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Efficient approach for exploring the multiple-channel bimolecular interactions of conformationally flexible reagents. Epoxide ring opening reaction

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Abstract

Algorithm for generation and assessment of probability of possible reaction pathways for multiple-channel bimolecular interactions is presented. The proposed algorithm comprises a combination of few steps. They include conformational search for reaction intermediate using the molecular mechanics (MMX) approach, based on the obtained conformation construction of structures of transition states and pre-reaction complexes, and calculation activation energies to further determine the probable reaction pathways. The proposed algorithm could be adopted for investigation of chemical and biochemical reactions of different types. Here, we have considered the reaction of bicyclo[2.2.1]hept-5-en-endo-2-ylmethylamine (1) with glycidyl ether (2) in a neutral environment that proceeds through SN2-like mechanism forming bipolar ion (3) which is a good starting point for identification of the reaction channels. Conformational properties of intermediate (3) have been investigated using stochastic conformational search. From the 95 localized conformations within 10 kcal/mol of global minimum that have been obtained, 63 unique transition state conformations were generated and optimized by using the PM7 and M062X/6-31G(d) methods for accurate estimation of overall rate constant of reaction. The most energetically favorable pathways have been investigated at the M062X/6-31G(d) level of theory taking into account the influence of solvent.

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Funding

The computation time was provided by the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation grant number ACI-1548562 and XSEDE award allocation Number TG-DMR110088. This study was supported by the Ministry of Education and Science of Ukraine (grant 0119U100724). Jerzy Leszczynski is thankful to the National Science Foundation (NSF/CREST HRD-1547754) for financial support.

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Authors and Affiliations

  1. Department of Physical, Organic and Inorganic Chemistry, Oles Honchar Dnipro National University, Dnipro, 49000, Ukraine

    Iryna O. Borysenko & Sergiy I. Okovytyy

  2. Department of General and Biological Chemistry N2, Donetsk National Medical University, 1 Velyka Perspectyvna Str., Kropyvnytskyi, 25015, Ukraine

    Liudmyla K. Sviatenko

  3. Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, Jackson, MS, 39217, USA

    Jerzy Leszczynski

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  1. Iryna O. Borysenko
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  2. Liudmyla K. Sviatenko
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  3. Sergiy I. Okovytyy
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Correspondence to Sergiy I. Okovytyy.

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Borysenko, I.O., Sviatenko, L.K., Okovytyy, S.I. et al. Efficient approach for exploring the multiple-channel bimolecular interactions of conformationally flexible reagents. Epoxide ring opening reaction. Struct Chem 32, 581–589 (2021). https://doi.org/10.1007/s11224-020-01663-0

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