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Towards an unified chemical model of secondary bonding

Journal of Molecular Modeling volume 26, Article number: 62 (2020) Cite this article

Abstract

The concept of secondary bond covers a wide range of non-covalent interactions involving an acceptor (or electrophilic) molecule and an electron donor (or nucleophilic) one. It involves triel, tetrel, pnictogen, chalcogen, halogen, and aerogen bonds as well as hydrogen bonds. Such interactions yield complexes in which the internuclear distance of the electrophilic and nucleophilic centers is intermediate between the sums of the covalent and van der Waals radii of these atoms. These complexes can be considered as precursors of hypothetical nucleophilic substitution or addition reactions. As a consequence of the least motion principle, in the complex, the arrangement of the ligands around the electrophilic center should look like that of the hypothetical transition state or addition product. In a same fashion, the geometry around the nucleophilic center is determined by the location of the lone pair or of the bond involved in the interaction. In this picture of secondary bonding, the structure of the valence shell of the electrophilic atoms determines the geometry of the complex rather than the group to which belongs the elemental atom. The reorganization of the complexes in terms of the arrangement of the bonding and non-bonding electronic domains around the electrophilic center enables to rationalize the geometries in a systematic fashion. A set of VSEPR inspired rules enabling the building up of secondary bonded isomers are proposed and checked by quantum chemical calculations performed on representative test systems of the AX4−nEn type.

An example of secondary interaction: FClO\(^{...}\textit {FCH}_{3}\)

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Notes

  1. Electronic domains can be defined as a region in which there is a high probability of finding an opposite spin pair or a single electron in the case of open-shell systems. This definition is consistent with the mathematical definition of domain: subset MA of the manifold M such as any two points belonging to MA can be connected by a path totally contained in MA; for example, in \(\mathbb {R}^{3}\), a volume enclosed by an isosurface is a domain.

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Affiliations

  1. Sorbonne Universités, UPMC, Univ Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris Cedex 05, France

    Bernard Silvi

  2. Sorbonne Universités, UPMC, Univ Paris 06, MONARIS, UMR 8233, 4 place Jussieu, F-75005, Paris Cedex 05, France

    Esmaïl Alikhani

  3. Faculty of Chemistry, University of Wroclław, 14 F. Joliot Curie Str. 50-383, Wrocław, Poland

    Henryk Ratajczak

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Silvi, B., Alikhani, E. & Ratajczak, H. Towards an unified chemical model of secondary bonding. J Mol Model 26, 62 (2020). https://doi.org/10.1007/s00894-019-4283-1

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Keywords

  • Non-covalent interactions
  • Secondary bonds