How to easily replace the independent atom model – the example of bergenin, a potential anti-HIV agent of traditional Asian medicine

Dittrich, Birger; Weber, Manuela; Kalinowski, Roman; Grabowsky, Simon; Hübschle, Christian B.; Luger, Peter (2009). How to easily replace the independent atom model – the example of bergenin, a potential anti-HIV agent of traditional Asian medicine. Acta crystallographica. Section B - Structural science, 65(6), pp. 749-756. Wiley-Blackwell 10.1107/S0108768109046060

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Bergenin, which has been isolated from a variety of tropical plants, has several pharmacological applications in traditional Asian medicine. Its electron-density distribution was obtained from a room-temperature low-resolution X-ray data set measured with point detection making use of multipole populations from the invariom library. Two refinement models were considered. In a first step, positional parameters and ADPs were refined with fixed library multipoles (model E1). This model was suitable to be input into a second refinement of multipoles (model E2), which converged smoothly although based on Cu Kalpha room-temperature data. Quantitative results of a topological analysis of the electron density from both models were compared with Hartree-Fock and density-functional calculations. With respect to the independent atom model (IAM) more information can be extracted from invariom modelling, including the electrostatic potential and hydrogen-bond energies, which are highly useful, especially for biologically active compounds. The reliability of the applied invariom formalism was assessed by a comparison of bond-topological properties of sucrose, for which high-resolution multipole and invariom densities were available. Since a conventional X-ray diffraction experiment using basic equipment was combined with the easy-to-use invariom formalism, the procedure described here for bergenin illustrates how it can be routinely applied in pharmacological research.

Item Type:

Journal Article (Original Article)


08 Faculty of Science > Department of Chemistry, Biochemistry and Pharmaceutical Sciences (DCBP)

UniBE Contributor:

Grabowsky, Simon


500 Science > 570 Life sciences; biology
500 Science > 540 Chemistry








Simon Grabowsky

Date Deposited:

05 Feb 2020 16:20

Last Modified:

05 Dec 2022 15:35

Publisher DOI:





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