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Studying the hydrogen atom position in the strong-short intermolecular hydrogen bond of pure and 5-substituted 9-hydroxyphenalenones by invariom refinement and ONIOM cluster computations

  • Irina Gruber , Lisa Bensch , Thomas J. J. Müller ORCID logo , Christoph Janiak ORCID logo and Birger Dittrich ORCID logo EMAIL logo


The solid-state structures of three H-bonded enol forms of 5-substituted 9-hydroxyphenalenones were investigated to accurately determine the H atom positions of the intramolecular hydrogen bond. For this purpose, single-crystal X-ray diffraction (SC-XRD) data were evaluated by invariom-model refinement. In addition, QM/MM computations of central molecules in their crystal environment show that results of an earlier standard independent atom model refinement, which pointed to the presence of a resonance-assisted hydrogen bond in unsubstituted 9-hydroxyphenalone, are misleading: in all our three and the earlier solid-state structures the lowest energy form is that of an asymmetric hydrogen bond (CS form). Apparent differences of results from SC-XRD and other analytical methods are explained.

Corresponding author: Birger Dittrich, Institut für Anorganische Chemie und Strukturchemie II, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany, E-mail:

Funding source: DFG

Award Identifier / Grant number: DI 921/6-1


We thank the DFG, project DI 921/6-1, for financial support.

  1. Author contribution: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.

  2. Research funding: B.D. acknowledges funding from the Deutsche Forschungsgemeinschaft DFG, project DI 921/6-1.

  3. Conflict of interest statement: The authors declare no conflicts of interest regarding this article.


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Supplementary Material

The online version of this article offers supplementary material (

Received: 2020-03-02
Accepted: 2020-05-04
Published Online: 2020-06-03
Published in Print: 2020-07-28

© 2020 Walter de Gruyter GmbH, Berlin/Boston

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