1
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Laplaza R, Wodrich MD, Corminboeuf C. Overcoming the Pitfalls of Computing Reaction Selectivity from Ensembles of Transition States. J Phys Chem Lett 2024; 15:7363-7370. [PMID: 38990895 DOI: 10.1021/acs.jpclett.4c01657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
The prediction of reaction selectivity is a challenging task for computational chemistry, not only because many molecules adopt multiple conformations but also due to the exponential relationship between effective activation energies and rate constants. To account for molecular flexibility, an increasing number of methods exist that generate conformational ensembles of transition state (TS) structures. Typically, these TS ensembles are Boltzmann weighted and used to compute selectivity assuming Curtin-Hammett conditions. This strategy, however, can lead to erroneous predictions if the appropriate filtering of the conformer ensembles is not conducted. Here, we demonstrate how any possible selectivity can be obtained by processing the same sets of TS ensembles for a model reaction. To address the burdensome filtering task in a consistent and automated way, we introduce marc, a tool for the modular analysis of representative conformers that aids in avoiding human errors while minimizing the number of reoptimization computations needed to obtain correct reaction selectivity.
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Affiliation(s)
- Ruben Laplaza
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- National Center for Competence in Research-Catalysis (NCCR-Catalysis), École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Matthew D Wodrich
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- National Center for Competence in Research-Catalysis (NCCR-Catalysis), École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Clemence Corminboeuf
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- National Center for Competence in Research-Catalysis (NCCR-Catalysis), École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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2
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Affiliation(s)
- Shuning Mao
- Department of Chemistry; Lishui University No. 1; Xueyuan Road 323000 Lishui City Zhejiang Province P. R. China
| | - Kaijun Chen
- Department of Chemistry; Lishui University No. 1; Xueyuan Road 323000 Lishui City Zhejiang Province P. R. China
| | - Guobing Yan
- Department of Chemistry; Lishui University No. 1; Xueyuan Road 323000 Lishui City Zhejiang Province P. R. China
| | - Dayun Huang
- Department of Chemistry; Lishui University No. 1; Xueyuan Road 323000 Lishui City Zhejiang Province P. R. China
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3
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Post-translational site-selective protein backbone α-deuteration. Nat Chem Biol 2018; 14:955-963. [DOI: 10.1038/s41589-018-0128-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 07/19/2018] [Indexed: 01/29/2023]
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4
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Gao W, Gong C, Yang Q, Yuan J, Xu L, Peng Y. Rh(III)-catalyzed oxidative ortho-C–H alkylation of 2,4-diarylquinazoline with potassium alkyltrifluoroborates. CAN J CHEM 2017. [DOI: 10.1139/cjc-2017-0258] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Alkyltrifluoroborates were used for Rh(III)-catalyzed ortho-alkylation of 2,4-disubstituted quinazoline via C–H bond activation. The reaction proceeded well with a broad substrate scope, providing a direct way to access high functional quinazoline core structure derivatives in yields up to 95%.
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Affiliation(s)
- Wei Gao
- Key Laboratory of Functional Small Organic Molecules, Ministry of Education; Jiangxi Province’s Key Laboratory of Green Chemistry and Jiangxi Normal University, Nanchang, Jiangxi 330022, China
- Jiangxi Academy of Forestry, Nanchang, Jiangxi 330013, China
| | - Chun Gong
- Jiangxi Academy of Forestry, Nanchang, Jiangxi 330013, China
| | - Qin Yang
- Key Laboratory of Functional Small Organic Molecules, Ministry of Education; Jiangxi Province’s Key Laboratory of Green Chemistry and Jiangxi Normal University, Nanchang, Jiangxi 330022, China
| | - Jianjun Yuan
- Key Laboratory of Functional Small Organic Molecules, Ministry of Education; Jiangxi Province’s Key Laboratory of Green Chemistry and Jiangxi Normal University, Nanchang, Jiangxi 330022, China
| | - Linchu Xu
- Jiangxi Academy of Forestry, Nanchang, Jiangxi 330013, China
| | - Yiyuan Peng
- Key Laboratory of Functional Small Organic Molecules, Ministry of Education; Jiangxi Province’s Key Laboratory of Green Chemistry and Jiangxi Normal University, Nanchang, Jiangxi 330022, China
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5
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Li Y, Jackson KE, Charlton A, Le Neve-Foster B, Khurshid A, Rudy HKA, Thompson AL, Paton RS, Hodgson DM. Asymmetric Induction in C-Alkylation of Tropane-Derived Enamines: Congruence Between Computation and Experiment. J Org Chem 2017; 82:10479-10488. [DOI: 10.1021/acs.joc.7b01954] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yifei Li
- Department of Chemistry,
Chemistry Research Laboratory, University of Oxford, Mansfield
Road, Oxford OX1 3TA, U.K
| | - Kelvin E. Jackson
- Department of Chemistry,
Chemistry Research Laboratory, University of Oxford, Mansfield
Road, Oxford OX1 3TA, U.K
| | - Andrew Charlton
- Department of Chemistry,
Chemistry Research Laboratory, University of Oxford, Mansfield
Road, Oxford OX1 3TA, U.K
| | - Ben Le Neve-Foster
- Department of Chemistry,
Chemistry Research Laboratory, University of Oxford, Mansfield
Road, Oxford OX1 3TA, U.K
| | - Asma Khurshid
- Department of Chemistry,
Chemistry Research Laboratory, University of Oxford, Mansfield
Road, Oxford OX1 3TA, U.K
| | - Heinrich-K. A. Rudy
- Department of Chemistry,
Chemistry Research Laboratory, University of Oxford, Mansfield
Road, Oxford OX1 3TA, U.K
| | - Amber L. Thompson
- Department of Chemistry,
Chemistry Research Laboratory, University of Oxford, Mansfield
Road, Oxford OX1 3TA, U.K
| | - Robert S. Paton
- Department of Chemistry,
Chemistry Research Laboratory, University of Oxford, Mansfield
Road, Oxford OX1 3TA, U.K
| | - David. M. Hodgson
- Department of Chemistry,
Chemistry Research Laboratory, University of Oxford, Mansfield
Road, Oxford OX1 3TA, U.K
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6
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Liu YW, Han P, Zhou W, Mao ZY, Si CM, Wei BG. Asymmetric syntheses of epohelmins A and B by In-mediated allylation. Org Biomol Chem 2016; 14:10714-10722. [PMID: 27805230 DOI: 10.1039/c6ob02212j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A diastereoselective new approach for the synthesis of trans-4-hydroxy-5-allyl-2-pyrrolidinone 9 has been developed through In-mediated allylation of α-chiral aldimine 8 with allyl bromide. The stereochemistry at the C-2 stereogenic center of 9 was controlled by both the α-OTBS substitution and the sulfinamide moiety. The utility of this asymmetric allylation is demonstrated by the asymmetric syntheses of epohelmins A (4) and B (10).
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Affiliation(s)
- Yi-Wen Liu
- Department of Natural Products Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, 201203, China.
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7
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Simón L, Paton RS. QM/MM study on the enantioselectivity of spiroacetalization catalysed by an imidodiphosphoric acid catalyst: how confinement works. Org Biomol Chem 2016; 14:3031-9. [DOI: 10.1039/c6ob00045b] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An explanation of why confined imidodiphosphoric acid catalyst succeeds where other chiral phosphoric acid catalysts fail.
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Affiliation(s)
- Luis Simón
- Facultad de Ciencias Químicas
- Universidad de Salamanca
- Salamanca E37004
- Spain
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8
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Asymmetric intramolecular α-cyclopropanation of aldehydes using a donor/acceptor carbene mimetic. Nat Commun 2015; 6:10041. [PMID: 26644194 PMCID: PMC4686670 DOI: 10.1038/ncomms10041] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 10/26/2015] [Indexed: 01/12/2023] Open
Abstract
Enantioselective α-alkylation of carbonyl is considered as one of the most important processes for asymmetric synthesis. Common alkylation agents, that is, alkyl halides, are notorious substrates for both Lewis acids and organocatalysts. Recently, olefins emerged as a benign alkylating species via photo/radical mechanisms. However, examples of enantioselective alkylation of aldehydes/ketones are scarce and direct asymmetric dialkylation remains elusive. Here we report an intramolecular α-cyclopropanation reaction of olefinic aldehydes to form chiral cyclopropane aldehydes. We demonstrate that an α-iodo aldehyde can function as a donor/acceptor carbene equivalent, which engages in a formal [2+1] annulation with a tethered double bond. Privileged bicyclo[3.1.0]hexane-type scaffolds are prepared in good optical purity using a chiral amine. The synthetic utility of the products is demonstrated by versatile transformations of the bridgehead formyl functionality. We expect the concept of using α-iodo iminium as a donor/acceptor carbene surrogate will find wide applications in chemical reaction development. The formation of chiral centres adjacent to carbonyl groups is a highly challenging task in asymmetric catalysis. Here, the authors report the asymmetric diakylation of carbonyls via an intramolceular α-cyclopropanation procedure.
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9
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Jackson KE, Mortimer CL, Odell B, McKenna JM, Claridge TDW, Paton RS, Hodgson DM. α- and α'-Lithiation-Electrophile Trapping of N-Thiopivaloyl and N-tert-Butoxythiocarbonyl α-Substituted Azetidines: Rationalization of the Regiodivergence Using NMR and Computation. J Org Chem 2015; 80:9838-46. [PMID: 26401908 DOI: 10.1021/acs.joc.5b01804] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
(1)H NMR and computational analyses provide insight into the regiodivergent (α- and α'-) lithiation-electrophile trapping of N-thiopivaloyl- and N-(tert-butoxythiocarbonyl)-α-alkylazetidines. The magnitudes of the rotation barriers in these azetidines indicate that rotamer interconversions do not occur at the temperature and on the time scale of the lithiations. The NMR and computational studies support the origin of regioselectivity as being thiocarbonyl-directed lithiation from the lowest energy amide-like rotameric forms (cis for N-thiopivaloyl and trans for N-tert-butoxythiocarbonyl).
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Affiliation(s)
- Kelvin E Jackson
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford , Mansfield Road, Oxford OX1 3TA, U.K
| | - Claire L Mortimer
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford , Mansfield Road, Oxford OX1 3TA, U.K
| | - Barbara Odell
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford , Mansfield Road, Oxford OX1 3TA, U.K
| | - Jeffrey M McKenna
- Novartis Institutes for BioMedical Research , Wimblehurst Road, Horsham, West Sussex RH12 5AB, U.K
| | - Timothy D W Claridge
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford , Mansfield Road, Oxford OX1 3TA, U.K
| | - Robert S Paton
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford , Mansfield Road, Oxford OX1 3TA, U.K
| | - David M Hodgson
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford , Mansfield Road, Oxford OX1 3TA, U.K
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10
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Si CM, Mao ZY, Liu YW, Du ZT, Wei BG, Lin GQ. Stereoselective formation of chiral trans-4-hydroxy-5-substituted 2-pyrrolidinones: syntheses of streptopyrrolidine and 3-epi-epohelmin A. Org Chem Front 2015. [DOI: 10.1039/c5qo00250h] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A highly diastereoselective approach for synthesis of trans-4-hydroxy-5-substituted 2-pyrrolidinones has been developed. The streptopyrrolidine and 3-epi-epohelmin A were synthesized by this one-pot cascade protocol.
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Affiliation(s)
- Chang-Mei Si
- Department of Natural Products Chemistry
- School of Pharmacy
- Fudan University
- Shanghai 201203
- China
| | - Zhuo-Ya Mao
- Department of Natural Products Chemistry
- School of Pharmacy
- Fudan University
- Shanghai 201203
- China
| | - Yi-Wen Liu
- Department of Natural Products Chemistry
- School of Pharmacy
- Fudan University
- Shanghai 201203
- China
| | - Zhen-Ting Du
- College of Science
- Northwest Agriculture and Forestry University
- Shaanxi, Yangling
- China
| | - Bang-Guo Wei
- Department of Natural Products Chemistry
- School of Pharmacy
- Fudan University
- Shanghai 201203
- China
| | - Guo-Qiang Lin
- Shanghai Institute of Organic Chemistry
- Chinese Academy of Sciences
- Shanghai 200032
- China
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11
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12
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Yu Y, Yang XF, Xu CF, Ding CH, Hou XL. Desymmetrization of Bicyclo[3.n.1]-3-one Derivatives by Palladium-Catalyzed Asymmetric Allylic Alkylation. Org Lett 2013; 15:3880-3. [DOI: 10.1021/ol4016207] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yang Yu
- State Key Laboratory of Organometallic Chemistry, Shanghai-Hong Kong Joint Laboratory in Chemical Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Xiao-Fei Yang
- State Key Laboratory of Organometallic Chemistry, Shanghai-Hong Kong Joint Laboratory in Chemical Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Chao-Fan Xu
- State Key Laboratory of Organometallic Chemistry, Shanghai-Hong Kong Joint Laboratory in Chemical Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Chang-Hua Ding
- State Key Laboratory of Organometallic Chemistry, Shanghai-Hong Kong Joint Laboratory in Chemical Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Xue-Long Hou
- State Key Laboratory of Organometallic Chemistry, Shanghai-Hong Kong Joint Laboratory in Chemical Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
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