Abstract
The electron density distribution (EDD) of a plant cyclic nonapeptide of orbitide type was studied. Crystal X-ray diffraction data was obtained from the Cambridge Structural Database (CSD) and refitted using scattering factors of the invariom library, thereby providing aspherical electron density. Bond topological, atomic properties and molecular surfaces (electrostatic potential and Hirshfeld surfaces) were derived. The partial double bond character of the peptide bond was confirmed by the ellipticity ε = 0.25. For eight N–H⋯O hydrogen bonds, atomic charges of contributing atoms differ depending on the type of the accepting oxygen atom. Atomic charge differences between negative main and positive side chains of this nonapeptide result in characteristic features of the electrostatic potential, which shows a positive isosurface around the molecule leading to repulsive interactions in the solid state structure. Weak intermolecular interactions are indicated by insignificant ED concentrations on the Hirshfeld surface except for weak signals at sites of intermolecular N–H⋯O and C–H⋯O hydrogen bonds.
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Research ethics: Not applicable.
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Author contributions: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.
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Competing interests: The authors declare no conflicts of interest regarding this article.
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Research funding: None declared.
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Data availability: Not applicable.
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Supplementary Material
This article contains supplementary material (https://doi.org/10.1515/znb-2023-0105).
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