abstract
Computational methods have emerged as a powerful tool to augment traditional experimental molecular catalyst design by providing useful predictions of catalyst performance and decreasing the time needed for catalyst screening. In this perspective, we discuss three approaches for computational molecular catalyst design: (i) the reaction mechanism-based approach that calculates all relevant elementary steps, finds the rate and selectivity determining steps, and ultimately makes predictions on catalyst performance based on kinetic analysis, (ii) the descriptor-based approach where physical/chemical considerations are used to find molecular properties as predictors of catalyst performance, and (iii) the data-driven approach where statistical analysis as well as machine learning (ML) methods are used to obtain relationships between available data/features and catalyst performance. Following an introduction to these approaches, we cover their strengths and weaknesses and highlight some recent key applications. Furthermore, we present an outlook on how the currently applied approaches may evolve in the near future by addressing how recent developments in building automated computational workflows and implementing advanced ML models hold promise for reducing human workload, eliminating human bias, and speeding up computational catalyst design at the same time. Finally, we provide our viewpoint on how some of the challenges associated with the up-and-coming approaches driven by automation and ML may be resolved.
Collapse
Affiliation(s)
- Ademola Soyemi
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, AL 35487, USA.
| | - Tibor Szilvási
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, AL 35487, USA.
| |
Collapse
|
42
|
Moskal M, Beker W, Szymkuć S, Grzybowski BA. Scaffold‐Directed Face Selectivity Machine‐Learned from Vectors of Non‐covalent Interactions. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101986] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Martyna Moskal
- Institute of Organic Chemistry Polish Academy of Sciences Ul. Kasprzaka 44/52 01-224 Warsaw Poland
- Allchemy, Inc. Highland IN USA
| | - Wiktor Beker
- Institute of Organic Chemistry Polish Academy of Sciences Ul. Kasprzaka 44/52 01-224 Warsaw Poland
- Allchemy, Inc. Highland IN USA
| | - Sara Szymkuć
- Institute of Organic Chemistry Polish Academy of Sciences Ul. Kasprzaka 44/52 01-224 Warsaw Poland
- Allchemy, Inc. Highland IN USA
| | - Bartosz A. Grzybowski
- Institute of Organic Chemistry Polish Academy of Sciences Ul. Kasprzaka 44/52 01-224 Warsaw Poland
- Allchemy, Inc. Highland IN USA
- IBS Center for Soft and Living Matter and Department of Chemistry UNIST 50, UNIST-gil, Eonyang-eup, Ulju-gun Ulsan South Korea
| |
Collapse
|
43
|
Moskal M, Beker W, Szymkuć S, Grzybowski BA. Scaffold-Directed Face Selectivity Machine-Learned from Vectors of Non-covalent Interactions. Angew Chem Int Ed Engl 2021; 60:15230-15235. [PMID: 33876554 DOI: 10.1002/anie.202101986] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/29/2021] [Indexed: 11/06/2022]
Abstract
This work describes a method to vectorize and Machine-Learn, ML, non-covalent interactions responsible for scaffold-directed reactions important in synthetic chemistry. Models trained on this representation predict correct face of approach in ca. 90 % of Michael additions or Diels-Alder cycloadditions. These accuracies are significantly higher than those based on traditional ML descriptors, energetic calculations, or intuition of experienced synthetic chemists. Our results also emphasize the importance of ML models being provided with relevant mechanistic knowledge; without such knowledge, these models cannot easily "transfer-learn" and extrapolate to previously unseen reaction mechanisms.
Collapse
Affiliation(s)
- Martyna Moskal
- Institute of Organic Chemistry, Polish Academy of Sciences, Ul. Kasprzaka 44/52, 01-224, Warsaw, Poland.,Allchemy, Inc., Highland, IN, USA
| | - Wiktor Beker
- Institute of Organic Chemistry, Polish Academy of Sciences, Ul. Kasprzaka 44/52, 01-224, Warsaw, Poland.,Allchemy, Inc., Highland, IN, USA
| | - Sara Szymkuć
- Institute of Organic Chemistry, Polish Academy of Sciences, Ul. Kasprzaka 44/52, 01-224, Warsaw, Poland.,Allchemy, Inc., Highland, IN, USA
| | - Bartosz A Grzybowski
- Institute of Organic Chemistry, Polish Academy of Sciences, Ul. Kasprzaka 44/52, 01-224, Warsaw, Poland.,Allchemy, Inc., Highland, IN, USA.,IBS Center for Soft and Living Matter and Department of Chemistry, UNIST, 50, UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan, South Korea
| |
Collapse
|
44
|
Rinehart NI, Zahrt AF, Henle JJ, Denmark SE. Dreams, False Starts, Dead Ends, and Redemption: A Chronicle of the Evolution of a Chemoinformatic Workflow for the Optimization of Enantioselective Catalysts. Acc Chem Res 2021; 54:2041-2054. [PMID: 33856771 DOI: 10.1021/acs.accounts.0c00826] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Catalyst design in enantioselective catalysis has historically been driven by empiricism. In this endeavor, experimentalists attempt to qualitatively identify trends in structure that lead to a desired catalyst function. In this body of work, we lay the groundwork for an improved, alternative workflow that uses quantitative methods to inform decision making at every step of the process. At the outset, we define a library of synthetically accessible permutations of a catalyst scaffold with the philosophy that the library contains every potential catalyst we are willing to make. To represent these chiral molecules, we have developed general 3D representations, which can be calculated for tens of thousands of structures. This defines the total chemical space of a given catalyst scaffold; it is constructed on the basis of catalyst structure only without regard to a specific reaction or mechanism. As such, any algorithmic subset selection method, which is unsupervised (i.e., only considers catalyst structure), should provide an ideal initial screening set for any new reaction that can be catalyzed by that scaffold. Notably, because this design strategy, the same set of catalysts can be used for any reaction that can be catalyzed with that parent catalyst scaffold. These are tested experimentally, and statistical learning tools can be used to create a model relating catalyst structure to catalyst function. Further, this model can be used to predict the performance of each catalyst candidate in the greater database of virtual catalyst candidates. In this way, it is possible estimate the performance of tens of thousands of catalysts by experimentally testing a smaller subset. Using error assessment metrics, it is possible to understand the confidence in new predictions. An experimentalist using this tool can balance the predicted results (reward) with the prediction confidence (risk) when deciding which catalysts to synthesize next in an optimization campaign. These catalysts are synthesized and tested experimentally. At this stage, either the optimization is a success or the predicted values were incorrect and further optimization is required. In the case of the latter, the information can be fed back into the statistical learning model to refine the model, and this iterative process can be used to determine the optimal catalyst. In this body of work, we not only establish this workflow but quantitatively establish how best to execute each step. Herein, we evaluate several 3D molecular representations to determine how best to represent molecules. Several selection protocols are examined to best decide which set of molecules can be used to represent the library of interest. In addition, the number of reactions needed to make accurate, statistical learning models is evaluated. Taken together these components establish a tool ready to progress from the development stage to the utility stage. As such, current research endeavors focus on applying these tools to optimize new reactions.
Collapse
Affiliation(s)
- N. Ian Rinehart
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Andrew F. Zahrt
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Jeremy J. Henle
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Scott E. Denmark
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| |
Collapse
|
45
|
Shoja A, Reid JP. Computational Insights into Privileged Stereocontrolling Interactions Involving Chiral Phosphates and Iminium Intermediates. J Am Chem Soc 2021; 143:7209-7215. [PMID: 33914528 DOI: 10.1021/jacs.1c03829] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The precise design of a catalyst for a given reaction is extremely difficult, often requiring a significant empirical screening campaign to afford products in high yields and enantiomeric excess. Design becomes even more challenging if one requires a catalyst that performs well for a diverse range of substrates. Such "privileged" catalysts exist, but little is known why they operate so generally. We report the results of computations which show that when substrate and catalyst features are conserved between significantly different mechanistic regimes, similar modes of activation can be invoked. As a validating case study, we explored a Hantzsch ester hydrogenation of α,β-unsaturated iminiums involving BINOL-derived chiral phosphates and find they impart asymmetric induction in an analogous fashion to their acid counterpart. Specifically, DFT calculations at the IEFPCM(1,4-dioxane)-B3LYP/6-311+G(d,p)//B3LYP/6-31G(d) level predicted enantioselectivity to be close to the experimental value (82% ee calculated, 96% ee experimental) and showed that the reaction proceeds via a transition state involving two hydrogen-bonding interactions from the iminium intermediate and nucleophile to the catalyst. These interactions lower the energy of the transition structure and provide extra rigidity to the system. This new model invokes "privileged" noncovalent interactions and leads to a new explanation for the enantioselectivity outcome, ultimately providing the basis for the development of general catalyst design principles and the translation of mechanistically disparate reaction profiles for the prediction of enantioselectivity outcomes using statistical models.
Collapse
Affiliation(s)
- Ali Shoja
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Jolene P Reid
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| |
Collapse
|
46
|
Zahrt AF, Rinehart NI, Denmark SE. A Conformer‐Dependent, Quantitative Quadrant Model. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Andrew F. Zahrt
- Roger Adams Laboratory Department of Chemistry University of Illinois 600 S. Mathews Ave Urbana, IL 61801 USA
| | - N. Ian Rinehart
- Roger Adams Laboratory Department of Chemistry University of Illinois 600 S. Mathews Ave Urbana, IL 61801 USA
| | - Scott E. Denmark
- Roger Adams Laboratory Department of Chemistry University of Illinois 600 S. Mathews Ave Urbana, IL 61801 USA
| |
Collapse
|
47
|
Gallarati S, Fabregat R, Laplaza R, Bhattacharjee S, Wodrich MD, Corminboeuf C. Reaction-based machine learning representations for predicting the enantioselectivity of organocatalysts. Chem Sci 2021; 12:6879-6889. [PMID: 34123316 PMCID: PMC8153079 DOI: 10.1039/d1sc00482d] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/01/2021] [Indexed: 12/12/2022] Open
Abstract
Hundreds of catalytic methods are developed each year to meet the demand for high-purity chiral compounds. The computational design of enantioselective organocatalysts remains a significant challenge, as catalysts are typically discovered through experimental screening. Recent advances in combining quantum chemical computations and machine learning (ML) hold great potential to propel the next leap forward in asymmetric catalysis. Within the context of quantum chemical machine learning (QML, or atomistic ML), the ML representations used to encode the three-dimensional structure of molecules and evaluate their similarity cannot easily capture the subtle energy differences that govern enantioselectivity. Here, we present a general strategy for improving molecular representations within an atomistic machine learning model to predict the DFT-computed enantiomeric excess of asymmetric propargylation organocatalysts solely from the structure of catalytic cycle intermediates. Mean absolute errors as low as 0.25 kcal mol-1 were achieved in predictions of the activation energy with respect to DFT computations. By virtue of its design, this strategy is generalisable to other ML models, to experimental data and to any catalytic asymmetric reaction, enabling the rapid screening of structurally diverse organocatalysts from available structural information.
Collapse
Affiliation(s)
- Simone Gallarati
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL) 1015 Lausanne Switzerland
| | - Raimon Fabregat
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL) 1015 Lausanne Switzerland
| | - Rubén Laplaza
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL) 1015 Lausanne Switzerland
- National Center for Competence in Research-Catalysis (NCCR-Catalysis), Ecole Polytechnique Fédérale de Lausanne (EPFL) 1015 Lausanne Switzerland
| | - Sinjini Bhattacharjee
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL) 1015 Lausanne Switzerland
- Indian Institute of Science Education and Research Dr Homi Bhabha Rd, Ward No. 8, NCL Colony, Pashan Pune Maharashtra 411008 India
| | - Matthew D Wodrich
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL) 1015 Lausanne Switzerland
- National Center for Competence in Research-Catalysis (NCCR-Catalysis), Ecole Polytechnique Fédérale de Lausanne (EPFL) 1015 Lausanne Switzerland
| | - Clemence Corminboeuf
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL) 1015 Lausanne Switzerland
- National Center for Competence in Research-Catalysis (NCCR-Catalysis), Ecole Polytechnique Fédérale de Lausanne (EPFL) 1015 Lausanne Switzerland
- National Center for Computational Design and Discovery of Novel Materials (MARVEL), Ecole Polytechnique Fédérale de Lausanne (EPFL) 1015 Lausanne Switzerland
| |
Collapse
|
48
|
Werth J, Sigman MS. Linear Regression Model Development for Analysis of Asymmetric Copper-Bisoxazoline Catalysis. ACS Catal 2021; 11:3916-3922. [PMID: 34671510 DOI: 10.1021/acscatal.1c00531] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Multivariate linear regression analysis (MLR) is used to unify and correlate different categories of asymmetric Cu-bisoxazoline (BOX) catalysis. The versatility of Cu-BOX complexes has been leveraged for several types of enantioselective transformations including cyclopropanation, Diels-Alder cycloadditions and difunctionalization of alkenes. Statistical tools and extensive molecular featurization has guided the development of an inclusive linear regression model, providing a predictive platform and readily interpretable descriptors. Mechanism-specific categorization of curated datasets and parameterization of reaction components allows for simultaneous analysis of disparate organometallic intermediates such as carbenes and Lewis acid adducts, all unified by a common ligand scaffold and metal ion. Additionally, this workflow permitted the development of a complementary linear regression model correlating analogous BOX-catalyzed reactions employing Ni, Fe, Mg, and Pd complexes. Comparison of ligand parameters in each model reveals the relevant structural requirements necessary for high selectivity. Overall, this strategy highlights the utility of MLR analysis in exploring mechanistically driven correlations across a diverse chemical space in organometallic chemistry and presents an applicable workflow for related ligand classes.
Collapse
Affiliation(s)
- Jacob Werth
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Matthew S. Sigman
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| |
Collapse
|
49
|
|
50
|
Maity B, Cao Z, Kumawat J, Gupta V, Cavallo L. A Multivariate Linear Regression Approach to Predict Ethene/1-Olefin Copolymerization Statistics Promoted by Group 4 Catalysts. ACS Catal 2021. [DOI: 10.1021/acscatal.0c04856] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Bholanath Maity
- King Abdullah University of Science and Technology (KAUST) KAUST Catalysis Center (KCC), Thuwal 23955-6900, Saudi Arabia
| | - Zhen Cao
- King Abdullah University of Science and Technology (KAUST) KAUST Catalysis Center (KCC), Thuwal 23955-6900, Saudi Arabia
| | - Jugal Kumawat
- Reliance Research & Development Centre, Reliance Corporate Park, Reliance Industries Limited, Navi Mumbai 400 701, India
| | - Virendrakumar Gupta
- Reliance Research & Development Centre, Reliance Corporate Park, Reliance Industries Limited, Navi Mumbai 400 701, India
| | - Luigi Cavallo
- King Abdullah University of Science and Technology (KAUST) KAUST Catalysis Center (KCC), Thuwal 23955-6900, Saudi Arabia
| |
Collapse
|