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Alkyne-Allene Transformation: Density Functional and in silico Studies of 5-bromo-1-(Propargyl)-7-azabenzimidazole and its 1,2-propadiene Analogue

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Abstract

Allenes are important precursors for various cycloaddition reactions and they are present in several natural and synthetic medicinal compounds. One of the simplest ways of allenes preparation is through alkyne transformation. An earlier report described the base-catalyzed (Cs2CO3 or K2CO3) isomerization of 5-bromo-1-(propargyl)-7-azabenzimidazole to 5-bromo-1-(1,2-propadiene)-7-azabenzimidazole. The current work probes this transformation by computational methods at the DFT/B3LYP(M06-2X)/6–31(d) level of theory. The two isomers were docked in malaria kinase enzyme model (PbCDPK-1). The molecular descriptors such as energy gap (ΔE), global softness (S), chemical potential (σ), electrophilicity (ω) were calulated. Relative energy of the isomers (ΔEiso), free energy change (ΔGiso), enthalpy change (ΔHiso) and entropy change (ΔSiso) for the propargyl-propadiene isomerization. Results obtained indicated that the isomers were polar and strong electrophiles with charge transfer tendency. 5-bromo-1-(1,2-propadiene)-7-azabenzimidazole exhibits improved chemical softness and kinetic instability. The propargyl-propadiene isomer showed negative values for ΔEiso, ΔGiso, ΔHiso and ΔSiso. Malaria enzyme binding data were also obtained for these isomers and the 5-bromo-1-(1,2-propadiene)-7-azabenzimidazole gave a better scoring function which may be attributed to its chemical softness.

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Acknowledgements

We acknowledge the Department of Chemical Sciences, Adekunle Ajasin University, Nigeria and the Department of Chemistry, University of Ibadan, Nigeria.

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Authors and Affiliations

  1. Department of Chemical Sciences, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria

    Kola A. Oluwafemi & Oluwatoba E. Oyeneyin

  2. Theoretical and Computational Chemistry Unit, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria

    Oluwatoba E. Oyeneyin

  3. Department of Chemistry, University of Ibadan, Ibadan, Oyo State, Nigeria

    Nathanael D. Ojo

  4. Department of Chemistry, Federal University of Technology, Akure, Ondo State, Nigeria

    Jane A. Aigbogun

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  1. Kola A. Oluwafemi
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Correspondence to Kola A. Oluwafemi.

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Oluwafemi, K.A., Oyeneyin, O.E., Ojo, N.D. et al. Alkyne-Allene Transformation: Density Functional and in silico Studies of 5-bromo-1-(Propargyl)-7-azabenzimidazole and its 1,2-propadiene Analogue. Chemistry Africa 6, 1117–1123 (2023). https://doi.org/10.1007/s42250-022-00538-7

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