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Voinarovska V, Kabeshov M, Dudenko D, Genheden S, Tetko IV. When Yield Prediction Does Not Yield Prediction: An Overview of the Current Challenges. J Chem Inf Model 2024; 64:42-56. [PMID: 38116926 PMCID: PMC10778086 DOI: 10.1021/acs.jcim.3c01524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 12/21/2023]
Abstract
Machine Learning (ML) techniques face significant challenges when predicting advanced chemical properties, such as yield, feasibility of chemical synthesis, and optimal reaction conditions. These challenges stem from the high-dimensional nature of the prediction task and the myriad essential variables involved, ranging from reactants and reagents to catalysts, temperature, and purification processes. Successfully developing a reliable predictive model not only holds the potential for optimizing high-throughput experiments but can also elevate existing retrosynthetic predictive approaches and bolster a plethora of applications within the field. In this review, we systematically evaluate the efficacy of current ML methodologies in chemoinformatics, shedding light on their milestones and inherent limitations. Additionally, a detailed examination of a representative case study provides insights into the prevailing issues related to data availability and transferability in the discipline.
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Affiliation(s)
- Varvara Voinarovska
- Molecular
AI, Discovery Sciences R&D, AstraZeneca, 431 83 Gothenburg, Sweden
- TUM
Graduate School, Faculty of Chemistry, Technical
University of Munich, 85748 Garching, Germany
| | - Mikhail Kabeshov
- Molecular
AI, Discovery Sciences R&D, AstraZeneca, 431 83 Gothenburg, Sweden
| | - Dmytro Dudenko
- Enamine
Ltd., 78 Chervonotkatska str., 02094 Kyiv, Ukraine
| | - Samuel Genheden
- Molecular
AI, Discovery Sciences R&D, AstraZeneca, 431 83 Gothenburg, Sweden
| | - Igor V. Tetko
- Molecular
Targets and Therapeutics Center, Helmholtz Munich − Deutsches
Forschungszentrum für Gesundheit und Umwelt (GmbH), Institute of Structural Biology, 85764 Neuherberg, Germany
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2
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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]
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3
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Moutaoukil Z, Serrano-Díez E, Collado IG, Jiménez-Tenorio M, Botubol-Ares JM. N-Alkylation of organonitrogen compounds catalyzed by methylene-linked bis-NHC half-sandwich ruthenium complexes. Org Biomol Chem 2022; 20:831-839. [PMID: 35018948 DOI: 10.1039/d1ob02214h] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
An efficient ruthenium-catalyzed N-alkylation of amines, amides and sulfonamides has been developed employing novel pentamethylcyclopentadienylruthenium(II) complexes bearing the methylene linked bis(NHC) ligand bis(3-methylimidazol-2-ylidene)methane. The acetonitrile complex 2 has proven particularly effective with a broad range of substrates with low catalyst loading (0.1-2.5 mol%) and high functional group tolerance under mild conditions. A total of 52 N-alkylated organonitrogen compounds including biologically relevant scaffolds were synthesized from (hetero)aromatic and aliphatic amines, amides and sulfonamides using alcohols or diols as alkylating agents in up to 99% isolated yield, even on gram-scale reactions. In the case of sulfonamides, it is the first example of N-alkylation employing a transition-metal complex bearing NHC ligands.
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Affiliation(s)
- Zakaria Moutaoukil
- University of Cadiz, Departamento de Química Orgánica-INBIO, Facultad de Ciencias, Torre Sur, 4° planta, 11510, Puerto Real, Cádiz.
| | - Emmanuel Serrano-Díez
- University of Cadiz, Departamento de Química Orgánica-INBIO, Facultad de Ciencias, Torre Sur, 4° planta, 11510, Puerto Real, Cádiz.
| | - Isidro G Collado
- University of Cadiz, Departamento de Química Orgánica-INBIO, Facultad de Ciencias, Torre Sur, 4° planta, 11510, Puerto Real, Cádiz.
| | - Manuel Jiménez-Tenorio
- University of Cadiz, Departamento de Ciencias de los Materiales e Ingeniería Metalúrgica y Química Inorgánica-INBIO, Facultad de Ciencias, Torre Norte, 1° planta, 11510, Puerto Real, Cádiz, Spain
| | - José Manuel Botubol-Ares
- University of Cadiz, Departamento de Química Orgánica-INBIO, Facultad de Ciencias, Torre Sur, 4° planta, 11510, Puerto Real, Cádiz.
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4
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Kearnes SM, Maser MR, Wleklinski M, Kast A, Doyle AG, Dreher SD, Hawkins JM, Jensen KF, Coley CW. The Open Reaction Database. J Am Chem Soc 2021; 143:18820-18826. [PMID: 34727496 DOI: 10.1021/jacs.1c09820] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Chemical reaction data in journal articles, patents, and even electronic laboratory notebooks are currently stored in various formats, often unstructured, which presents a significant barrier to downstream applications, including the training of machine-learning models. We present the Open Reaction Database (ORD), an open-access schema and infrastructure for structuring and sharing organic reaction data, including a centralized data repository. The ORD schema supports conventional and emerging technologies, from benchtop reactions to automated high-throughput experiments and flow chemistry. The data, schema, supporting code, and web-based user interfaces are all publicly available on GitHub. Our vision is that a consistent data representation and infrastructure to support data sharing will enable downstream applications that will greatly improve the state of the art with respect to computer-aided synthesis planning, reaction prediction, and other predictive chemistry tasks.
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Affiliation(s)
- Steven M Kearnes
- Relay Therapeutics, Cambridge, Massachusetts 02139, United States
| | - Michael R Maser
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Michael Wleklinski
- Chemistry Capabilities Accelerating Therapeutics, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Anton Kast
- Google LLC, Mountain View, California 94043, United States
| | - Abigail G Doyle
- Department of Chemistry & Biochemistry, University of California at Los Angeles, Los Angeles, California 90095, United States
| | - Spencer D Dreher
- Chemistry Capabilities Accelerating Therapeutics, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Joel M Hawkins
- Chemical Research and Development, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Klavs F Jensen
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Connor W Coley
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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5
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Liu RY, Buchwald SL. CuH-Catalyzed Olefin Functionalization: From Hydroamination to Carbonyl Addition. Acc Chem Res 2020; 53:1229-1243. [PMID: 32401530 DOI: 10.1021/acs.accounts.0c00164] [Citation(s) in RCA: 231] [Impact Index Per Article: 46.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In organic synthesis, ligand-modified copper(I) hydride (CuH) complexes have become well-known reagents and catalysts for selective reduction, particularly toward Michael acceptors and carbonyl compounds. Recently, our group and others have found that these hydride complexes undergo migratory insertion (hydrocupration) with relatively unactivated and electronically unpolarized olefins, producing alkylcopper intermediates that can be leveraged to forge a variety of useful bonds. The resulting formal hydrofunctionalization reactions have formed the basis for a resurgence of research in CuH catalysis. This Account chronicles the development of this concept in our research group, highlighting its origin in the context of asymmetric hydroamination, evolution to more general C-X bond-forming reactions, and applications in the addition of olefin-derived nucleophiles to carbonyl derivatives.Hydroamination, the formal insertion of an olefin into the N-H bond of an amine, is a process of significant academic and industrial interest, due to its potential to transform widely available alkenes and alkynes into valuable complex amines. We developed a polarity-reversed strategy for catalytic enantioselective hydroamination relying on the reaction of olefins with CuH to generate chiral organocopper intermediates, which are intercepted by electrophilic amine reagents. By engineering the auxiliary ligand, amine electrophile, and reaction conditions, the scope of this method has since been extended to include many types of olefins, including challenging internal olefins. Further, the scope of amine reagents has been expanded to enable the synthesis of primary, secondary, and tertiary amines as well as amides, N-alkylated heterocycles, and anilines. All of these reactions exhibit high regio- and stereoselectivity and, due to the mild conditions required, excellent tolerance for heterocycles and polar functional groups.Though the generation of alkylcopper species from olefins was originally devised as a means to solve the hydroamination problem, we soon found that these intermediates could react efficiently with an unexpectedly broad range of electrophiles, including alkyl halides, silicon reagents, arylpalladium species, heterocycles, and carbonyl derivatives. The general ability of olefins to function as precursors for nucleophilic intermediates has proved particularly advantageous in carbonyl addition reactions because it overcomes many of the disadvantages associated with traditional organometallic reagents. By removing the need for pregeneration of the nucleophile in a separate operation, CuH-catalyzed addition reactions of olefin-derived nucleophiles feature improved step economy, enhanced functional group tolerance, and the potential for catalyst control over regio- and stereoselectivity. Following this paradigm, feedstock olefins such as allene, butadiene, and styrene have been employed as reagents for asymmetric alkylation of ketones, imines, and aldehydes.
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Affiliation(s)
- Richard Y. Liu
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, United States
| | - Stephen L. Buchwald
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, United States
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Yang Q, Li S, Wang J(J. Asymmetric Synthesis of Chiral Chromanes by Copper‐Catalyzed Hydroamination of 2
H
‐Chromenes. ChemCatChem 2020. [DOI: 10.1002/cctc.202000601] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Qingjing Yang
- School of Chemistry and Chemical EngineeringHarbin Institute of Technology Harbin 150080 P. R. China
- Department of ChemistrySouthern University of Science and Technology Shenzhen Guangdong 518055 P. R. China
| | - Sifeng Li
- Department of ChemistrySouthern University of Science and Technology Shenzhen Guangdong 518055 P. R. China
| | - Jun (Joelle) Wang
- Department of ChemistrySouthern University of Science and Technology Shenzhen Guangdong 518055 P. R. China
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Xu-Xu QF, Zhang X, You SL. Enantioselective Synthesis of 4-Aminotetrahydroquinolines via 1,2-Reductive Dearomatization of Quinolines and Copper(I) Hydride-Catalyzed Asymmetric Hydroamination. Org Lett 2019; 21:5357-5362. [PMID: 31247783 DOI: 10.1021/acs.orglett.9b02034] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A 1,2-reductive dearomatization of quinolines and copper(II) acetate monohydrate/( R, R)-Ph-BPE/P( p-tolyl)3-catalyzed enantioselective hydroamination sequence was developed, affording diverse 4-amino-1,2,3,4-tetrahydroquinolines with high levels of enantioselectivity in either a stepwise or one-pot fashion. Pleasingly, internal cis-cyclic alkenes, which are challenging substrates in copper hydride-catalyzed enantioselective hydroamination reactions, were transformed efficiently under mild conditions.
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Affiliation(s)
- Qing-Feng Xu-Xu
- State Key Laboratory of Organometallic Chemistry, Center for Excellence in Molecular Synthesis , Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences , 345 Lingling Lu , Shanghai 200032 , China
| | - Xiao Zhang
- State Key Laboratory of Organometallic Chemistry, Center for Excellence in Molecular Synthesis , Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences , 345 Lingling Lu , Shanghai 200032 , China
| | - Shu-Li You
- State Key Laboratory of Organometallic Chemistry, Center for Excellence in Molecular Synthesis , Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences , 345 Lingling Lu , Shanghai 200032 , China.,Collaborative Innovation Center of Chemical Science and Engineering , Tianjin 300072 , China
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8
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Liu RY, Zhou Y, Yang Y, Buchwald SL. Enantioselective Allylation Using Allene, a Petroleum Cracking Byproduct. J Am Chem Soc 2019; 141:2251-2256. [PMID: 30685967 DOI: 10.1021/jacs.8b13907] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Allene (C3H4) gas is produced and separated on million-metric-ton scale per year during petroleum refining but is rarely employed in organic synthesis. Meanwhile, the addition of an allyl group (C3H5) to ketones is among the most common and prototypical reactions in synthetic chemistry. Herein, we report that the combination of allene gas with inexpensive and environmentally benign hydrosilanes, such as PMHS, can serve as a replacement for stoichiometric quantities of allylmetal reagents, which are required in most enantioselective ketone allylation reactions. This process is catalyzed by copper salts and commercially available ligands, operates without specialized equipment or pressurization, and tolerates a broad range of functional groups. Furthermore, the exceptional chemoselectivity of this catalyst system enables industrially relevant C3 hydrocarbon mixtures of allene with methylacetylene and propylene to be applied directly.
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Affiliation(s)
- Richard Y Liu
- Department of Chemistry , Massachusetts Institute of Technology , 77 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Yujing Zhou
- Department of Chemistry , Massachusetts Institute of Technology , 77 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Yang Yang
- Department of Chemistry , Massachusetts Institute of Technology , 77 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Stephen L Buchwald
- Department of Chemistry , Massachusetts Institute of Technology , 77 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
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9
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Xu‐Xu Q, Liu Q, Zhang X, You S. Copper‐Catalyzed Ring Opening of Benzofurans and an Enantioselective Hydroamination Cascade. Angew Chem Int Ed Engl 2018; 57:15204-15208. [DOI: 10.1002/anie.201809003] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 09/06/2018] [Indexed: 11/07/2022]
Affiliation(s)
- Qing‐Feng Xu‐Xu
- State Key Laboratory of Organometallic ChemistryShanghai Institute of Organic ChemistryUniversity of Chinese Academy of SciencesChinese Academy of Sciences 345 Lingling Lu Shanghai 200032 China
| | - Qiang‐Qiang Liu
- State Key Laboratory of Organometallic ChemistryShanghai Institute of Organic ChemistryUniversity of Chinese Academy of SciencesChinese Academy of Sciences 345 Lingling Lu Shanghai 200032 China
| | - Xiao Zhang
- State Key Laboratory of Organometallic ChemistryShanghai Institute of Organic ChemistryUniversity of Chinese Academy of SciencesChinese Academy of Sciences 345 Lingling Lu Shanghai 200032 China
| | - Shu‐Li You
- State Key Laboratory of Organometallic ChemistryShanghai Institute of Organic ChemistryUniversity of Chinese Academy of SciencesChinese Academy of Sciences 345 Lingling Lu Shanghai 200032 China
- Collaborative Innovation Center of, Chemical Science and Engineering Tianjin 300072 China
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10
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Thomas AA, Speck K, Kevlishvili I, Lu Z, Liu P, Buchwald SL. Mechanistically Guided Design of Ligands That Significantly Improve the Efficiency of CuH-Catalyzed Hydroamination Reactions. J Am Chem Soc 2018; 140:13976-13984. [PMID: 30244567 PMCID: PMC6469493 DOI: 10.1021/jacs.8b09565] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Using a mechanically guided ligand design approach, a new ligand (SEGFAST) for the CuH-catalyzed hydroamination reaction of unactivated terminal olefins has been developed, providing a 62-fold rate increase over reactions compared to DTBM-SEGPHOS, the previous optimal ligand. Combining the respective strengths of computational chemistry and experimental kinetic measurements, we were able to quickly identify potential modifications that lead to more effective ligands, thus avoiding synthesizing and testing a large library of ligands. By optimizing the combination of attractive, noncovalent ligand-substrate interactions and the stability of the catalyst under the reaction conditions, we were able to identify a finely tuned hybrid ligand that greatly enables accelerated hydrocupration rates with unactivated alkenes. Moreover, a modular and robust synthetic sequence was devised, which allowed for the practical, gram-scale synthesis of these novel hybrid ligand structures.
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Affiliation(s)
- Andy A Thomas
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Klaus Speck
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Ilia Kevlishvili
- Department of Chemistry , University of Pittsburgh , Pittsburgh , Pennsylvania 15260 , United States
| | - Zhaohong Lu
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Peng Liu
- Department of Chemistry , University of Pittsburgh , Pittsburgh , Pennsylvania 15260 , United States
| | - Stephen L Buchwald
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
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11
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Xu‐Xu Q, Liu Q, Zhang X, You S. Copper‐Catalyzed Ring Opening of Benzofurans and an Enantioselective Hydroamination Cascade. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201809003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Qing‐Feng Xu‐Xu
- State Key Laboratory of Organometallic ChemistryShanghai Institute of Organic ChemistryUniversity of Chinese Academy of SciencesChinese Academy of Sciences 345 Lingling Lu Shanghai 200032 China
| | - Qiang‐Qiang Liu
- State Key Laboratory of Organometallic ChemistryShanghai Institute of Organic ChemistryUniversity of Chinese Academy of SciencesChinese Academy of Sciences 345 Lingling Lu Shanghai 200032 China
| | - Xiao Zhang
- State Key Laboratory of Organometallic ChemistryShanghai Institute of Organic ChemistryUniversity of Chinese Academy of SciencesChinese Academy of Sciences 345 Lingling Lu Shanghai 200032 China
| | - Shu‐Li You
- State Key Laboratory of Organometallic ChemistryShanghai Institute of Organic ChemistryUniversity of Chinese Academy of SciencesChinese Academy of Sciences 345 Lingling Lu Shanghai 200032 China
- Collaborative Innovation Center of, Chemical Science and Engineering Tianjin 300072 China
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