1
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Yamaguchi S. Molecular field analysis for data-driven molecular design in asymmetric catalysis. Org Biomol Chem 2022; 20:6057-6071. [PMID: 35791843 DOI: 10.1039/d2ob00228k] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This review highlights the recent advances (2019-present) in the use of MFA (molecular field analysis) for data-driven catalyst design, enabling to improve selectivities/reaction outcomes in asymmetric catalysis. Successful examples of MFA-based molecular design and how to design molecules by MFA are described, including how to generate and evaluate MFA-based regression models, and future challenges in MFA-based molecular design in molecular catalysis.
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Affiliation(s)
- Shigeru Yamaguchi
- RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
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2
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Lustosa DM, Milo A. Mechanistic Inference from Statistical Models at Different Data-Size Regimes. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Danilo M. Lustosa
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Anat Milo
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
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3
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4
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Golub T, Kano T, Maruoka K, Merten C. VCD spectroscopy distinguishes the enamine and iminium ion of a 1,1’-binaphthyl azepine. Chem Commun (Camb) 2022; 58:8412-8415. [DOI: 10.1039/d2cc02863h] [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
We present a VCD spectroscopic characterization of a chiral 1,1’-binaphthyl azepine catalyst and show that the VCD spectra of an in-situ generated enamine and an ex-situ prepared iminium ion are...
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5
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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.
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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.
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6
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Maley SM, Kwon DH, Rollins N, Stanley JC, Sydora OL, Bischof SM, Ess DH. Quantum-mechanical transition-state model combined with machine learning provides catalyst design features for selective Cr olefin oligomerization. Chem Sci 2020; 11:9665-9674. [PMID: 34094231 PMCID: PMC8161675 DOI: 10.1039/d0sc03552a] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 08/20/2020] [Indexed: 12/20/2022] Open
Abstract
The use of data science tools to provide the emergence of non-trivial chemical features for catalyst design is an important goal in catalysis science. Additionally, there is currently no general strategy for computational homogeneous, molecular catalyst design. Here, we report the unique combination of an experimentally verified DFT-transition-state model with a random forest machine learning model in a campaign to design new molecular Cr phosphine imine (Cr(P,N)) catalysts for selective ethylene oligomerization, specifically to increase 1-octene selectivity. This involved the calculation of 1-hexene : 1-octene transition-state selectivity for 105 (P,N) ligands and the harvesting of 14 descriptors, which were then used to build a random forest regression model. This model showed the emergence of several key design features, such as Cr-N distance, Cr-α distance, and Cr distance out of pocket, which were then used to rapidly design a new generation of Cr(P,N) catalyst ligands that are predicted to give >95% selectivity for 1-octene.
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Affiliation(s)
- Steven M Maley
- Department of Chemistry and Biochemistry, Brigham Young University Provo Utah 84602 USA
| | - Doo-Hyun Kwon
- Department of Chemistry and Biochemistry, Brigham Young University Provo Utah 84602 USA
| | - Nick Rollins
- Department of Chemistry and Biochemistry, Brigham Young University Provo Utah 84602 USA
| | - Johnathan C Stanley
- Department of Chemistry and Biochemistry, Brigham Young University Provo Utah 84602 USA
| | - Orson L Sydora
- Research and Technology, Chevron Phillips Chemical Company LP 1862, Kingwood Drive Kingwood Texas 77339 USA
| | - Steven M Bischof
- Research and Technology, Chevron Phillips Chemical Company LP 1862, Kingwood Drive Kingwood Texas 77339 USA
| | - Daniel H Ess
- Department of Chemistry and Biochemistry, Brigham Young University Provo Utah 84602 USA
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7
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Gerosa GG, Marcarino MO, Spanevello RA, Suárez AG, Sarotti AM. Re-Engineering Organocatalysts for Asymmetric Friedel–Crafts Alkylation of Indoles through Computational Studies. J Org Chem 2020; 85:9969-9978. [DOI: 10.1021/acs.joc.0c01256] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Gabriela G. Gerosa
- Instituto de Quı́mica Rosario (CONICET-UNR), Facultad de Ciencias Bioquı́micas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina
| | - Maribel O. Marcarino
- Instituto de Quı́mica Rosario (CONICET-UNR), Facultad de Ciencias Bioquı́micas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina
| | - Rolando A. Spanevello
- Instituto de Quı́mica Rosario (CONICET-UNR), Facultad de Ciencias Bioquı́micas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina
| | - Alejandra G. Suárez
- Instituto de Quı́mica Rosario (CONICET-UNR), Facultad de Ciencias Bioquı́micas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina
| | - Ariel M. Sarotti
- Instituto de Quı́mica Rosario (CONICET-UNR), Facultad de Ciencias Bioquı́micas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina
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8
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Zahrt AF, Athavale SV, Denmark SE. Quantitative Structure-Selectivity Relationships in Enantioselective Catalysis: Past, Present, and Future. Chem Rev 2020; 120:1620-1689. [PMID: 31886649 PMCID: PMC7018559 DOI: 10.1021/acs.chemrev.9b00425] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The dawn of the 21st century has brought with it a surge of research related to computer-guided approaches to catalyst design. In the past two decades, chemoinformatics, the application of informatics to solve problems in chemistry, has increasingly influenced prediction of activity and mechanistic investigations of organic reactions. The advent of advanced statistical and machine learning methods, as well as dramatic increases in computational speed and memory, has contributed to this emerging field of study. This review summarizes strategies to employ quantitative structure-selectivity relationships (QSSR) in asymmetric catalytic reactions. The coverage is structured by initially introducing the basic features of these methods. Subsequent topics are discussed according to increasing complexity of molecular representations. As the most applied subfield of QSSR in enantioselective catalysis, the application of local parametrization approaches and linear free energy relationships (LFERs) along with multivariate modeling techniques is described first. This section is followed by a description of global parametrization methods, the first of which is continuous chirality measures (CCM) because it is a single parameter derived from the global structure of a molecule. Chirality codes, global, multivariate descriptors, are then introduced followed by molecular interaction fields (MIFs), a global descriptor class that typically has the highest dimensionality. To highlight the current reach of QSSR in enantioselective transformations, a comprehensive collection of examples is presented. When combined with traditional experimental approaches, chemoinformatics holds great promise to predict new catalyst structures, rationalize mechanistic behavior, and profoundly change the way chemists discover and optimize reactions.
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Affiliation(s)
- Andrew F. Zahrt
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, IL 61801
| | - Soumitra V. Athavale
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, IL 61801
| | - Scott E. Denmark
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, IL 61801
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9
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Affiliation(s)
- Marco Foscato
- Department of Chemistry, University of Bergen, Allégaten 41, N-5007 Bergen, Norway
| | - Vidar R. Jensen
- Department of Chemistry, University of Bergen, Allégaten 41, N-5007 Bergen, Norway
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10
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Cheng C, Li Y, Zhang J, Zhao Y, Zhang L, Li C, Yang Y, Tang L, Yang Y. Organo‐Catalyzed Asymmetric Amination of 4‐Arylisoquinoline‐1,3(2
H
,4
H
)‐dione Derivatives in the Construction of Quaternary Stereocenters. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201900980] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Cheng Cheng
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, School of PharmacyGuizhou Medical University Guiyang 550014 People's Republic of China
| | - Ying‐Xian Li
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, School of PharmacyGuizhou Medical University Guiyang 550014 People's Republic of China
| | - Ji‐Quan Zhang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, School of PharmacyGuizhou Medical University Guiyang 550014 People's Republic of China
| | - Yong‐Long Zhao
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, School of PharmacyGuizhou Medical University Guiyang 550014 People's Republic of China
| | - Lin Zhang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, School of PharmacyGuizhou Medical University Guiyang 550014 People's Republic of China
| | - Chun Li
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, School of PharmacyGuizhou Medical University Guiyang 550014 People's Republic of China
| | - Yu‐she Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia MedicaChinese Academy of Sciences Shanghai 201203 People's Republic of China
| | - Lei Tang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, School of PharmacyGuizhou Medical University Guiyang 550014 People's Republic of China
| | - Yuan‐Yong Yang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, School of PharmacyGuizhou Medical University Guiyang 550014 People's Republic of China
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11
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Yamaguchi S, Sodeoka M. Molecular Field Analysis Using Intermediates in Enantio-Determining Steps Can Extract Information for Data-Driven Molecular Design in Asymmetric Catalysis. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2019. [DOI: 10.1246/bcsj.20190132] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Shigeru Yamaguchi
- RIKEN Center for Sustainable Resource Science, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Mikiko Sodeoka
- RIKEN Center for Sustainable Resource Science, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- RIKEN Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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12
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Ahn S, Hong M, Sundararajan M, Ess DH, Baik MH. Design and Optimization of Catalysts Based on Mechanistic Insights Derived from Quantum Chemical Reaction Modeling. Chem Rev 2019; 119:6509-6560. [DOI: 10.1021/acs.chemrev.9b00073] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Seihwan Ahn
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Mannkyu Hong
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Mahesh Sundararajan
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Daniel H. Ess
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Mu-Hyun Baik
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
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13
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14
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Voss M, Das D, Genz M, Kumar A, Kulkarni N, Kustosz J, Kumar P, Bornscheuer UT, Höhne M. In Silico Based Engineering Approach to Improve Transaminases for the Conversion of Bulky Substrates. ACS Catal 2018. [DOI: 10.1021/acscatal.8b03900] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Moritz Voss
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Devashish Das
- Quantumzyme, LLP, No. 110/8, Krishnappa Layout, Lalbagh Road, Bangalore 560027, India
| | - Maika Genz
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Anurag Kumar
- Quantumzyme, LLP, No. 110/8, Krishnappa Layout, Lalbagh Road, Bangalore 560027, India
| | - Naveen Kulkarni
- Quantumzyme, LLP, No. 110/8, Krishnappa Layout, Lalbagh Road, Bangalore 560027, India
| | - Jakub Kustosz
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Pravin Kumar
- Quantumzyme, LLP, No. 110/8, Krishnappa Layout, Lalbagh Road, Bangalore 560027, India
| | - Uwe T. Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Matthias Höhne
- Protein Biochemistry, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
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15
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Rosales AR, Quinn TR, Wahlers J, Tomberg A, Zhang X, Helquist P, Wiest O, Norrby PO. Application of Q2MM to predictions in stereoselective synthesis. Chem Commun (Camb) 2018; 54:8294-8311. [PMID: 29971313 DOI: 10.1039/c8cc03695k] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Quantum-Guided Molecular Mechanics (Q2MM) can be used to derive transition state force fields (TSFFs) that allow the fast and accurate predictions of stereoselectivity for a wide range of catalytic enantioselective reactions. The basic ideas behind the derivation of TSFFs using Q2MM are discussed and the steps involved in obtaining a TSFF using the Q2MM code, publically available at github.com/q2mm, are shown. The applicability for a range of reactions, including several non-standard applications of Q2MM, is demonstrated. Future developments of the method are also discussed.
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Affiliation(s)
- Anthony R Rosales
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
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16
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Huber R, Passera A, Gubler E, Mezzetti A. P-Stereogenic PN(H)P Iron(II) Catalysts for the Asymmetric Hydrogenation of Ketones: The Importance of Non-Covalent Interactions in Rational Ligand Design by Computation. Adv Synth Catal 2018. [DOI: 10.1002/adsc.201800433] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Raffael Huber
- Dept. of Chemistry and Applied Biosciences; ETH Zürich; Switzerland
| | | | - Erik Gubler
- Dept. of Chemistry and Applied Biosciences; ETH Zürich; Switzerland
| | - Antonio Mezzetti
- Dept. of Chemistry and Applied Biosciences; ETH Zürich; Switzerland
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17
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Zhu F, Xie Y, Zhang J, Tian G, Qin H, Yang X, Hu T, He Y, Aisa HA, Shen J. A Facile Epoxide Aminolysis Promoted by ( t-BuO) 2Mg and Its Application to the Synthesis of Efinaconazole. Org Process Res Dev 2018. [DOI: 10.1021/acs.oprd.8b00081] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Fuqiang Zhu
- Key Laboratory of Plant Resources and Chemistry in Arid Regions, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, South Beijing Road 40-1, Urumqi, Xinjiang 830011, P. R. China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, P. R. China
| | - Yuanchao Xie
- CAS Key Laboratory for Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
| | - Jian Zhang
- Topharman Shanghai Co., Ltd., Building 1, No. 388 Jialilue Road, Zhangjiang Hitech Park, Shanghai 201209, P. R. China
| | - Guanghui Tian
- Topharman Shanghai Co., Ltd., Building 1, No. 388 Jialilue Road, Zhangjiang Hitech Park, Shanghai 201209, P. R. China
| | - Hongjian Qin
- Topharman Shanghai Co., Ltd., Building 1, No. 388 Jialilue Road, Zhangjiang Hitech Park, Shanghai 201209, P. R. China
| | - Xiaojun Yang
- Topharman Shanghai Co., Ltd., Building 1, No. 388 Jialilue Road, Zhangjiang Hitech Park, Shanghai 201209, P. R. China
| | - Tianwen Hu
- Topharman Shanghai Co., Ltd., Building 1, No. 388 Jialilue Road, Zhangjiang Hitech Park, Shanghai 201209, P. R. China
| | - Yang He
- CAS Key Laboratory for Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
| | - Haji A. Aisa
- Key Laboratory of Plant Resources and Chemistry in Arid Regions, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, South Beijing Road 40-1, Urumqi, Xinjiang 830011, P. R. China
| | - Jingshan Shen
- CAS Key Laboratory for Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
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18
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Pastor J, Rezabal E, Voituriez A, Betzer JF, Marinetti A, Frison G. Revised Theoretical Model on Enantiocontrol in Phosphoric Acid Catalyzed H-Transfer Hydrogenation of Quinoline. J Org Chem 2018; 83:2779-2787. [DOI: 10.1021/acs.joc.7b03248] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Julien Pastor
- LCM,
CNRS, Ecole polytechnique, Université Paris-Saclay, 91128 Palaiseau, France
| | - Elixabete Rezabal
- LCM,
CNRS, Ecole polytechnique, Université Paris-Saclay, 91128 Palaiseau, France
- Kimika
Fakultatea, Euskal Herriko Unibertsitatea UPV/EHU, Donostia International Physics Center (DIPC), P.K. 1072, 20080 Donostia, Euskadi Spain
| | - Arnaud Voituriez
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Jean-François Betzer
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Angela Marinetti
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Gilles Frison
- LCM,
CNRS, Ecole polytechnique, Université Paris-Saclay, 91128 Palaiseau, France
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19
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Kwon DH, Fuller JT, Kilgore UJ, Sydora OL, Bischof SM, Ess DH. Computational Transition-State Design Provides Experimentally Verified Cr(P,N) Catalysts for Control of Ethylene Trimerization and Tetramerization. ACS Catal 2018. [DOI: 10.1021/acscatal.7b04026] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Doo-Hyun Kwon
- Department
of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Jack T. Fuller
- Department
of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Uriah J. Kilgore
- Research and Technology, Chevron Phillips Chemical Company LP, 1862 Kingwood Drive, Kingwood, Texas 77339, 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
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20
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Korenaga T, Sasaki R, Takemoto T, Yasuda T, Watanabe M. Computationally-Led Ligand Modification using Interplay between Theory and Experiments: Highly Active Chiral Rhodium Catalyst Controlled by Electronic Effects and CH-π Interactions. Adv Synth Catal 2018. [DOI: 10.1002/adsc.201701191] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Toshinobu Korenaga
- Department of Chemistry and Biological Sciences, Faculty of Science and Engineering; Iwate University; 4-3-5 Ueda Morioka, Iwate 020-8551 Japan
| | - Ryo Sasaki
- Department of Chemistry and Biological Sciences, Faculty of Science and Engineering; Iwate University; 4-3-5 Ueda Morioka, Iwate 020-8551 Japan
| | - Toshihide Takemoto
- Central Research Laboratory, Technology and Development Division; Kanto Chemical Co., Inc., Soka; Saitama 340-0003 Japan
| | - Toshihisa Yasuda
- Central Research Laboratory, Technology and Development Division; Kanto Chemical Co., Inc., Soka; Saitama 340-0003 Japan
| | - Masahito Watanabe
- Central Research Laboratory, Technology and Development Division; Kanto Chemical Co., Inc., Soka; Saitama 340-0003 Japan
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21
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Fianchini M. Synthesis meets theory: Past, present and future of rational chemistry. PHYSICAL SCIENCES REVIEWS 2017. [DOI: 10.1515/psr-2017-0134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Abstract
Chemical synthesis has its roots in the empirical approach of alchemy. Nonetheless, the birth of the scientific method, the technical and technological advances (exploiting revolutionary discoveries in physics) and the improved management and sharing of growing databases greatly contributed to the evolution of chemistry from an esoteric ground into a mature scientific discipline during these last 400 years. Furthermore, thanks to the evolution of computational resources, platforms and media in the last 40 years, theoretical chemistry has added to the puzzle the final missing tile in the process of “rationalizing” chemistry. The use of mathematical models of chemical properties, behaviors and reactivities is nowadays ubiquitous in literature. Theoretical chemistry has been successful in the difficult task of complementing and explaining synthetic results and providing rigorous insights when these are otherwise unattainable by experiment. The first part of this review walks the reader through a concise historical overview on the evolution of the “model” in chemistry. Salient milestones have been highlighted and briefly discussed. The second part focuses more on the general description of recent state-of-the-art computational techniques currently used worldwide by chemists to produce synergistic models between theory and experiment. Each section is complemented by key-examples taken from the literature that illustrate the application of the technique discussed therein.
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22
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Ardkhean R, Roth PMC, Maksymowicz RM, Curran A, Peng Q, Paton RS, Fletcher SP. Enantioselective Conjugate Addition Catalyzed by a Copper Phosphoramidite Complex: Computational and Experimental Exploration of Asymmetric Induction. ACS Catal 2017. [DOI: 10.1021/acscatal.7b01453] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Ruchuta Ardkhean
- Chemistry
Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Philippe M. C. Roth
- Chemistry
Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Rebecca M. Maksymowicz
- Chemistry
Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Alex Curran
- Chemistry
Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Qian Peng
- State
Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, People’s Republic of China
| | - Robert S. Paton
- Chemistry
Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Stephen P. Fletcher
- Chemistry
Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
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23
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García-López D, Cid J, Marqués R, Fernández E, Carbó JJ. Quantitative Structure-Activity Relationships for the Nucleophilicity of Trivalent Boron Compounds. Chemistry 2017; 23:5066-5075. [DOI: 10.1002/chem.201605798] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Diego García-López
- Departament de Química Física i Inorgànica; Universitat Rovira i Virgili; Marcel⋅lí Domingo 1 43007 Tarragona Spain
| | - Jessica Cid
- Departament de Química Física i Inorgànica; Universitat Rovira i Virgili; Marcel⋅lí Domingo 1 43007 Tarragona Spain
| | - Ruben Marqués
- Departament de Química Física i Inorgànica; Universitat Rovira i Virgili; Marcel⋅lí Domingo 1 43007 Tarragona Spain
| | - Elena Fernández
- Departament de Química Física i Inorgànica; Universitat Rovira i Virgili; Marcel⋅lí Domingo 1 43007 Tarragona Spain
| | - Jorge J. Carbó
- Departament de Química Física i Inorgànica; Universitat Rovira i Virgili; Marcel⋅lí Domingo 1 43007 Tarragona Spain
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24
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Yamaguchi S, Nishimura T, Hibe Y, Nagai M, Sato H, Johnston I. Regularized regression analysis of digitized molecular structures in organic reactions for quantification of steric effects. J Comput Chem 2017; 38:1825-1833. [DOI: 10.1002/jcc.24791] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 02/03/2017] [Accepted: 03/05/2017] [Indexed: 01/18/2023]
Affiliation(s)
- Shigeru Yamaguchi
- RIKEN Center for Sustainable Resource Science; 2-1 Hirosawa, Wako Saitama 351-0198 Japan
| | - Takahiro Nishimura
- Department of Chemistry; Graduate School of Science, Kyoto University; Sakyo-ku Kyoto 606-8502 Japan
| | - Yuta Hibe
- Department of Chemistry; Graduate School of Science, Kyoto University; Sakyo-ku Kyoto 606-8502 Japan
| | - Masaki Nagai
- Department of Chemistry; Graduate School of Science, Kyoto University; Sakyo-ku Kyoto 606-8502 Japan
| | - Hirofumi Sato
- Department of Molecular Engineering; Graduate School of Engineering, Kyoto University; Nishikyo-ku Kyoto 610-8510 Japan
| | - Ian Johnston
- Department of Mathematics and Statistics; Boston University; 111 Cummington Mall Boston Massachusetts 02215
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25
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Poree C, Schoenebeck F. A Holy Grail in Chemistry: Computational Catalyst Design: Feasible or Fiction? Acc Chem Res 2017; 50:605-608. [PMID: 28945392 DOI: 10.1021/acs.accounts.6b00606] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Efficient and selective catalysis lies at the heart of much of chemistry, enabling the synthesis of molecules and materials with enormous societal and technological impact. Modern in silico tools should allow us to develop new catalysts faster and better than ever before; this contribution discusses the feasibility and potential of computational catalyst design.
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Affiliation(s)
- Carl Poree
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52074 Aachen, Germany
| | - Franziska Schoenebeck
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52074 Aachen, Germany
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26
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Karukurichi KR, Fei X, Swyka RA, Broussy S, Shen W, Dey S, Roy SK, Berkowitz DB. Mini-ISES identifies promising carbafructopyranose-based salens for asymmetric catalysis: Tuning ligand shape via the anomeric effect. SCIENCE ADVANCES 2015; 1:e1500066. [PMID: 26501130 PMCID: PMC4613784 DOI: 10.1126/sciadv.1500066] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Accepted: 05/11/2015] [Indexed: 05/24/2023]
Abstract
This study introduces new methods of screening for and tuning chiral space and in so doing identifies a promising set of chiral ligands for asymmetric synthesis. The carbafructopyranosyl-1,2-diamine(s) and salens constructed therefrom are particularly compelling. It is shown that by removing the native anomeric effect in this ligand family, one can tune chiral ligand shape and improve chiral bias. This concept is demonstrated by a combination of (i) x-ray crystallographic structure determination, (ii) assessment of catalytic performance, and (iii) consideration of the anomeric effect and its underlying dipolar basis. The title ligands were identified by a new mini version of the in situ enzymatic screening (ISES) procedure through which catalyst-ligand combinations are screened in parallel, and information on relative rate and enantioselectivity is obtained in real time, without the need to quench reactions or draw aliquots. Mini-ISES brings the technique into the nanomole regime (200 to 350 nmol catalyst/20 μml organic volume) commensurate with emerging trends in reaction development/process chemistry. The best-performing β-d-carbafructopyranosyl-1,2-diamine-derived salen ligand discovered here outperforms the best known organometallic and enzymatic catalysts for the hydrolytic kinetic resolution of 3-phenylpropylene oxide, one of several substrates examined for which the ligand is "matched." This ligand scaffold defines a new swath of chiral space, and anomeric effect tunability defines a new concept in shaping that chiral space. Both this ligand set and the anomeric shape-tuning concept are expected to find broad application, given the value of chiral 1,2-diamines and salens constructed from these in asymmetric catalysis.
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27
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Chen Y, Xiao H, Zheng J, Liang G. Structure-thermodynamics-antioxidant activity relationships of selected natural phenolic acids and derivatives: an experimental and theoretical evaluation. PLoS One 2015; 10:e0121276. [PMID: 25803685 PMCID: PMC4372407 DOI: 10.1371/journal.pone.0121276] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 01/29/2015] [Indexed: 11/18/2022] Open
Abstract
Phenolic acids and derivatives have potential biological functions, however, little is known about the structure-activity relationships and the underlying action mechanisms of these phenolic acids to date. Herein we investigate the structure-thermodynamics-antioxidant relationships of 20 natural phenolic acids and derivatives using DPPH• scavenging assay, density functional theory calculations at the B3LYP/6-311++G(d,p) levels of theory, and quantitative structure-activity relationship (QSAR) modeling. Three main working mechanisms (HAT, SETPT and SPLET) are explored in four micro-environments (gas-phase, benzene, water and ethanol). Computed thermodynamics parameters (BDE, IP, PDE, PA and ETE) are compared with the experimental radical scavenging activities against DPPH•. Available theoretical and experimental investigations have demonstrated that the extended delocalization and intra-molecular hydrogen bonds are the two main contributions to the stability of the radicals. The C = O or C = C in COOH, COOR, C = CCOOH and C = CCOOR groups, and orthodiphenolic functionalities are shown to favorably stabilize the specific radical species to enhance the radical scavenging activities, while the presence of the single OH in the ortho position of the COOH group disfavors the activities. HAT is the thermodynamically preferred mechanism in the gas phase and benzene, whereas SPLET in water and ethanol. Furthermore, our QSAR models robustly represent the structure-activity relationships of these explored compounds in polar media.
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Affiliation(s)
- Yuzhen Chen
- School of Mathematical Sciences, Henan Institute of Science and Technology, Xinxiang 453003, P. R. China
| | - Huizhi Xiao
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, School of Bioengineering, Chongqing University, Chongqing 400044, P. R. China
| | - Jie Zheng
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States of America
| | - Guizhao Liang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, School of Bioengineering, Chongqing University, Chongqing 400044, P. R. China
- * E-mail:
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28
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Yang X, Toste FD. Direct asymmetric amination of α-branched cyclic ketones catalyzed by a chiral phosphoric acid. J Am Chem Soc 2015; 137:3205-8. [PMID: 25719604 DOI: 10.1021/jacs.5b00229] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Here we report the direct asymmetric amination of α-substituted cyclic ketones catalyzed by a chiral phosphoric acid, yielding products with a N-containing quaternary stereocenter in high yields and excellent enantioselectivities. Kinetic resolution of the starting ketone was also found to occur on some of the substrates under milder conditions, providing enantioenriched α-branched ketones, another important building block in organic synthesis. The utility of this methodology was demonstrated in the short synthesis of (S)-ketamine, the more active enantiomer of this versatile pharmaceutical.
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Affiliation(s)
- Xiaoyu Yang
- Department of Chemistry, University of California , Berkeley, California 94720, United States
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29
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Sun Z, Wang Q, Xu Y, Wang Z. A computationally designed titanium-mediated amination of allylic alcohols for the synthesis of secondary allylamines. RSC Adv 2015. [DOI: 10.1039/c5ra18503c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A direct amination on allylic alcohols under mild conditions was enlightened by computational investigations and implemented in secondary allylamines synthesis.
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Affiliation(s)
- Zunming Sun
- State Key Laboratory and Institute of Elemento-Organic Chemistry
- Nankai University
- Tianjin 300071
- China
| | - Qingxia Wang
- State Key Laboratory and Institute of Elemento-Organic Chemistry
- Nankai University
- Tianjin 300071
- China
| | - Yi Xu
- State Key Laboratory and Institute of Elemento-Organic Chemistry
- Nankai University
- Tianjin 300071
- China
| | - Zhihong Wang
- State Key Laboratory and Institute of Elemento-Organic Chemistry
- Nankai University
- Tianjin 300071
- China
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30
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Buitrago Santanilla A, Regalado EL, Pereira T, Shevlin M, Bateman K, Campeau LC, Schneeweis J, Berritt S, Shi ZC, Nantermet P, Liu Y, Helmy R, Welch CJ, Vachal P, Davies IW, Cernak T, Dreher SD. Nanomole-scale high-throughput chemistry for the synthesis of complex molecules. Science 2014; 347:49-53. [DOI: 10.1126/science.1259203] [Citation(s) in RCA: 346] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
At the forefront of new synthetic endeavors, such as drug discovery or natural product synthesis, large quantities of material are rarely available and timelines are tight. A miniaturized automation platform enabling high-throughput experimentation for synthetic route scouting to identify conditions for preparative reaction scale-up would be a transformative advance. Because automated, miniaturized chemistry is difficult to carry out in the presence of solids or volatile organic solvents, most of the synthetic “toolkit” cannot be readily miniaturized. Using palladium-catalyzed cross-coupling reactions as a test case, we developed automation-friendly reactions to run in dimethyl sulfoxide at room temperature. This advance enabled us to couple the robotics used in biotechnology with emerging mass spectrometry–based high-throughput analysis techniques. More than 1500 chemistry experiments were carried out in less than a day, using as little as 0.02 milligrams of material per reaction.
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31
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Tsang ASK, Sanhueza IA, Schoenebeck F. Combining Experimental and Computational Studies to Understand and Predict Reactivities of Relevance to Homogeneous Catalysis. Chemistry 2014; 20:16432-41. [DOI: 10.1002/chem.201404725] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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32
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Bess EN, Bischoff AJ, Sigman MS. Designer substrate library for quantitative, predictive modeling of reaction performance. Proc Natl Acad Sci U S A 2014; 111:14698-703. [PMID: 25267648 PMCID: PMC4205662 DOI: 10.1073/pnas.1409522111] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Assessment of reaction substrate scope is often a qualitative endeavor that provides general indications of substrate sensitivity to a measured reaction outcome. Unfortunately, this field standard typically falls short of enabling the quantitative prediction of new substrates' performance. The disconnection between a reaction's development and the quantitative prediction of new substrates' behavior limits the applicative usefulness of many methodologies. Herein, we present a method by which substrate libraries can be systematically developed to enable quantitative modeling of reaction systems and the prediction of new reaction outcomes. Presented in the context of rhodium-catalyzed asymmetric transfer hydrogenation, these models quantify the molecular features that influence enantioselection and, in so doing, lend mechanistic insight to the modes of asymmetric induction.
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Affiliation(s)
- Elizabeth N Bess
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112
| | - Amanda J Bischoff
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112
| | - Matthew S Sigman
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112
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33
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A mathematical expression for the enantioselectivity and thermodynamic factors in the conformational equilibrium of catalysts in the addition of diethylzinc to benzaldehyde. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.tetasy.2014.09.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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34
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Huang H, Zong H, Bian G, Yue H, Song L. Correlating the Effects of the N-Substituent Sizes of Chiral 1,2-Amino Phosphinamide Ligands on Enantioselectivities in Catalytic Asymmetric Henry Reaction Using Physical Steric Parameters. J Org Chem 2014; 79:9455-64. [DOI: 10.1021/jo500982j] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Huayin Huang
- The State
Key Lab of Structural
Chemistry, the Key Laboratory of Coal to Ethylene Glycol and Its Related
Technology, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
| | - Hua Zong
- The State
Key Lab of Structural
Chemistry, the Key Laboratory of Coal to Ethylene Glycol and Its Related
Technology, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
| | - Guangling Bian
- The State
Key Lab of Structural
Chemistry, the Key Laboratory of Coal to Ethylene Glycol and Its Related
Technology, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
| | - Huifeng Yue
- The State
Key Lab of Structural
Chemistry, the Key Laboratory of Coal to Ethylene Glycol and Its Related
Technology, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
| | - Ling Song
- The State
Key Lab of Structural
Chemistry, the Key Laboratory of Coal to Ethylene Glycol and Its Related
Technology, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
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35
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Nielsen MC, Bonney KJ, Schoenebeck F. Computational ligand design for the reductive elimination of ArCF₃ from a small bite angle Pd(II) complex: remarkable effect of a perfluoroalkyl phosphine. Angew Chem Int Ed Engl 2014; 53:5903-6. [PMID: 24840791 DOI: 10.1002/anie.201400837] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Indexed: 11/09/2022]
Abstract
To date only three ligands are known to trigger the challenging reductive elimination of ArCF3 from Pd(II). We report the computational design of a bidentate trifluoromethylphosphine ligand that although exhibiting a generally ineffective small bite angle is predicted to give facile reductive elimination. Our experimental verification gave quantitative formation of ArCF3 at 80 °C within 2 h. This highlights the distinct effect of P-CF3 in organometallic reactivity and constitutes a proof-of-principle study of computational reactivity design.
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Affiliation(s)
- Mads C Nielsen
- ETH Zürich, Laboratory for Organic Chemistry, Vladimir-Prelog-Weg 3, 8093 Zürich (Switzerland)
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36
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Nielsen MC, Bonney KJ, Schoenebeck F. Computational Ligand Design for the Reductive Elimination of ArCF3from a Small Bite Angle PdIIComplex: Remarkable Effect of a Perfluoroalkyl Phosphine. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201400837] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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37
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Bonney KJ, Schoenebeck F. Experiment and computation: a combined approach to study the reactivity of palladium complexes in oxidation states 0 toiv. Chem Soc Rev 2014; 43:6609-38. [DOI: 10.1039/c4cs00061g] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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38
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QSAR analysis of the catalytic asymmetric ethylation of ketone using physical steric parameters of chiral ligand substituents. Tetrahedron 2014. [DOI: 10.1016/j.tet.2013.12.054] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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39
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Jindal G, Sunoj RB. Rational design of catalysts for asymmetric diamination reaction using transition state modeling. Org Biomol Chem 2014; 12:2745-53. [DOI: 10.1039/c3ob42520g] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
DFT calculations have been used to design chiral phosphoramidite ligands for the asymmetric diamination of vicinal diamines. The substituents at both the 3,3′ positions of the binol framework and the amido nitrogen play a vital role in the stereochemical outcome.
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Affiliation(s)
- Garima Jindal
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai 400076, India
| | - Raghavan B. Sunoj
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai 400076, India
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40
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Liu Y, Zhang J, Chen X, Zheng J, Wang G, Liang G. Insights into the adsorption of simple benzene derivatives on carbon nanotubes. RSC Adv 2014. [DOI: 10.1039/c4ra10195b] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
This work characterizes the adsorption characteristics of simple benzene derivatives on carbon nanotubes.
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Affiliation(s)
- Yonglan Liu
- Key Laboratory of Biorheological Science and Technology
- Ministry of Education
- School of Bioengineering
- Chongqing University
- Chongqing 400044, P. R. China
| | - Jin Zhang
- Key Laboratory of Biorheological Science and Technology
- Ministry of Education
- School of Bioengineering
- Chongqing University
- Chongqing 400044, P. R. China
| | - Xiaohua Chen
- School of Chemistry and Chemical Engineering
- Chongqing University
- Chongqing, P. R. China
| | - Jie Zheng
- Department of Chemical and Biomolecular Engineering
- The University of Akron
- Akron, USA
| | - Guixue Wang
- Key Laboratory of Biorheological Science and Technology
- Ministry of Education
- School of Bioengineering
- Chongqing University
- Chongqing 400044, P. R. China
| | - Guizhao Liang
- Key Laboratory of Biorheological Science and Technology
- Ministry of Education
- School of Bioengineering
- Chongqing University
- Chongqing 400044, P. R. China
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41
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Liang G, Liu Y, Shi B, Zhao J, Zheng J. An index for characterization of natural and non-natural amino acids for peptidomimetics. PLoS One 2013; 8:e67844. [PMID: 23935845 PMCID: PMC3720802 DOI: 10.1371/journal.pone.0067844] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 05/22/2013] [Indexed: 11/19/2022] Open
Abstract
Bioactive peptides and peptidomimetics play a pivotal role in the regulation of many biological processes such as cellular apoptosis, host defense, and biomineralization. In this work, we develop a novel structural matrix, Index of Natural and Non-natural Amino Acids (NNAAIndex), to systematically characterize a total of 155 physiochemical properties of 22 natural and 593 non-natural amino acids, followed by clustering the structural matrix into 6 representative property patterns including geometric characteristics, H-bond, connectivity, accessible surface area, integy moments index, and volume and shape. As a proof-of-principle, the NNAAIndex, combined with partial least squares regression or linear discriminant analysis, is used to develop different QSAR models for the design of new peptidomimetics using three different peptide datasets, i.e., 48 bitter-tasting dipeptides, 58 angiotensin-converting enzyme inhibitors, and 20 inorganic-binding peptides. A comparative analysis with other QSAR techniques demonstrates that the NNAAIndex method offers a stable and predictive modeling technique for in silico large-scale design of natural and non-natural peptides with desirable bioactivities for a wide range of applications.
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Affiliation(s)
- Guizhao Liang
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College Chongqing University, Chongqing, China
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio, United States of America
| | - Yonglan Liu
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College Chongqing University, Chongqing, China
| | - Bozhi Shi
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College Chongqing University, Chongqing, China
| | - Jun Zhao
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio, United States of America
| | - Jie Zheng
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio, United States of America
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42
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Harper KC, Vilardi SC, Sigman MS. Prediction of Catalyst and Substrate Performance in the Enantioselective Propargylation of Aliphatic Ketones by a Multidimensional Model of Steric Effects. J Am Chem Soc 2013; 135:2482-5. [DOI: 10.1021/ja4001807] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kaid C. Harper
- Department
of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112,
United States
| | - Sarah C. Vilardi
- 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
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43
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Mori K, Ichikawa Y, Kobayashi M, Shibata Y, Yamanaka M, Akiyama T. Prediction of suitable catalyst by 1H NMR: asymmetric synthesis of multisubstituted biaryls by chiral phosphoric acid catalyzed asymmetric bromination. Chem Sci 2013. [DOI: 10.1039/c3sc52142g] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
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44
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Huang H, Zong H, Bian G, Song L. Constructing a Quantitative Correlation between N-Substituent Sizes of Chiral Ligands and Enantioselectivities in Asymmetric Addition Reactions of Diethylzinc with Benzaldehyde. J Org Chem 2012; 77:10427-34. [DOI: 10.1021/jo3016715] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Huayin Huang
- The State Key Lab of Structural
Chemistry, the Key
Laboratory of Coal to Ethylene Glycol and Its Related Technology,
Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002,
China
| | - Hua Zong
- The State Key Lab of Structural
Chemistry, the Key
Laboratory of Coal to Ethylene Glycol and Its Related Technology,
Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002,
China
| | - Guangling Bian
- The State Key Lab of Structural
Chemistry, the Key
Laboratory of Coal to Ethylene Glycol and Its Related Technology,
Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002,
China
| | - Ling Song
- The State Key Lab of Structural
Chemistry, the Key
Laboratory of Coal to Ethylene Glycol and Its Related Technology,
Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002,
China
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45
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Aguado-Ullate S, Urbano-Cuadrado M, Villalba I, Pires E, García JI, Bo C, Carbó JJ. Predicting the Enantioselectivity of the Copper-Catalysed Cyclopropanation of Alkenes by Using Quantitative Quadrant-Diagram Representations of the Catalysts. Chemistry 2012; 18:14026-36. [DOI: 10.1002/chem.201201135] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 07/16/2012] [Indexed: 11/08/2022]
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46
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Harper KC, Bess EN, Sigman MS. Multidimensional steric parameters in the analysis of asymmetric catalytic reactions. Nat Chem 2012; 4:366-74. [DOI: 10.1038/nchem.1297] [Citation(s) in RCA: 186] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 02/07/2012] [Indexed: 11/09/2022]
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Aguado-Ullate S, Guasch L, Urbano-Cuadrado M, Bo C, Carbó JJ. 3D-QSPR models for predicting the enantioselectivity and the activity for asymmetric hydroformylation of styrene catalyzed by Rh–diphosphane. Catal Sci Technol 2012. [DOI: 10.1039/c2cy20089a] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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48
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Affiliation(s)
- Olaf Wiest
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
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49
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Weill N, Corbeil CR, De Schutter JW, Moitessier N. Toward a computational tool predicting the stereochemical outcome of asymmetric reactions: Development of the molecular mechanics‐based program ACE and application to asymmetric epoxidation reactions. J Comput Chem 2011; 32:2878-89. [DOI: 10.1002/jcc.21869] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Revised: 05/05/2011] [Accepted: 05/21/2011] [Indexed: 01/22/2023]
Affiliation(s)
- Nathanael Weill
- Department of Chemistry, McGill University, Montreal, Quebec, Canada H3A 2K6
| | | | | | - Nicolas Moitessier
- Department of Chemistry, McGill University, Montreal, Quebec, Canada H3A 2K6
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Denmark SE, Gould ND, Wolf LM. A systematic investigation of quaternary ammonium ions as asymmetric phase-transfer catalysts. Application of quantitative structure activity/selectivity relationships. J Org Chem 2011; 76:4337-57. [PMID: 21446723 DOI: 10.1021/jo2005457] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although the synthetic utility of asymmetric phase-transfer catalysis continues to expand, the number of proven catalyst types and design criteria remains limited. At the origin of this scarcity is a lack in understanding of how catalyst structural features affect the rate and enantioselectivity of phase transfer catalyzed reactions. Described in this paper is the development of quantitative structure-activity relationships (QSAR) and -selectivity relationships (QSSR) for the alkylation of a protected glycine imine with libraries of quaternary ammonium ion catalysts. Catalyst descriptors including ammonium ion accessibility, interfacial adsorption affinity, and partition coefficient were found to correlate meaningfully with catalyst activity. The physical nature of the descriptors was rationalized through differing contributions of the interfacial and extraction mechanisms to the reaction under study. The variation in the observed enantioselectivity was rationalized employing a comparative molecular field analysis (CoMFA) using both the steric and electrostatic fields of the catalysts. A qualitative analysis of the developed model reveals preferred regions for catalyst binding to afford both configurations of the alkylated product.
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Affiliation(s)
- Scott E Denmark
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States.
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