1
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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.
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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
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2
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Monti A, López-Serrano J, Prieto A, Nicasio MC. Broad-Scope Amination of Aryl Sulfamates Catalyzed by a Palladium Phosphine Complex. ACS Catal 2023; 13:10945-10952. [PMID: 37614522 PMCID: PMC10443792 DOI: 10.1021/acscatal.3c03166] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 07/20/2023] [Indexed: 08/25/2023]
Abstract
Among phenol-derived electrophiles, aryl sulfamates are attractive substrates since they can be employed as directing groups for C-H functionalization prior to catalysis. However, their use in C-N coupling is limited only to Ni catalysis. Here, we describe a Pd-based catalyst with a broad scope for the amination of aryl sulfamates. We show that the N-methyl-2-aminobiphenyl palladacycle supported by the PCyp2ArXyl2 ligand (Cyp = cyclopentyl; ArXyl2 = 2,6-bis(2,6-dimethylphenyl)phenyl) efficiently catalyzes the C-N coupling of aryl sulfamates with a variety of nitrogen nucleophiles, including anilines, primary and secondary alkyl amines, heteroaryl amines, N-heterocycles, and primary amides. DFT calculations support that the oxidative addition of the aryl sulfamate is the rate-determining step. The C-N coupling takes place through a cationic pathway in the polar protic medium.
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Affiliation(s)
- Andrea Monti
- Departamento
de Química Inorgánica, Universidad
de Sevilla, Aptdo 1203, 41071 Sevilla, Spain
| | - Joaquín López-Serrano
- Instituto
de Investigaciones Químicas (IIQ), Departamento de Química
Inorgánica and Centro de Innovación Química Avanzada
(ORFEO-CINQA), Universidad de Sevilla and
CSIC, 41092 Sevilla, Spain
| | - Auxiliadora Prieto
- Laboratorio
de Catálisis Homogénea, Unidad Asociada al CSIC, CIQSO-Centro
de Investigación en Química Sostenible and Departamento
de Química, Universidad de Huelva, Campus de El Carmen s/n, 21007 Huelva, Spain
| | - M. Carmen Nicasio
- Departamento
de Química Inorgánica, Universidad
de Sevilla, Aptdo 1203, 41071 Sevilla, Spain
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3
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Lavigne C, Gomes G, Pollice R, Aspuru-Guzik A. Guided discovery of chemical reaction pathways with imposed activation. Chem Sci 2022; 13:13857-13871. [PMID: 36544742 PMCID: PMC9710306 DOI: 10.1039/d2sc05135d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/09/2022] [Indexed: 11/12/2022] Open
Abstract
Computational power and quantum chemical methods have improved immensely since computers were first applied to the study of reactivity, but the de novo prediction of chemical reactions has remained challenging. We show that complex reaction pathways can be efficiently predicted in a guided manner using chemical activation imposed by geometrical constraints of specific reactive modes, which we term imposed activation (IACTA). Our approach is demonstrated on realistic and challenging chemistry, such as a triple cyclization cascade involved in the total synthesis of a natural product, a water-mediated Michael addition, and several oxidative addition reactions of complex drug-like molecules. Notably and in contrast with traditional hand-guided computational chemistry calculations, our method requires minimal human involvement and no prior knowledge of the products or the associated mechanisms. We believe that IACTA will be a transformational tool to screen for chemical reactivity and to study both by-product formation and decomposition pathways in a guided way.
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Affiliation(s)
- Cyrille Lavigne
- Department of Computer Science, University of Toronto214 College St.TorontoOntarioM5T 3A1Canada
| | - Gabe Gomes
- Department of Computer Science, University of Toronto214 College St.TorontoOntarioM5T 3A1Canada,Chemical Physics Theory Group, Department of Chemistry, University of Toronto80 St George StTorontoOntarioM5S 3H6Canada
| | - Robert Pollice
- Department of Computer Science, University of Toronto214 College St.TorontoOntarioM5T 3A1Canada,Chemical Physics Theory Group, Department of Chemistry, University of Toronto80 St George StTorontoOntarioM5S 3H6Canada
| | - Alán Aspuru-Guzik
- Department of Computer Science, University of Toronto214 College St.TorontoOntarioM5T 3A1Canada,Chemical Physics Theory Group, Department of Chemistry, University of Toronto80 St George StTorontoOntarioM5S 3H6Canada,Department of Chemical Engineering & Applied Chemistry, University of Toronto200 College St.OntarioM5S 3E5Canada,Department of Materials Science & Engineering, University of Toronto184 College St.OntarioM5S 3E4Canada,Vector Institute for Artificial Intelligence661 University Ave Suite 710TorontoOntarioM5G 1M1Canada,Lebovic Fellow, Canadian Institute for Advanced Research (CIFAR)661 University AveTorontoOntarioM5GCanada
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4
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Verdugo F, Rodiño R, Calvelo M, Mascareñas JL, López F. Palladium-Catalyzed Tandem Cycloisomerization/Cross-Coupling of Carbonyl- and Imine-Tethered Alkylidenecyclopropanes. Angew Chem Int Ed Engl 2022; 61:e202202295. [PMID: 35348273 PMCID: PMC9324954 DOI: 10.1002/anie.202202295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Indexed: 11/12/2022]
Abstract
Pd0 catalysts featuring phosphorus-based monodentate ligands can detour the reactivity of carbonyl-tethered alkylidenecyclopropanes (ACPs) from standard (3+2) cycloadditions towards tandem cycloisomerization/cross-coupling processes. This new reactivity lies on the formation of key π-allyl oxapalladacyclic intermediates, which are subsequently trapped with external nucleophilic partners, instead of undergoing canonical C-O reductive eliminations. Importantly, the use of imine-tethered ACP's is also feasible. Therefore, the method provides a straightforward and stereoselective entry to a wide variety of highly functionalized cyclic alcohols and amines.
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Affiliation(s)
- Felipe Verdugo
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química OrgánicaUniversidad de Santiago de CompostelaSpain
| | - Ricardo Rodiño
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química OrgánicaUniversidad de Santiago de CompostelaSpain
| | - Martín Calvelo
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química OrgánicaUniversidad de Santiago de CompostelaSpain
| | - José Luis Mascareñas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química OrgánicaUniversidad de Santiago de CompostelaSpain
| | - Fernando López
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química OrgánicaUniversidad de Santiago de CompostelaSpain
- Misión Biológica de Galicia (MBG), ConsejoSuperior de Investigaciones Científicas (CSIC)36680PontevedraSpain
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5
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Verdugo F, Rodiño R, Calvelo M, Mascareñas JL, López F. Palladium‐Catalyzed Tandem Cycloisomerization/Cross‐Coupling of Carbonyl‐ and Imine‐Tethered Alkylidenecyclopropanes. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202202295] [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)
- Felipe Verdugo
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica Universidad de Santiago de Compostela Spain
| | - Ricardo Rodiño
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica Universidad de Santiago de Compostela Spain
| | - Martín Calvelo
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica Universidad de Santiago de Compostela Spain
| | - José Luis Mascareñas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica Universidad de Santiago de Compostela Spain
| | - Fernando López
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica Universidad de Santiago de Compostela Spain
- Misión Biológica de Galicia (MBG), Consejo Superior de Investigaciones Científicas (CSIC) 36680 Pontevedra Spain
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6
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Dardir AH, Casademont-Reig I, Balcells D, Ellefsen JD, Espinosa MR, Hazari N, Smith NE. Synthesis of Triarylmethanes via Palladium-Catalyzed Suzuki–Miyaura Reactions of Diarylmethyl Esters. Organometallics 2021; 40:2332-2344. [DOI: 10.1021/acs.organomet.1c00085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Amira H. Dardir
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520, United States
| | - Irene Casademont-Reig
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, P.O. Box 1033, Blindern, N-0315 Oslo, Norway
- Donostia International Physics Center (DIPC), 20018 Donostia, Euskadi, Spain
- Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), 20080 Donostia, Euskadi, Spain
| | - David Balcells
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, P.O. Box 1033, Blindern, N-0315 Oslo, Norway
| | - Jonathan D. Ellefsen
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520, United States
| | - Matthew R. Espinosa
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520, United States
| | - Nilay Hazari
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520, United States
| | - Nicholas E. Smith
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520, United States
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7
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Verdugo F, da Concepción E, Rodiño R, Calvelo M, Mascareñas JL, López F. Pd-Catalyzed (3 + 2) Heterocycloadditions between Alkylidenecyclopropanes and Carbonyls: Straightforward Assembly of Highly Substituted Tetrahydrofurans. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01827] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Felipe Verdugo
- Centro Singular de Investigación en Quı́mica Biolóxica e Materiais Moleculares (CiQUS) and Departamento de Quı́mica Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Eduardo da Concepción
- Centro Singular de Investigación en Quı́mica Biolóxica e Materiais Moleculares (CiQUS) and Departamento de Quı́mica Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Ricardo Rodiño
- Centro Singular de Investigación en Quı́mica Biolóxica e Materiais Moleculares (CiQUS) and Departamento de Quı́mica Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Martín Calvelo
- Centro Singular de Investigación en Quı́mica Biolóxica e Materiais Moleculares (CiQUS) and Departamento de Quı́mica Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - José L. Mascareñas
- Centro Singular de Investigación en Quı́mica Biolóxica e Materiais Moleculares (CiQUS) and Departamento de Quı́mica Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Fernando López
- Centro Singular de Investigación en Quı́mica Biolóxica e Materiais Moleculares (CiQUS) and Departamento de Quı́mica Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
- Instituto de Quı́mica Orgánica General (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
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8
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Yang JJ, Xu Z, Nie YX, Lu SQ, Zhang J, Xu LW. Long-Distance Chirality Transfer from P-Ligand to Prochiral Dihydrosilanes via Pd(II) Aryl Iodide Complex in Pd-Catalyzed Silylation of Aryl Iodide: A DFT Study. J Org Chem 2020; 85:14360-14368. [DOI: 10.1021/acs.joc.0c00202] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jing-Jing Yang
- Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education, and Key Laboratory of Organosilicon Material Technology of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, P.R. China
| | - Zheng Xu
- Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education, and Key Laboratory of Organosilicon Material Technology of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, P.R. China
| | - Yi-Xue Nie
- Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education, and Key Laboratory of Organosilicon Material Technology of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, P.R. China
| | - Si-Qi Lu
- Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education, and Key Laboratory of Organosilicon Material Technology of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, P.R. China
| | - Jin Zhang
- Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education, and Key Laboratory of Organosilicon Material Technology of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, P.R. China
| | - Li-Wen Xu
- Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education, and Key Laboratory of Organosilicon Material Technology of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, P.R. China
- State Key Laboratory for Oxo Synthesis and Selective Oxidation, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, P.R. China
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9
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Three-phenyl transfer in palladium-catalyzed C C coupling reactions by triarylbismuths: A mechanistic study. MOLECULAR CATALYSIS 2020. [DOI: 10.1016/j.mcat.2019.110649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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10
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Wagschal S, Perego LA, Simon A, Franco-Espejo A, Tocqueville C, Albaneze-Walker J, Jutand A, Grimaud L. Formation of XPhos-Ligated Palladium(0) Complexes and Reactivity in Oxidative Additions. Chemistry 2019; 25:6980-6987. [PMID: 30920694 DOI: 10.1002/chem.201900451] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Indexed: 12/17/2022]
Abstract
Understanding the nature of the intermediate species operating within a palladium catalytic cycle is crucial for developing efficient cross-coupling reactions. Even though the XPhos/Pd(OAc)2 catalytic system has found numerous applications, the nature of the active catalytic species remains elusive. A Pd0 complex ligated to XPhos has been detected and characterized in situ for the first time using cyclic voltammetry and NMR techniques. In the presence of XPhos, Pd(OAc)2 initially associates with the ligand to form a complex in solution, which has been characterized as PdII (OAc)2 (XPhos). This PdII center is then reduced to the Pd0 (XPhos)2 species by an intramolecular process. This study also sheds light on the formation of PdI -PdI dimers. Finally, a kinetic study probes a dissociative mechanism for the oxidative addition with aryl halides involving Pd0 (XPhos) as the reactive species in equilibrium with the unreactive Pd0 (XPhos)2 . Remarkably, the reportedly poorly reactive PhCl reacts at room temperature in the oxidative addition, which confirms the crucial role of the XPhos ligand in the activation of aryl chlorides.
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Affiliation(s)
- Simon Wagschal
- Discovery Product Development and Supply, Janssen Pharmaceutica, Hochstrasse 201, 8200, Schaffhausen, Switzerland
| | - Luca Alessandro Perego
- PASTEUR, Département de Chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Alexandre Simon
- PASTEUR, Département de Chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Aida Franco-Espejo
- PASTEUR, Département de Chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Chanelle Tocqueville
- PASTEUR, Département de Chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Jennifer Albaneze-Walker
- Discovery Product Development and Supply, Janssen Pharmaceutica, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Anny Jutand
- PASTEUR, Département de Chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Laurence Grimaud
- PASTEUR, Département de Chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
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11
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Uthayopas C, Surawatanawong P. Aryl C–O oxidative addition of phenol derivatives to nickel supported by an N-heterocyclic carbene via a Ni0 five-centered complex. Dalton Trans 2019; 48:7817-7827. [DOI: 10.1039/c9dt00455f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An aryl ether with the assistance of organoaluminum, an aryl sulfonate/sulfamate and an ester/carbamate proceeds towards C–O bond cleavage via a Ni0 five-centered complex.
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Affiliation(s)
- Chayapat Uthayopas
- Department of Chemistry and Center of Excellence for Innovation in Chemistry
- Faculty of Science
- Mahidol University
- Bangkok 10400
- Thailand
| | - Panida Surawatanawong
- Department of Chemistry and Center of Excellence for Innovation in Chemistry
- Faculty of Science
- Mahidol University
- Bangkok 10400
- Thailand
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