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Theoretical analysis of C–F bond cleavage mediated by cob[I]alamin-based structures

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Abstract

In the present work, C–F bond cleavage mediated by the super-reduced form of cobalamin (i.e., CoICbl) was theoretically studied at the ONIOM(BP86/6-311++G(d,p):PM6) + SMD level of theory. Dispersion effects were introduced by employing Grimme’s empirical dispersion at the ONIOM(BP86-D/6-311++G(d,p):PM6) + SMD level. In the first stage of the study, cobalamin was characterized in terms of the coordination number of the central cobalt atom. The ONIOM(BP86/6-311++G(d,p):PM6) results showed that the base-off form of the system is slightly more stable than its base-on counterpart (ΔE = E base-off – E base-on ~ −2 kcal/mol). The inclusion of dispersive forces in the description of the system stabilizes the base-on form, which becomes as stable as its base-off counterpart. Moreover, in the latter case, the energy barrier separating both structures was found to be negligible, with a computed value of 1.02 kcal/mol. In the second stage of the work, the reaction CoICbl + CH3F → MeCbl + F− was studied considering the base-off and the base-on forms of CoICbl. The reaction that occurs in the presence of the base-on form of CoICbl was found to be kinetically more favorable (ΔE ≠ = 13.7 kcal/mol) than that occurring in the presence of the base-off form (ΔE ≠ = 41.2 kcal/mol). Further reaction-force analyses of the processes showed that the energy barrier to C–F bond cleavage arises largely due to structural rearrangements when the reaction occurs on the base-on form of the CoICbl complex, but is mainly due to electronic rearrangements when the reaction takes place on the base-off form of the complex. The latter behavior emerges from differences in the synchronicity of the bond strengthening/weakening processes along the reaction path; the base-on mode of CoICbl is able to decrease the synchronicity of the chemical events. This work gives new molecular-level insights into the role of Cbl-based systems in the cleavage of C–F bonds. These insights have potential implications for research into processes for degrading fluorine-containing pollutants.

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Acknowledgements

The present work was mainly carried out using the resources of the high-performance computing systems of UBx and USFQ. Corporación para el Desarrollo de Internet Avanzado (CEDIA) is also acknowledged for providing computing hours in its computational infrastructure. F.J.T., L.R., and J.M. thank the USFQ’s POLI-GRANTS program for financial support. D.E. Ortega is also acknowledged for useful discussions.

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Authors and Affiliations

  1. Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Ignacio Valdivieso 2409, P.O. Box 8940577, San Joaquín, Santiago, Chile

    D. Cortés-Arriagada

  2. Nucleus Millennium Chemical Processes and Catalysis (CPC), Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Casilla 306, Correo 22, Santiago, Chile

    A. Toro-Labbe

  3. Instituto de Simulación Computacional (ISC-USFQ), Diego de Robles y Vía Interoceánica, Universidad San Francisco de Quito, 17-1200-841, Quito, Ecuador

    J. R. Mora, L. Rincón & F. J. Torres

  4. Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Diego de Robles y Vía Interoceánica, Universidad San Francisco de Quito, 17-1200-841, Quito, Ecuador

    J. R. Mora, L. Rincón & F. J. Torres

  5. Université de Bordeaux, ISM, UMR 5255, 351 Cours de la Libération, F-33405, Talence, France

    R. Mereau

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  1. D. Cortés-Arriagada
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  2. A. Toro-Labbe
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Correspondence to F. J. Torres.

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This paper belongs to Topical Collection QUITEL 2016

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Cortés-Arriagada, D., Toro-Labbe, A., Mora, J.R. et al. Theoretical analysis of C–F bond cleavage mediated by cob[I]alamin-based structures. J Mol Model 23, 264 (2017). https://doi.org/10.1007/s00894-017-3431-8

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