Understanding chemical reactivity using the activation strain model
| Autor: | Trevor A. Hamlin, Pascal Vermeeren, Célia Fonseca Guerra, Stephanie C. C. van der Lubbe, F. Matthias Bickelhaupt |
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| Přispěvatelé: | AIMMS, Theoretical Chemistry, Chemistry and Pharmaceutical Sciences |
| Rok vydání: | 2020 |
| Předmět: |
0303 health sciences
Materials science Supramolecular chemistry Stationary point Chemical reaction General Biochemistry Genetics and Molecular Biology Reaction coordinate 03 medical and health sciences 0302 clinical medicine Potential energy surface Reactivity (chemistry) SDG 7 - Affordable and Clean Energy Biological system Theoretical Chemistry Protocol (object-oriented programming) 030217 neurology & neurosurgery Energy (signal processing) 030304 developmental biology |
| Zdroj: | Nature Protocols Vermeeren, P, van der Lubbe, S C C, Fonseca Guerra, C, Bickelhaupt, F M & Hamlin, T A 2020, ' Understanding chemical reactivity using the activation strain model ', Nature Protocols, vol. 15, no. 2, pp. 649-667 . https://doi.org/10.1038/s41596-019-0265-0 Nature Protocols, 15(2), 649-667. Nature Publishing Group |
| ISSN: | 1754-2189 |
| DOI: | 10.1038/s41596-019-0265-0 |
| Popis: | Understanding chemical reactivity through the use of state-of-the-art computational techniques enables chemists to both predict reactivity and rationally design novel reactions. This protocol aims to provide chemists with the tools to implement a powerful and robust method for analyzing and understanding any chemical reaction using PyFrag 2019. The approach is based on the so-called activation strain model (ASM) of reactivity, which relates the relative energy of a molecular system to the sum of the energies required to distort the reactants into the geometries required to react plus the strength of their mutual interactions. Other available methods analyze only a stationary point on the potential energy surface, but our methodology analyzes the change in energy along a reaction coordinate. The use of this methodology has been proven to be critical to the understanding of reactions, spanning the realms of the inorganic and organic, as well as the supramolecular and biochemical, fields. This protocol provides step-by-step instructions—starting from the optimization of the stationary points and extending through calculation of the potential energy surface and analysis of the trend-decisive energy terms—that can serve as a guide for carrying out the analysis of any given reaction of interest within hours to days, depending on the size of the molecular system. |
| Databáze: | OpenAIRE |
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