Format

Send to

Choose Destination
IUCrJ. 2019 Jul 15;6(Pt 5):868-883. doi: 10.1107/S2052252519007358. eCollection 2019 Sep 1.

Energetics of interactions in the solid state of 2-hydroxy-8-X-quinoline derivatives (X = Cl, Br, I, S-Ph): comparison of Hirshfeld atom, X-ray wavefunction and multipole refinements.

Author information

1
Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Zwirki i Wigury 101, Warszawa 02-089, Poland.
2
Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.
3
College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences (MISMaP), University of Warsaw, Stefana Banacha 2C, Warszawa 02-097, Poland.
4
Department of Drug Chemistry, Faculty of Pharmacy, Medicinal University of Warsaw, Stefana Banacha 1, Warszawa 02-091, Poland.
5
Department of Pharmacodynamics, Centre of Preclinical Research and Technology, Faculty of Pharmacy, Medical University of Warsaw, Stefana Banacha 1, Warszawa 02-091, Poland.
6
Department of Chemistry, University of Warsaw, Pasteura 1, Warszawa 02-093, Poland.

Abstract

In this work, two methods of high-resolution X-ray data refinement: multipole refinement (MM) and Hirshfeld atom refinement (HAR) - together with X-ray wavefunction refinement (XWR) - are applied to investigate the refinement of positions and anisotropic thermal motion of hydrogen atoms, experiment-based reconstruction of electron density, refinement of anharmonic thermal vibrations, as well as the effects of excluding the weakest reflections in the refinement. The study is based on X-ray data sets of varying quality collected for the crystals of four quinoline derivatives with Cl, Br, I atoms and the -S-Ph group as substituents. Energetic investigations are performed, comprising the calculation of the energy of intermolecular interactions, cohesive and geometrical relaxation energy. The results obtained for experimentally derived structures are verified against the values calculated for structures optimized using dispersion-corrected periodic density functional theory. For the high-quality data sets (the Cl and -S-Ph compounds), both MM and XWR could be successfully used to refine the atomic displacement parameters and the positions of hydrogen atoms; however, the bond lengths obtained with XWR were more precise and closer to the theoretical values. In the application to the more challenging data sets (the Br and I compounds), only XWR enabled free refinement of hydrogen atom geometrical parameters, nevertheless, the results clearly showed poor data quality. For both refinement methods, the energy values (intermolecular interactions, cohesive and relaxation) calculated for the experimental structures were in similar agreement with the values associated with the optimized structures - the most significant divergences were observed when experimental geometries were biased by poor data quality. XWR was found to be more robust in avoiding incorrect distortions of the reconstructed electron density as a result of data quality issues. Based on the problem of anharmonic thermal motion refinement, this study reveals that for the most correct interpretation of the obtained results, it is necessary to use the complete data set, including the weak reflections in order to draw conclusions.

KEYWORDS:

X-ray wavefunction refinement; anharmonic thermal motion; charge, spin and momentum densities; energy calculations; high-resolution X-ray crystallography; intermolecular interactions; molecular crystals; multipole refinement

Supplemental Content

Full text links

Icon for International Union of Crystallography Icon for PubMed Central
Loading ...
Support Center