1
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Janssen K, Kirchmair J, Proppe J. Relevance and Potential Applications of C2-Carboxylated 1,3-Azoles. ChemMedChem 2024; 19:e202400307. [PMID: 39022854 DOI: 10.1002/cmdc.202400307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 07/12/2024] [Accepted: 07/16/2024] [Indexed: 07/20/2024]
Abstract
Carbon dioxide (CO2) is an economically viable and abundant carbon source that can be incorporated into compounds such as C2-carboxylated 1,3-azoles relevant to the pharmaceutical, cosmetics, and pesticide industries. Of the 2.4 million commercially available C2-unsubstituted 1,3-azole compounds, less than 1 % are currently purchasable as their C2-carboxylated derivatives, highlighting the substantial gap in compound availability. This availability gap leaves ample opportunities for exploring the synthetic accessibility and use of carboxylated azoles in bioactive compounds. In this study, we analyze and quantify the relevance of C2-carboxylated 1,3-azoles in small-molecule research. An analysis of molecular databases such as ZINC, ChEMBL, COSMOS, and DrugBank identified relevant C2-carboxylated 1,3-azoles as anticoagulant and aroma-giving compounds. Moreover, a pharmacophore analysis highlights promising pharmaceutical potential associated with C2-carboxylated 1,3-azoles, revealing the ATP-sensitive inward rectifier potassium channel 1 (KATP) and Kinesin-like protein KIF18 A as targets that can potentially be addressed with C2-carboxylated 1,3-azoles. Moreover, we identified several bioisosteres of C2-carboxylated 1,3-azoles. In conclusion, further exploration of the chemical space of C2-carboxylated 1,3-azoles is recommended to harness their full potential in drug discovery and related fields.
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Affiliation(s)
- Kerrin Janssen
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, 38106, Braunschweig, Germany
| | - Johannes Kirchmair
- Christian Doppler Laboratory for Molecular Informatics in the Biosciences and Department of Pharmaceutical Sciences, University of Vienna, 1090, Vienna, Austria
| | - Jonny Proppe
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, 38106, Braunschweig, Germany
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2
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Schmid SP, Schlosser L, Glorius F, Jorner K. Catalysing (organo-)catalysis: Trends in the application of machine learning to enantioselective organocatalysis. Beilstein J Org Chem 2024; 20:2280-2304. [PMID: 39290209 PMCID: PMC11406055 DOI: 10.3762/bjoc.20.196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 08/09/2024] [Indexed: 09/19/2024] Open
Abstract
Organocatalysis has established itself as a third pillar of homogeneous catalysis, besides transition metal catalysis and biocatalysis, as its use for enantioselective reactions has gathered significant interest over the last decades. Concurrent to this development, machine learning (ML) has been increasingly applied in the chemical domain to efficiently uncover hidden patterns in data and accelerate scientific discovery. While the uptake of ML in organocatalysis has been comparably slow, the last two decades have showed an increased interest from the community. This review gives an overview of the work in the field of ML in organocatalysis. The review starts by giving a short primer on ML for experimental chemists, before discussing its application for predicting the selectivity of organocatalytic transformations. Subsequently, we review ML employed for privileged catalysts, before focusing on its application for catalyst and reaction design. Concluding, we give our view on current challenges and future directions for this field, drawing inspiration from the application of ML to other scientific domains.
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Affiliation(s)
- Stefan P Schmid
- Institute of Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich CH-8093, Switzerland
| | - Leon Schlosser
- Organisch-Chemisches Institut, Universität Münster, 48149 Münster, Germany
| | - Frank Glorius
- Organisch-Chemisches Institut, Universität Münster, 48149 Münster, Germany
| | - Kjell Jorner
- Institute of Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich CH-8093, Switzerland
- National Centre of Competence in Research (NCCR) Catalysis, ETH Zurich, Zurich CH-8093, Switzerland
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3
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Saida AB, Mahaut D, Tumanov N, Wouters J, Champagne B, Vanthuyne N, Robiette R, Berionni G. Reactivity and Steric Parameters from 2D to 3D Bulky Pyridines: Increasing Steric Demand at Nitrogen with Chiral Azatriptycenes. Angew Chem Int Ed Engl 2024; 63:e202407503. [PMID: 38781114 DOI: 10.1002/anie.202407503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 05/25/2024]
Abstract
Sterically hindered pyridines embedded in a three-dimensional triptycene framework have been synthesized, and their resolution by chiral HPLC enabled access to unprecedented enantiopure pyridines exceeding the known steric limits. The design principles for new axially chiral pyridine derivatives are then described. To rationalize their associations with Lewis acids and transition metals, a comprehensive determination of the steric and electronic parameters for this new class of pyridines was performed. This led to the general parameterization of the steric parameters (percent buried volume %VBur, Tolman cone angle θ, and He8_steric descriptor) for a large set of two- and three-dimensional pyridine derivatives. These parameters are shown to describe quantitatively their interactions with carbon- and boron-centered Lewis acids and were used to predict the ΔG° of association with the prototypical B(C6F5)3 Lewis acid widely used in frustrated Lewis pair catalysis. This first parameterization of pyridine sterics is a fundamental basis for the future development of predictive reactivity models and for guiding new applications of bulky and chiral pyridines in organocatalysis, frustrated Lewis pairs, and transition-metal catalysis.
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Affiliation(s)
- Ali Ben Saida
- Department of Chemistry and Namur Institute of Structured Matter, Université de Namur, 61 Rue de Bruxelles, 5000, Namur, Belgium
| | - Damien Mahaut
- Department of Chemistry and Namur Institute of Structured Matter, Université de Namur, 61 Rue de Bruxelles, 5000, Namur, Belgium
| | - Nikolay Tumanov
- Department of Chemistry and Namur Institute of Structured Matter, Université de Namur, 61 Rue de Bruxelles, 5000, Namur, Belgium
| | - Johan Wouters
- Department of Chemistry and Namur Institute of Structured Matter, Université de Namur, 61 Rue de Bruxelles, 5000, Namur, Belgium
| | - Benoît Champagne
- Department of Chemistry and Namur Institute of Structured Matter, Université de Namur, 61 Rue de Bruxelles, 5000, Namur, Belgium
| | - Nicolas Vanthuyne
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Raphaël Robiette
- Institute of Condensed Matter and Nanosciences, Université catholique de Louvain, Place Louis Pasteur 1 Box L4.01.02, 1348, Louvain-la-Neuve, Belgium
| | - Guillaume Berionni
- Department of Chemistry and Namur Institute of Structured Matter, Université de Namur, 61 Rue de Bruxelles, 5000, Namur, Belgium
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4
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Chen Z, Song G, Qi L, Gunasekar R, Aïssa C, Robertson C, Steiner A, Xue D, Xiao J. Reductive Transamination of Pyridinium Salts to N-Aryl Piperidines. J Org Chem 2024; 89:9352-9359. [PMID: 38872240 PMCID: PMC11232014 DOI: 10.1021/acs.joc.4c00493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/30/2024] [Accepted: 06/05/2024] [Indexed: 06/15/2024]
Abstract
Saturated N-heterocycles are found in numerous bioactive natural products and are prevalent in pharmaceuticals and agrochemicals. While there are many methods for their synthesis, each has its limitations, such as scope and functional group tolerance. Herein, we describe a rhodium-catalyzed transfer hydrogenation of pyridinium salts to access N-(hetero)aryl piperidines. The reaction proceeds via a reductive transamination process, involving the initial formation of a dihydropyridine intermediate via reduction of the pyridinium ion with HCOOH, which is intercepted by water and then hydrolyzed. Subsequent reductive amination with an exogenous (hetero)aryl amine affords an N-(hetero)aryl piperidine. This reductive transamination method thus allows for access of N-(hetero)aryl piperidines from readily available pyridine derivatives, expanding the toolbox of dearomatization and skeletal editing.
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Affiliation(s)
- Zhenyu Chen
- Department
of Chemistry, University of Liverpool, Liverpool L69 7ZD, U.K.
| | - Geyang Song
- Key
Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education
and School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an 710119, China
| | - Leiming Qi
- Department
of Chemistry, University of Liverpool, Liverpool L69 7ZD, U.K.
| | | | - Christophe Aïssa
- Department
of Chemistry, University of Liverpool, Liverpool L69 7ZD, U.K.
| | - Craig Robertson
- Department
of Chemistry, University of Liverpool, Liverpool L69 7ZD, U.K.
| | - Alexander Steiner
- Department
of Chemistry, University of Liverpool, Liverpool L69 7ZD, U.K.
| | - Dong Xue
- Key
Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education
and School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an 710119, China
| | - Jianliang Xiao
- Department
of Chemistry, University of Liverpool, Liverpool L69 7ZD, U.K.
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5
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Escayola S, Bahri-Laleh N, Poater A. % VBur index and steric maps: from predictive catalysis to machine learning. Chem Soc Rev 2024; 53:853-882. [PMID: 38113051 DOI: 10.1039/d3cs00725a] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Steric indices are parameters used in chemistry to describe the spatial arrangement of atoms or groups of atoms in molecules. They are important in determining the reactivity, stability, and physical properties of chemical compounds. One commonly used steric index is the steric hindrance, which refers to the obstruction or hindrance of movement in a molecule caused by bulky substituents or functional groups. Steric hindrance can affect the reactivity of a molecule by altering the accessibility of its reactive sites and influencing the geometry of its transition states. Notably, the Tolman cone angle and %VBur are prominent among these indices. Actually, steric effects can also be described using the concept of steric bulk, which refers to the space occupied by a molecule or functional group. Steric bulk can affect the solubility, melting point, boiling point, and viscosity of a substance. Even though electronic indices are more widely used, they have certain drawbacks that might shift preferences towards others. They present a higher computational cost, and often, the weight of electronics in correlation with chemical properties, e.g. binding energies, falls short in comparison to %VBur. However, it is worth noting that this may be because the steric index inherently captures part of the electronic content. Overall, steric indices play an important role in understanding the behaviour of chemical compounds and can be used to predict their reactivity, stability, and physical properties. Predictive chemistry is an approach to chemical research that uses computational methods to anticipate the properties and behaviour of these compounds and reactions, facilitating the design of new compounds and reactivities. Within this domain, predictive catalysis specifically targets the prediction of the performance and behaviour of catalysts. Ultimately, the goal is to identify new catalysts with optimal properties, leading to chemical processes that are both more efficient and sustainable. In this framework, %VBur can be a key metric for deepening our understanding of catalysis, emphasizing predictive catalysis and sustainability. Those latter concepts are needed to direct our efforts toward identifying the optimal catalyst for any reaction, minimizing waste, and reducing experimental efforts while maximizing the efficacy of the computational methods.
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Affiliation(s)
- Sílvia Escayola
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, c/Mª Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain.
- Donostia International Physics Center (DIPC), 20018 Donostia, Euskadi, Spain
| | - Naeimeh Bahri-Laleh
- Iran Polymer and Petrochemical Institute (IPPI), P.O. Box 14965/115, Tehran, Iran
- Institute for Sustainability with Knotted Chiral Meta Matter (WPI-SKCM), Hiroshima University, Hiroshima, 739-8526, Japan
| | - Albert Poater
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, c/Mª Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain.
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6
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Eckhoff M, Diedrich JV, Mücke M, Proppe J. Quantitative Structure-Reactivity Relationships for Synthesis Planning: The Benzhydrylium Case. J Phys Chem A 2024; 128:343-354. [PMID: 38113457 PMCID: PMC10788916 DOI: 10.1021/acs.jpca.3c07289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 11/28/2023] [Accepted: 12/01/2023] [Indexed: 12/21/2023]
Abstract
Selective and feasible reactions are among the top targets in synthesis planning. Mayr's approach to quantifying chemical reactivity has greatly facilitated the planning process, but reactivity parameters for new compounds require time-consuming experiments. In the past decade, data-driven modeling has been gaining momentum in the field, as it shows promise in terms of efficient reactivity prediction. However, state-of-the-art models use quantum chemical data as input, which prevent access to real-time planning in organic synthesis. Here, we present a novel data-driven workflow for predicting reactivity parameters of molecules that takes only structural information as input, enabling de facto real-time reactivity predictions. We use the well-understood chemical space of benzhydrylium ions as an example to demonstrate the functionality of our approach and the performance of the resulting quantitative structure-reactivity relationships (QSRRs). Our results suggest that it is straightforward to build low-cost QSRR models that are accurate, interpretable, and transferable to unexplored systems within a given scope of application. Moreover, our QSRR approach suggests that Hammett σ parameters are only approximately additive.
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Affiliation(s)
- Maike Eckhoff
- Institute
of Physical and Theoretical Chemistry, TU
Braunschweig, Braunschweig 38106, Germany
| | - Johannes V. Diedrich
- Institute
of Physical and Theoretical Chemistry, TU
Braunschweig, Braunschweig 38106, Germany
- Institute
of Physical Chemistry, University of Göttingen, Göttingen 37077, Germany
| | - Maike Mücke
- Institute
of Physical and Theoretical Chemistry, TU
Braunschweig, Braunschweig 38106, Germany
- Institute
of Physical Chemistry, University of Göttingen, Göttingen 37077, Germany
| | - Jonny Proppe
- Institute
of Physical and Theoretical Chemistry, TU
Braunschweig, Braunschweig 38106, Germany
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7
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Di Terlizzi L, Nicchio L, Callegari C, Scaringi S, Neuville L, Fagnoni M, Protti S, Masson G. Visible-Light-Mediated Divergent and Regioselective Vicinal Difunctionalization of Styrenes with Arylazo Sulfones. Org Lett 2023; 25:9047-9052. [PMID: 38085821 DOI: 10.1021/acs.orglett.3c03786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Activated by visible light, arylazo sulfones can serve as multifaceted reactants and are employed in diazenylation, sulfonylation, and arylation reactions under (photo)catalyst-free conditions. Such versatile reactivity enabled us to develop an operationally simple, regioselective, and tunable difunctionalization of styrenes with arylazo sulfones to produce α-sulfonyl arylhydrazones and 1,2-alkoxyarylated products in moderate to excellent yields. Furthermore, such difunctionalized products have been exploited as key building blocks for the synthesis of various heterocycles.
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Affiliation(s)
- Lorenzo Di Terlizzi
- Institut de Chimie des Substances Naturelles (ICSN), CNRS UPR 2301, Université Paris-Saclay, 1 avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France
- PhotoGreen Lab, Department of Chemistry, University of Pavia, Pavia 27100, Italy
| | - Luca Nicchio
- Institut de Chimie des Substances Naturelles (ICSN), CNRS UPR 2301, Université Paris-Saclay, 1 avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France
- PhotoGreen Lab, Department of Chemistry, University of Pavia, Pavia 27100, Italy
| | - Camilla Callegari
- Institut de Chimie des Substances Naturelles (ICSN), CNRS UPR 2301, Université Paris-Saclay, 1 avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France
- PhotoGreen Lab, Department of Chemistry, University of Pavia, Pavia 27100, Italy
| | - Simone Scaringi
- Institut de Chimie des Substances Naturelles (ICSN), CNRS UPR 2301, Université Paris-Saclay, 1 avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France
- PhotoGreen Lab, Department of Chemistry, University of Pavia, Pavia 27100, Italy
| | - Luc Neuville
- Institut de Chimie des Substances Naturelles (ICSN), CNRS UPR 2301, Université Paris-Saclay, 1 avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France
- HitCat, Seqens-CNRS joint laboratory, Seqens'Lab, 8 Rue de Rouen, 78440 Porcheville, France
| | - Maurizio Fagnoni
- PhotoGreen Lab, Department of Chemistry, University of Pavia, Pavia 27100, Italy
| | - Stefano Protti
- PhotoGreen Lab, Department of Chemistry, University of Pavia, Pavia 27100, Italy
| | - Geraldine Masson
- Institut de Chimie des Substances Naturelles (ICSN), CNRS UPR 2301, Université Paris-Saclay, 1 avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France
- HitCat, Seqens-CNRS joint laboratory, Seqens'Lab, 8 Rue de Rouen, 78440 Porcheville, France
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8
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Lorandi F, Fantin M, Jafari H, Gorczynski A, Szczepaniak G, Dadashi-Silab S, Isse AA, Matyjaszewski K. Reactivity Prediction of Cu-Catalyzed Halogen Atom Transfer Reactions Using Data-Driven Techniques. J Am Chem Soc 2023; 145:21587-21599. [PMID: 37733464 DOI: 10.1021/jacs.3c07711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Abstract
In catalysis, linear free energy relationships (LFERs) are commonly used to identify reaction descriptors that enable the prediction of outcomes and the design of more effective catalysts. Herein, LFERs are established for the reductive cleavage of the C(sp3)-X bond in alkyl halides (RX) by Cu complexes. This reaction represents the activation step in atom transfer radical polymerization and atom transfer radical addition/cyclization. The values of the activation rate constant, kact, for 107 Cu complex/RX couples in 5 different solvents spanning over 13 orders of magnitude were effectively interpolated by the equation: log kact = sC(I + C + S), where I, C, and S are, respectively, the initiator, catalyst, and solvent parameters, and sC is the catalyst-specific sensitivity parameter. Furthermore, each of these parameters was correlated to relevant descriptors, which included the bond dissociation free energy of RX and its Tolman cone angle θ, the electron affinity of X, the radical stabilization energy, the standard reduction potential of the Cu complex, the polarizability parameter π* of the solvent, and the distortion energy of the complex in its transition state. This set of descriptors establishes the fundamental properties of Cu complexes and RX that determine their reactivity and that need to be considered when designing novel systems for atom transfer radical reactions. Finally, a multivariate linear regression (MLR) approach was adopted to develop an objective model that surpassed the predictive capability of the LFER equation. Thus, the MLR model was employed to predict kact values for >2000 Cu complex/RX pairs.
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Affiliation(s)
- Francesca Lorandi
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
- Department of Chemical Sciences, University of Padova, via Marzolo 1, Padova 35131, Italy
| | - Marco Fantin
- Department of Chemical Sciences, University of Padova, via Marzolo 1, Padova 35131, Italy
| | - Hossein Jafari
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Adam Gorczynski
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614 Poznań, Poland
| | - Grzegorz Szczepaniak
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Sajjad Dadashi-Silab
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Abdirisak A Isse
- Department of Chemical Sciences, University of Padova, via Marzolo 1, Padova 35131, Italy
| | - Krzysztof Matyjaszewski
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
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9
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Lu Y, Chen C. Exceptional reactivity of the bridgehead amine on bicyclo[1.1.1]pentane. ARKIVOC 2023; 2023:202312003. [PMID: 37786812 PMCID: PMC10544781 DOI: 10.24820/ark.5550190.p012.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023] Open
Abstract
Bicyclo[1.1.1]pentane (BCP) has received substantial interest in the field of synthetic chemistry recently for its potential use as a benzene isostere in medicinal chemistry. Whereas bicyclo[2.2.2]octane (BCO) has also been used as a bioisostere of benzene, the condensation of BCP-amine with nadic anhydride is significantly easier than that of BCO-amine. Analyses of the geometries and the frontier molecular orbitals of these amines suggest that the low steric hindrance and high intrinsic nucleophilicity of BCP-amine together contribute to its exceptional reactivity.
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Affiliation(s)
- Yong Lu
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9038
| | - Chuo Chen
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9038
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10
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Li L, Mayer RJ, Ofial AR, Mayr H. One-Bond-Nucleophilicity and -Electrophilicity Parameters: An Efficient Ordering System for 1,3-Dipolar Cycloadditions. J Am Chem Soc 2023; 145:7416-7434. [PMID: 36952671 DOI: 10.1021/jacs.2c13872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
Diazoalkanes are ambiphilic 1,3-dipoles that undergo fast Huisgen cycloadditions with both electron-rich and electron-poor dipolarophiles but react slowly with alkenes of low polarity. Frontier molecular orbital (FMO) theory considering the 3-center-4-electron π-system of the propargyl fragment of diazoalkanes is commonly applied to rationalize these reactivity trends. However, we recently found that a change in the mechanism from cycloadditions to azo couplings takes place due to the existence of a previously overlooked lower-lying unoccupied molecular orbital. We now propose an alternative approach to analyze 1,3-dipolar cycloaddition reactions, which relies on the linear free energy relationship lg k2(20 °C) = sN(N + E) (eq 1) with two solvent-dependent parameters (N, sN) to characterize nucleophiles and one parameter (E) for electrophiles. Rate constants for the cycloadditions of diazoalkanes with dipolarophiles were measured and compared with those calculated for the formation of zwitterions by eq 1. The difference between experimental and predicted Gibbs energies of activation is interpreted as the energy of concert, i.e., the stabilization of the transition states by the concerted formation of two new bonds. By linking the plot of lg k2 vs N for nucleophilic dipolarophiles with that of lg k2 vs E for electrophilic dipolarophiles, one obtains V-shaped plots which provide absolute rate constants for the stepwise reactions on the borderlines. These plots furthermore predict relative reactivities of dipolarophiles in concerted, highly asynchronous cycloadditions more precisely than the classical correlations of rate constants with FMO energies or ionization potentials. DFT calculations using the SMD solvent model confirm these interpretations.
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Affiliation(s)
- Le Li
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - Robert J Mayer
- CNRS, ISIS, Université de Strasbourg, 8 Allee Gaspard Monge, 67000 Strasbourg, France
| | - Armin R Ofial
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - Herbert Mayr
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
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11
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Abstract
Reactivity scales are useful research tools for chemists, both experimental and computational. However, to determine the reactivity of a single molecule, multiple measurements need to be carried out, which is a time-consuming and resource-intensive task. In this Tutorial Review, we present alternative approaches for the efficient generation of quantitative structure-reactivity relationships that are based on quantum chemistry, supervised learning, and uncertainty quantification. First published in 2002, we observe a tendency for these relationships to become not only more predictive but also more interpretable over time.
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Affiliation(s)
- Maike Vahl
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany.
| | - Jonny Proppe
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany.
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12
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Zahrt AF, Mo Y, Nandiwale KY, Shprints R, Heid E, Jensen KF. Machine-Learning-Guided Discovery of Electrochemical Reactions. J Am Chem Soc 2022; 144:22599-22610. [PMID: 36459170 DOI: 10.1021/jacs.2c08997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The molecular structures synthesizable by organic chemists dictate the molecular functions they can create. The invention and development of chemical reactions are thus critical for chemists to access new and desirable functional molecules in all disciplines of organic chemistry. This work seeks to expedite the exploration of emerging areas of organic chemistry by devising a machine-learning-guided workflow for reaction discovery. Specifically, this study uses machine learning to predict competent electrochemical reactions. To this end, we first develop a molecular representation that enables the production of general models with limited training data. Next, we employ automated experimentation to test a large number of electrochemical reactions. These reactions are categorized as competent or incompetent mixtures, and a classification model was trained to predict reaction competency. This model is used to screen 38,865 potential reactions in silico, and the predictions are used to identify a number of reactions of synthetic or mechanistic interest, 80% of which are found to be competent. Additionally, we provide the predictions for the 38,865-member set in the hope of accelerating the development of this field. We envision that adopting a workflow such as this could enable the rapid development of many fields of chemistry.
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Affiliation(s)
- Andrew F Zahrt
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02142, United States
| | - Yiming Mo
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02142, United States.,College of Chemical and Biological Engineering, Zhejiang University, Hangzhou310027, China
| | - Kakasaheb Y Nandiwale
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02142, United States
| | - Ron Shprints
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02142, United States
| | - Esther Heid
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02142, United States.,Institute of Materials Chemistry, TU Wien, Vienna1060, Austria
| | - Klavs F Jensen
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02142, United States
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13
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Lu J, Paci I, Leitch DC. A broadly applicable quantitative relative reactivity model for nucleophilic aromatic substitution (S NAr) using simple descriptors. Chem Sci 2022; 13:12681-12695. [PMID: 36519044 PMCID: PMC9645419 DOI: 10.1039/d2sc04041g] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/17/2022] [Indexed: 07/22/2023] Open
Abstract
We report a multivariate linear regression model able to make accurate predictions for the relative rate and regioselectivity of nucleophilic aromatic substitution (SNAr) reactions based on the electrophile structure. This model uses a diverse training/test set from experimentally-determined relative SNAr rates between benzyl alcohol and 74 unique electrophiles, including heterocycles with multiple substitution patterns. There is a robust linear relationship between the experimental SNAr free energies of activation and three molecular descriptors that can be obtained computationally: the electron affinity (EA) of the electrophile; the average molecular electrostatic potential (ESP) at the carbon undergoing substitution; and the sum of average ESP values for the ortho and para atoms relative to the reactive center. Despite using only simple descriptors calculated from ground state wavefunctions, this model demonstrates excellent correlation with previously measured SNAr reaction rates, and is able to accurately predict site selectivity for multihalogenated substrates: 91% prediction accuracy across 82 individual examples. The excellent agreement between predicted and experimental outcomes makes this easy-to-implement reactivity model a potentially powerful tool for synthetic planning.
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Affiliation(s)
- Jingru Lu
- Department of Chemistry, University of Victoria 3800 Finnerty Rd. Victoria BC CANADA V8P 5C2
| | - Irina Paci
- Department of Chemistry, University of Victoria 3800 Finnerty Rd. Victoria BC CANADA V8P 5C2
| | - David C Leitch
- Department of Chemistry, University of Victoria 3800 Finnerty Rd. Victoria BC CANADA V8P 5C2
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14
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Zeng L. Analysis of the Stage Performance Effect of Environmental Protection Music and Dance Drama Based on Artificial Intelligence Technology. JOURNAL OF ENVIRONMENTAL AND PUBLIC HEALTH 2022; 2022:2891993. [PMID: 36193396 PMCID: PMC9526563 DOI: 10.1155/2022/2891993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/01/2022] [Accepted: 09/05/2022] [Indexed: 11/23/2022]
Abstract
There are a lot of environmental protection musicals and dances in public entertainment life to support the concept of environmental protection and to entice people to support the cause of environmental protection. As we all know, in a musical performance, the distance between the audience and the actors, the design of the stage environment, the training of the actors, the costumes of the actors, the makeup of the actors, and the musical accompaniment will all have more or less influence on the stage performance effects. In order to make environmental protection music and dance dramas profoundly meaningful to social production and human activities, it is especially important to analyze the stage performance of such music and dance dramas. The analysis of stage performance effects is not only beneficial to making the ideas spread by the music and dance drama penetrate into people's hearts but can also provide guiding suggestions for the production of music and dance drama. Therefore, this paper proposes a linear regression algorithm based on artificial intelligence to deeply explore and analyze the influence of the above six factors on the stage performance effects of environmental protection music and dance drama. In our method, first we preprocess the data collected by classification to remove the odd values from the data so that the various types of data conform to a normal distribution. Secondly, we obtained linear fit plots of the six factors with the stage performance effect scores by using a linear regression algorithm to deeply analyze the correlation between various types of data and the stage performance effect scores. Finally, through numerical calculations, we found that the distance between the audience and the actors, the training of the actors, and the musical accompaniment have a greater influence on the performance effect of the musical cabaret in the environmental protection category. Meanwhile, the costumes of the actors, the makeup of the actors, and the design of the stage environment have less influence on the performance effect of the musical cabaret. Therefore, in the production and performance of environmental protection music and dance dramas, producers and performers should pay more attention to the distance between the audience and the actors, the design of musical accompaniment, and the training of actors. To sum up, this paper has made a scientific, detailed, and reasonable analysis of the performance effect of environmental protection music and dance dramas on stage, contributing to the dissemination of environmental protection ideas.
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Affiliation(s)
- Li Zeng
- Jiangxi Science & Technology Normal University, Nanchang 330000, China
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15
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Solvent effect, quantification and correlation analysis of the nucleophilicities of cyclic secondary amines. CHEMICAL PAPERS 2022. [DOI: 10.1007/s11696-022-02483-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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16
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Nie W, Liu D, Li S, Yu H, Fu Y. Nucleophilicity Prediction Using Graph Neural Networks. J Chem Inf Model 2022; 62:4319-4328. [PMID: 36097394 DOI: 10.1021/acs.jcim.2c00696] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The quantitative description between chemical reaction rates and nucleophilicity parameters plays a crucial role in organic chemistry. In this regard, the formula proposed by Mayr et al. and the constructed reactivity database are important representatives. However, the determination of Mayr's nucleophilicity parameter N often requires time-consuming experiments with reference electrophiles in the solvent. Several machine learning (ML)-based models have been proposed to realize the data-driven prediction of N in recent years. However, in addition to DFT-calculated electronic descriptors, most of them also use a set of artificially predefined structural descriptors as input, which may result in a biased representation of the nucleophile's structural information depending on descriptors' definition preference. Compared with traditional ML algorithms, graph neural networks (GNNs) can naturally take the molecule's structural information into account by applying the message passing technique. We herein proposed a SchNet-based GNN model that only takes the molecular conformation and solvent type as input. The model achieves a comparable performance to the previous benchmark study on 10-fold cross-validation of 894 data points (R2 = 0.91, RMSE = 2.25). To enhance the model's ability to capture the molecule's electronic information, some DFT-calculated parameters are then incorporated into the model via graph global features, and substantial improvement is achieved in the prediction precision (R2 = 0.95, RMSE = 1.63). These results demonstrate that both structural and electronic information are important for the prediction of N, and GNN can integrate these two kinds of information more effectively.
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Affiliation(s)
- Wan Nie
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Urban Pollutant Conversion, Anhui Province Key Laboratory of Biomass Clean Energy, Center for Excellence in Molecular Synthesis of CAS, Institute of Energy, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230026, China.,Department of Computer Science, City University of Hong Kong, Hong Kong 999077, China
| | - Deguang Liu
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Urban Pollutant Conversion, Anhui Province Key Laboratory of Biomass Clean Energy, Center for Excellence in Molecular Synthesis of CAS, Institute of Energy, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230026, China
| | - Shuaicheng Li
- Department of Computer Science, City University of Hong Kong, Hong Kong 999077, China
| | - Haizhu Yu
- Department of Chemistry and Centre for Atomic Engineering of Advanced Materials, Anhui Province Key Laboratory of Chemistry for Inorganic/Organic Hybrid Functionalized Materials, Anhui University, Hefei 230601, China
| | - Yao Fu
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Urban Pollutant Conversion, Anhui Province Key Laboratory of Biomass Clean Energy, Center for Excellence in Molecular Synthesis of CAS, Institute of Energy, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230026, China
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17
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Trifonova EA, Ankudinov NM, Chusov DA, Nelyubina YV, Perekalin DS. Asymmetric cyclopropanation of electron-rich alkenes by the racemic diene rhodium catalyst: the chiral poisoning approach. Chem Commun (Camb) 2022; 58:6709-6712. [PMID: 35593764 DOI: 10.1039/d2cc01648f] [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
Asymmetric cyclopropanation of alkenes by aryldiazoacetates was achieved using the readily-available racemic (diene)rhodium complex in combination with the chiral oxazoline-phenol ligand, which acts as the chiral poison and selectively inhibits one of the enantiomers of the catalyst. This approach eliminates a common problematic step of the synthesis of chiral catalysts.
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Affiliation(s)
- Evgeniya A Trifonova
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, 28 Vavilova str., 119991, Moscow, Russia.
| | - Nikita M Ankudinov
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, 28 Vavilova str., 119991, Moscow, Russia.
| | - Denis A Chusov
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, 28 Vavilova str., 119991, Moscow, Russia.
| | - Yulia V Nelyubina
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, 28 Vavilova str., 119991, Moscow, Russia.
| | - Dmitry S Perekalin
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, 28 Vavilova str., 119991, Moscow, Russia.
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18
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Zhang X, Su C, Cao C, Gong G, Huang L, Wang Z, Song S, Zhu B. Gut Microbiota of Individuals Could Be Balanced by a 14-Day Supplementation With Laminaria japonica and Differed in Metabolizing Alginate and Galactofucan. Front Nutr 2022; 9:881464. [PMID: 35662929 PMCID: PMC9158320 DOI: 10.3389/fnut.2022.881464] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
Laminaria japonica is rich in alginate (Alg) and galactofucan (GF) which have both been reported to regulate gut microbiota composition. To reveal the effect of L. japonica on human gut microbiota, the fecal microbiota of 12 volunteers before and after 14-day L. japonica intake was sequenced and compared, and the capabilities of the gut microbiota to utilize Alg and GF were also investigated. The 16S rRNA gene sequencing results demonstrated that Firmicutes/Bacteroidetes ratio could be balanced by L. japonica supplementation. The ability of gut microbiota to utilize Alg was significantly enhanced by L. japonica supplementation. Furthermore, the multiple linear regression analysis suggested that bacteria from Bacteroidaceae and Ruminococcaceae were positively correlated with Alg utilization while those from Erysipelotrichaceae, Bacteroidaceae, and Prevotellaceae participated in GF degradation. Moreover, the production of acetic acid and the total short-chain fatty acids (SCFAs) in fermentation were consistent with the consumption of Alg or GF, and propionic acid content was positively correlated with Alg consumption. In addition, the percentage of monosaccharides in the consumed GF after the fermentation suggested that gut microbiota from individuals could consume GF with different monosaccharide preferences. These findings shed a light on the impacts of dietary L. japonica on human health.
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Affiliation(s)
- Xueqian Zhang
- College of Food Science and Technology, Northwest University, Xi'an, China
| | - Changyu Su
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
| | - Cui Cao
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an, China
| | - Guiping Gong
- College of Food Science and Technology, Northwest University, Xi'an, China
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an, China
| | - Linjuan Huang
- College of Food Science and Technology, Northwest University, Xi'an, China
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an, China
| | - Zhongfu Wang
- College of Food Science and Technology, Northwest University, Xi'an, China
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an, China
- *Correspondence: Zhongfu Wang
| | - Shuang Song
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
- National & Local Joint Engineering Laboratory for Marine Bioactive Polysaccharide Development and Application, Dalian Polytechnic University, Dalian, China
- Shuang Song
| | - Beiwei Zhu
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
- National & Local Joint Engineering Laboratory for Marine Bioactive Polysaccharide Development and Application, Dalian Polytechnic University, Dalian, China
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19
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He C, Tang X, He X, Zhou Y, Liu X, Feng X. Regio- and enantioselective conjugate addition of β-nitro α,β-unsaturated carbonyls to construct 3-alkenyl disubstituted oxindoles. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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20
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Influence of the features of the spatial and electronic structure of α-substituted β-ethoxyvinyl trifluoromethyl ketones and secondary amines on their reactivity. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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21
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Proppe J, Kircher J. Uncertainty Quantification of Reactivity Scales. Chemphyschem 2022; 23:e202200061. [PMID: 35189024 PMCID: PMC9314972 DOI: 10.1002/cphc.202200061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/16/2022] [Indexed: 11/09/2022]
Abstract
According to Mayr, polar organic synthesis can be rationalized by a simple empirical relationship linking bimolecular rate constants to as few as three reactivity parameters. Here, we propose an extension to Mayr's reactivity method that is rooted in uncertainty quantification and transforms the reactivity parameters into probability distributions. Through uncertainty propagation, these distributions can be transformed into uncertainty estimates for bimolecular rate constants. Chemists can exploit these virtual error bars to enhance synthesis planning and to decrease the ambiguity of conclusions drawn from experimental data. We demonstrate the above at the example of the reference data set released by Mayr and co-workers [J. Am. Chem. Soc. 2001, 123, 9500; J. Am. Chem. Soc. 2012, 134, 13902]. As by-product of the new approach, we obtain revised reactivity parameters for 36 π-nucleophiles and 32 benzhydrylium ions.
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Affiliation(s)
- Jonny Proppe
- Georg-August UniversityInstitute of Physical ChemistryTammannstrasse 637077GöttingenGermany
- Present address: Technische Universität BraunschweigInstitute of Physical and Theoretical ChemistryGaussstrasse 1738106BraunschweigGermany
| | - Johannes Kircher
- Georg-August UniversityInstitute of Physical ChemistryTammannstrasse 637077GöttingenGermany
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22
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Haas BC, Goetz AE, Bahamonde A, McWilliams JC, Sigman MS. Predicting relative efficiency of amide bond formation using multivariate linear regression. Proc Natl Acad Sci U S A 2022; 119:e2118451119. [PMID: 35412905 PMCID: PMC9169781 DOI: 10.1073/pnas.2118451119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 02/09/2022] [Indexed: 01/29/2023] Open
Abstract
Amides are ubiquitous in biologically active natural products and commercial drugs. The most common strategy for introducing this functional group is the coupling of a carboxylic acid with an amine, which requires the use of a coupling reagent to facilitate elimination of water. However, the optimal reaction conditions often appear rather arbitrary to the specific reaction. Herein, we report the development of statistical models correlating measured rates to physical organic descriptors to enable the prediction of reaction rates for untested carboxylic acid/amine pairs. The key to the success of this endeavor was the development of an end-to-end data science–based workflow to select a set of coupling partners that are appropriately distributed in chemical space to facilitate statistical model development. By using a parameterization, dimensionality reduction, and clustering protocol, a training set was identified. Reaction rates for a range of carboxylic acid and primary alkyl amine couplings utilizing carbonyldiimidazole (CDI) as the coupling reagent were measured. The collected rates span five orders of magnitude, confirming that the designed training set encompasses a wide range of chemical space necessary for effective model development. Regressing these rates with high-level density functional theory (DFT) descriptors allowed for identification of a statistical model wherein the molecular features of the carboxylic acid are primarily responsible for the observed rates. Finally, out-of-sample amide couplings are used to determine the limitations and effectiveness of the model.
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Affiliation(s)
- Brittany C. Haas
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112
| | - Adam E. Goetz
- Chemical Research and Development, Groton Laboratories, Pfizer Worldwide Research and Development, Groton, CT 06340
| | - Ana Bahamonde
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112
| | - J. Christopher McWilliams
- Chemical Research and Development, Groton Laboratories, Pfizer Worldwide Research and Development, Groton, CT 06340
| | - Matthew S. Sigman
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112
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23
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24
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Saini V, Sharma A, Nivatia D. A machine learning approach for predicting the nucleophilicity of organic molecules. Phys Chem Chem Phys 2022; 24:1821-1829. [PMID: 34986215 DOI: 10.1039/d1cp05072a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Nucleophilicity provides important information about the chemical reactivity of organic molecules. Experimental determination of the nucleophilicity parameter is a tedious and resource-intensive approach. Herein, we present a novel machine learning protocol that uses key structural descriptors to predict the nucleophilicities of organic molecules, which agree well with the experimental values. A data driven approach was used where quantum mechanical molecular and thermodynamic descriptors from a wide range of structurally diverse nucleophiles and relevant solvents were extracted and modelled using advanced algorithms against the experimentally available nucleophilicity values. Despite the structural diversity of nucleophiles, we are able to achieve statistically robust models with a high predictive power using tree-based and neural network algorithms trained on an in-house developed unique dataset consisting of 752 nucleophilicity values and 27 molecular descriptors.
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Affiliation(s)
- Vaneet Saini
- Department of Chemistry & Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India.
| | - Aditya Sharma
- Department of Chemistry & Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India.
| | - Dhruv Nivatia
- IT Department, University Institute of Engineering & Technology, Panjab University, Chandigarh 160014, India
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25
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Franceschi P, Nicoletti C, Bonetto R, Bonchio M, Natali M, Dell'Amico L, Sartorel A. Basicity as a Thermodynamic Descriptor of Carbanions Reactivity with Carbon Dioxide: Application to the Carboxylation of α,β-Unsaturated Ketones. Front Chem 2021; 9:783993. [PMID: 34900942 PMCID: PMC8652261 DOI: 10.3389/fchem.2021.783993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 10/28/2021] [Indexed: 12/24/2022] Open
Abstract
The utilization of carbon dioxide as a raw material represents nowadays an appealing strategy in the renewable energy, organic synthesis, and green chemistry fields. Besides reduction strategies, carbon dioxide can be exploited as a single-carbon-atom building block through its fixation into organic scaffolds with the formation of new C-C bonds (carboxylation processes). In this case, activation of the organic substrate is commonly required, upon formation of a carbanion C-, being sufficiently reactive toward the addition of CO2. However, the prediction of the reactivity of C- with CO2 is often problematic with the process being possibly associated with unfavorable thermodynamics. In this contribution, we present a thermodynamic analysis combined with density functional theory calculations on 50 organic molecules enabling the achievement of a linear correlation of the standard free energy (ΔG0) of the carboxylation reaction with the basicity of the carbanion C-, expressed as the pKa of the CH/C- couple. The analysis identifies a threshold pKa of ca 36 (in CH3CN) for the CH/C- couple, above which the ΔG0 of the carboxylation reaction is negative and indicative of a favorable process. We then apply the model to a real case involving electrochemical carboxylation of flavone and chalcone as model compounds of α,β-unsaturated ketones. Carboxylation occurs in the β-position from the doubly reduced dianion intermediates of flavone and chalcone (calculated ΔG0 of carboxylation in β = -12.8 and -20.0 Kcalmol-1 for flavone and chalcone, respectively, associated with pKa values for the conjugate acids of 50.6 and 51.8, respectively). Conversely, the one-electron reduced radical anions are not reactive toward carboxylation (ΔG0 > +20 Kcalmol-1 for both substrates, in either α or β position, consistent with pKa of the conjugate acids < 18.5). For all the possible intermediates, the plot of calculated ΔG0 of carboxylation vs. pKa is consistent with the linear correlation model developed. The application of the ΔG0 vs. pKa correlation is finally discussed for alternative reaction mechanisms and for carboxylation of other C=C and C=O double bonds. These results offer a new mechanistic tool for the interpretation of the reactivity of CO2 with organic intermediates.
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Affiliation(s)
- Pietro Franceschi
- Nano and Molecular Catalysis Laboratory, Department of Chemical Sciences, University of Padova, Padova, Italy
| | - Catia Nicoletti
- Nano and Molecular Catalysis Laboratory, Department of Chemical Sciences, University of Padova, Padova, Italy
| | - Ruggero Bonetto
- Nano and Molecular Catalysis Laboratory, Department of Chemical Sciences, University of Padova, Padova, Italy
| | - Marcella Bonchio
- Nano and Molecular Catalysis Laboratory, Department of Chemical Sciences, University of Padova, Padova, Italy
| | - Mirco Natali
- Department of Chemical, Pharmaceutical and Agricultural Sciences (DOCPAS), University of Ferrara, and Centro Interuniversitario per La Conversione Chimica Dell'Energia Solare (SOLARCHEM), Ferrara, Italy
| | - Luca Dell'Amico
- Nano and Molecular Catalysis Laboratory, Department of Chemical Sciences, University of Padova, Padova, Italy
| | - Andrea Sartorel
- Nano and Molecular Catalysis Laboratory, Department of Chemical Sciences, University of Padova, Padova, Italy
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26
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Yang XP, Lv HP, Yang HD, Wang BL, Wang XW. Box-copper catalyzed cascade asymmetric amidation for chiral exo-methylene aminoindoline derivatives. Org Biomol Chem 2021; 19:9373-9378. [PMID: 34673876 DOI: 10.1039/d1ob01242h] [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
Enantioselective copper-catalyzed cascade inter- and intramolecular amidation was achieved between ethynyl benzoxazinanones and α-halohydroxamates in the presence of an indapybox ligand. The one-pot cascade transformation was triggered by the attack of hydroxamates to dipolar copper-allenylidene intermediates, followed by a nucleophilic annulation reaction. Thus, a series of exo-methylene 3-aminoindoline derivatives were obtained in good yields with high enantioselectivities under mild reaction conditions.
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Affiliation(s)
- Xiao-Peng Yang
- Key Laboratory of Organic Synthesis of Jiangsu Province, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, P. R. China.
| | - Hao-Peng Lv
- Key Laboratory of Organic Synthesis of Jiangsu Province, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, P. R. China.
| | - Hao-Di Yang
- Key Laboratory of Organic Synthesis of Jiangsu Province, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, P. R. China.
| | - Bai-Lin Wang
- Key Laboratory of Organic Synthesis of Jiangsu Province, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, P. R. China.
| | - Xing-Wang Wang
- Key Laboratory of Organic Synthesis of Jiangsu Province, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, P. R. China.
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27
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Boobier S, Liu Y, Sharma K, Hose DRJ, Blacker AJ, Kapur N, Nguyen BN. Predicting Solvent-Dependent Nucleophilicity Parameter with a Causal Structure Property Relationship. J Chem Inf Model 2021; 61:4890-4899. [PMID: 34549957 DOI: 10.1021/acs.jcim.1c00610] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Solvent-dependent reactivity is a key aspect of synthetic science, which controls reaction selectivity. The contemporary focus on new, sustainable solvents highlights a need for reactivity predictions in different solvents. Herein, we report the excellent machine learning prediction of the nucleophilicity parameter N in the four most-common solvents for nucleophiles in the Mayr's reactivity parameter database (R2 = 0.93 and 81.6% of predictions within ±2.0 of the experimental values with Extra Trees algorithm). A Causal Structure Property Relationship (CSPR) approach was utilized, with focus on the physicochemical relationships between the descriptors and the predicted parameters, and on rational improvements of the prediction models. The nucleophiles were represented with a series of electronic and steric descriptors and the solvents were represented with principal component analysis (PCA) descriptors based on the ACS Solvent Tool. The models indicated that steric factors do not contribute significantly, because of bias in the experimental database. The most important descriptors are solvent-dependent HOMO energy and Hirshfeld charge of the nucleophilic atom. Replacing DFT descriptors with Parameterization Method 6 (PM6) descriptors for the nucleophiles led to an 8.7-fold decrease in computational time, and an ∼10% decrease in the percentage of predictions within ±2.0 and ±1.0 of the experimental values.
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Affiliation(s)
- Samuel Boobier
- Institute of Process Research & Development, School of Chemistry, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Yufeng Liu
- Institute of Process Research & Development, School of Chemistry, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Krishna Sharma
- Institute of Process Research & Development, School of Chemistry, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - David R J Hose
- Chemical Development, Pharmaceutical Technology and Development, Operations, AstraZeneca, Macclesfield SK10 2NA, United Kingdom
| | - A John Blacker
- Institute of Process Research & Development, School of Chemistry, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Nikil Kapur
- School of Mechanical Engineering, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Bao N Nguyen
- Institute of Process Research & Development, School of Chemistry, University of Leeds, Leeds, LS2 9JT, United Kingdom
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28
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Matić M, Denegri B. Prediction of the kinetic stability of
N
‐alkyl‐X‐pyridinium ions in dichloromethane. J PHYS ORG CHEM 2021. [DOI: 10.1002/poc.4248] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Mirela Matić
- Faculty of Pharmacy and Biochemistry University of Zagreb Zagreb Croatia
| | - Bernard Denegri
- Faculty of Pharmacy and Biochemistry University of Zagreb Zagreb Croatia
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