The origin of synthons and supramolecular motifs: beyond atoms and functional groups
A four-membered R22(4) supramolecular motif formed by S...S and S...I chalcogen-bonding interactions in the crystal structure of 4-iodo-1,3-dithiol-2-one (C3HIOS2, IDT) is analysed and compared with a similar R22(4) motif (stabilized by Se...Se and Se...O chalcogen bonds) observed in the previously...
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International Union of Crystallography
2025-05-01
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| Online Access: | https://journals.iucr.org/paper?S2052252525001447 |
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| author | Rahul Shukla Emmanuel Aubert Mariya Brezgunova Sébastien Lebègue Marc Fourmigué Enrique Espinosa |
| author_facet | Rahul Shukla Emmanuel Aubert Mariya Brezgunova Sébastien Lebègue Marc Fourmigué Enrique Espinosa |
| author_sort | Rahul Shukla |
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| description | A four-membered R22(4) supramolecular motif formed by S...S and S...I chalcogen-bonding interactions in the crystal structure of 4-iodo-1,3-dithiol-2-one (C3HIOS2, IDT) is analysed and compared with a similar R22(4) motif (stabilized by Se...Se and Se...O chalcogen bonds) observed in the previously reported crystal structure of selenaphthalic anhydride (C8H4O2Se, SePA) through detailed charge density analysis. Our investigation reveals that the chalcogen-bonding interactions participating in the R22(4) motifs observed in the two structures have the same characteristic orientation of local electrostatic electrophilic...nucleophilic interactions while involving different types of atoms. We carried out Cambridge Structural Database searches for synthons and supramolecular motifs involving chalcogen-, halogen- and hydrogen-bonding (ChB, XB and HB) interactions. Geometrical characterizations and topological analyses of the electron density ρ(r) and its negative Laplacian function [L(r) = −∇2ρ(r)] indicate that all the bonding interactions forming the motifs are driven by local electrophilic...nucleophilic interactions between complementary charge concentration (CC) and charge depletion (CD) sites present in the valence shells of the atoms, regardless of the atoms and functional groups involved. The graph-set assignment Gda(n) (G = C, R, D or S), formerly developed by Etter [Acc. Chem. Res. (1990), 23, 120–126] for HB interactions, is a convenient way to describe the connectivity in supramolecular motifs based on electrophilic...nucleophilic interactions (such as ChB, XB and HB interactions), exchanging the number of atomic acceptors (a) and donors (d) with the number of nucleophilic (n: CC) and electrophilic (e: CD) sites, and the number of atoms building the motif n by m, leading to the new graph-set assignment Gen(m) (G = C, R, D or S). Geometrical preferences in the molecular assembly of synthons and other supramolecular motifs are governed by the relative positions of CC and CD sites through CC...CD interactions that, in most cases, align with the internuclear directions within a <15° range despite low interaction energies. Accordingly, beyond atoms and functional groups, the origin of recurrent supramolecular structures embedded within different molecular environments is found in the local electrostatic complementarity of electrophilic and nucleophilic regions that are placed at particular geometries, driving the formation and the geometry of synthons and supramolecular motifs by directional and locally stabilizing electrostatic interactions. |
| format | Article |
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| publishDate | 2025-05-01 |
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| spelling | doaj-art-fa6de1b3ce1b457eaf8f0a7dd6fbc2a62025-08-20T01:48:26ZengInternational Union of CrystallographyIUCrJ2052-25252025-05-0112333435710.1107/S2052252525001447pen5012The origin of synthons and supramolecular motifs: beyond atoms and functional groupsRahul Shukla0Emmanuel Aubert1Mariya Brezgunova2Sébastien Lebègue3Marc Fourmigué4Enrique Espinosa5CRM2, Université de Lorraine, CNRS, Nancy F-54500, FranceCRM2, Université de Lorraine, CNRS, Nancy F-54500, FranceCRM2, Université de Lorraine, CNRS, Nancy F-54500, FranceCRM2, Université de Lorraine, CNRS, Nancy F-54500, FranceInstitut des Sciences Chimiques de Rennes, Université Rennes 1, UMR CNRS 6226, Campus de Beaulieu 35042, FranceCRM2, Université de Lorraine, CNRS, Nancy F-54500, FranceA four-membered R22(4) supramolecular motif formed by S...S and S...I chalcogen-bonding interactions in the crystal structure of 4-iodo-1,3-dithiol-2-one (C3HIOS2, IDT) is analysed and compared with a similar R22(4) motif (stabilized by Se...Se and Se...O chalcogen bonds) observed in the previously reported crystal structure of selenaphthalic anhydride (C8H4O2Se, SePA) through detailed charge density analysis. Our investigation reveals that the chalcogen-bonding interactions participating in the R22(4) motifs observed in the two structures have the same characteristic orientation of local electrostatic electrophilic...nucleophilic interactions while involving different types of atoms. We carried out Cambridge Structural Database searches for synthons and supramolecular motifs involving chalcogen-, halogen- and hydrogen-bonding (ChB, XB and HB) interactions. Geometrical characterizations and topological analyses of the electron density ρ(r) and its negative Laplacian function [L(r) = −∇2ρ(r)] indicate that all the bonding interactions forming the motifs are driven by local electrophilic...nucleophilic interactions between complementary charge concentration (CC) and charge depletion (CD) sites present in the valence shells of the atoms, regardless of the atoms and functional groups involved. The graph-set assignment Gda(n) (G = C, R, D or S), formerly developed by Etter [Acc. Chem. Res. (1990), 23, 120–126] for HB interactions, is a convenient way to describe the connectivity in supramolecular motifs based on electrophilic...nucleophilic interactions (such as ChB, XB and HB interactions), exchanging the number of atomic acceptors (a) and donors (d) with the number of nucleophilic (n: CC) and electrophilic (e: CD) sites, and the number of atoms building the motif n by m, leading to the new graph-set assignment Gen(m) (G = C, R, D or S). Geometrical preferences in the molecular assembly of synthons and other supramolecular motifs are governed by the relative positions of CC and CD sites through CC...CD interactions that, in most cases, align with the internuclear directions within a <15° range despite low interaction energies. Accordingly, beyond atoms and functional groups, the origin of recurrent supramolecular structures embedded within different molecular environments is found in the local electrostatic complementarity of electrophilic and nucleophilic regions that are placed at particular geometries, driving the formation and the geometry of synthons and supramolecular motifs by directional and locally stabilizing electrostatic interactions.https://journals.iucr.org/paper?S2052252525001447chalcogen bondinghalogen bondinghydrogen bondingelectrophilic–nucleophilic interactionselectron densitylaplacian of electron densitytopological analysiscrystal engineering |
| spellingShingle | Rahul Shukla Emmanuel Aubert Mariya Brezgunova Sébastien Lebègue Marc Fourmigué Enrique Espinosa The origin of synthons and supramolecular motifs: beyond atoms and functional groups IUCrJ chalcogen bonding halogen bonding hydrogen bonding electrophilic–nucleophilic interactions electron density laplacian of electron density topological analysis crystal engineering |
| title | The origin of synthons and supramolecular motifs: beyond atoms and functional groups |
| title_full | The origin of synthons and supramolecular motifs: beyond atoms and functional groups |
| title_fullStr | The origin of synthons and supramolecular motifs: beyond atoms and functional groups |
| title_full_unstemmed | The origin of synthons and supramolecular motifs: beyond atoms and functional groups |
| title_short | The origin of synthons and supramolecular motifs: beyond atoms and functional groups |
| title_sort | origin of synthons and supramolecular motifs beyond atoms and functional groups |
| topic | chalcogen bonding halogen bonding hydrogen bonding electrophilic–nucleophilic interactions electron density laplacian of electron density topological analysis crystal engineering |
| url | https://journals.iucr.org/paper?S2052252525001447 |
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