Efficient approach for exploring the multiple-channel bimolecular interactions of conformationally flexible reagents. Ep
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ORIGINAL RESEARCH
Efficient approach for exploring the multiple-channel bimolecular interactions of conformationally flexible reagents. Epoxide ring opening reaction Iryna O. Borysenko 1 & Liudmyla K. Sviatenko 2 & Sergiy I. Okovytyy 1
&
Jerzy Leszczynski 3
Received: 30 September 2020 / Accepted: 8 October 2020 # Springer Science+Business Media, LLC, part of Springer Nature 2020
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. Keywords Multiple-channel bimolecular reaction . Conformational analysis . Epoxide cycle opening . Glycidyl ethers
Introduction One of the most important tasks in the theoretical investigation of the mechanism of chemical reactions is finding all possible reaction pathways and locating transition state (TS) for them. The reaction pathways and TS structures therein could be Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11224-020-01663-0) contains supplementary material, which is available to authorized users. * Sergiy I. Okovytyy [email protected] 1
Department of Physical, Organic and Inorganic Chemistry, Oles Honchar Dnipro National University, Dnipro 49000, Ukraine
2
Department of General and Biological Chemistry N2, Donetsk National Medical University, 1 Velyka Perspectyvna Str., Kropyvnytskyi 25015, Ukraine
3
Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, Jackson, MS 39217, USA
guessed using researcher’s intuition or evaluated and approximated by various interpolation tools before optimization. Over the last decades, several automatic methods for systematic searching reac
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