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Palladium(II)-catalyzed annulation of N-methoxy amides and arynes: computational mechanistic insights and substituents effects

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Abstract

Context

The combined use of transition metal-catalyzed C–H activation with aryne annulation reactions has emerged as an important strategy in organic synthesis. In this study, the mechanisms of the palladium(II)-catalyzed annulation reaction of N-methoxy amides and arynes were computationally investigated by density functional theory. The role of methoxy amide as a directing group was elucidated through the calculation of three different pathways for the C–H activation step, showing that the pathway where amide nitrogen acts as a directing group is preferable. At the reductive elimination transition state, an unstable seven-membered ring is formed preventing the lactam formation. A substituent effect study based on an NBO analysis, Hammet, and using a More O’Ferall-Jenks plot indicates that the C–H activation step proceeds via an electrophilic concerted metalation-deprotonation (eCMD) mechanism. The results show that electron-withdrawing groups increase the activation barrier and contribute to an early Pd–C bond formation and a late C–H bond breaking when compared with electron-donating substituents. Our computational results are in agreement with the experimental data provided in the literature.

Methods

All calculations were performed using Gaussian 16 software. Geometry optimizations, frequency analyses at 393.15 K, and IRC calculations were conducted at the M06L/Def2-SVP level of theory. Corrected electronic energies, NBO charges, and Wiberg bond indexes were computed at the M06L/Def2-TZVP//M06L/Def2-SVP level of theory. Implicit solvent effects were considered in all calculations using the SMD model, with acetonitrile employed as the solvent.

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Data availability

The inputs and outputs files of the calculations presented in the article are available in the ioChem-BD repository (https://doi.org/10.19061/iochem-bd-6-343). Additional data is provided in the supplementary information.

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Acknowledgements

The authors acknowledge the Superintendência de Tecnologia da Informação from University of São Paulo (STI-USP), CNPq, CAPES and the São Paulo Research Foundation (FAPESP).

Funding

A.A.C.B. received financial support from São Paulo Research Foundation (FAPESP) (Grant #2015/01491-3), the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) of Brazil (Grants 312550/2020-0 and 313720/2023-1), and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES) that partially supported this work (Finance Code 001). E.H.S.A. received financial support from FAPESP (Grant #2022/16623-6). D.A.S.O. received financial support from FAPESP (Grant #2022/01685-6) and CNPq (Grant #162366/2021-3).

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  1. Departament of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, 05508-000, São Paulo, Brazil

    Erick H. S. Alves, Daniel A. S. Oliveira & Ataualpa A. C. Braga

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Erick H. S. Alves: conceptualization, methodology, performed computations, formal analysis, writing—original draft; Daniel A. S. Oliveira: conceptualization, methodology, performed computations, formal analysis, writing—original draft; Ataualpa A. C. Braga: conceptualization, methodology, formal analysis, supervision, writing-review and edition.

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Alves, E.H.S., Oliveira, D.A.S. & Braga, A.A.C. Palladium(II)-catalyzed annulation of N-methoxy amides and arynes: computational mechanistic insights and substituents effects. J Mol Model 30, 152 (2024). https://doi.org/10.1007/s00894-024-05930-3

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