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

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.

Further Validation of Quantum Crystallography Approaches

“…value is used as a reference. Based on our studies [ 12 , 17 ] and literature data [ 11 , 40 ], we propose that good agreement is achieved for an value equal to or less than 1. Notably, the value is a reliable parameter for the analysis of ADPs with high accordance.…”

“…In HAR, the wavefunctions calculated in all refinements were obtained using the DFT method, applying the BLYP functional and the cc-pVDZ basis set. In accordance with previous studies [ 17 , 33 , 39 ], the cluster size of the atomic charges and dipoles was set to a standard size of 8 Å. For all refinements, the full range of reflections (excluding those with negative intensities) was used [ 17 ].…”

“…In accordance with previous studies [ 17 , 33 , 39 ], the cluster size of the atomic charges and dipoles was set to a standard size of 8 Å. For all refinements, the full range of reflections (excluding those with negative intensities) was used [ 17 ]. The ADPs of hydrogen atoms obtained via the NoMoRe method were used for the Hirshfeld atom refinement (HAR) as fixed constraints.…”

“…In this work, we discuss the influence of the applied model of electron density ( Section 3.2 ), the approach to modelling hydrogen atom ADPs ( Section 3.3 ), and the source of radiation ( Section 3.4 ) on the parameters of charge density distribution. Some of these aspects were discussed in previous studies; for instance, the influence of H-atom ADPs on charge density results [ 13 , 14 ], the application of low-resolution Cu Kα data [ 12 , 15 , 16 ], and the differences between quantum crystallography models [ 17 , 18 , 19 , 20 , 21 , 22 ]. In this complementary work, we consider the effects of the refinement of hydrogen atoms with the NoMoRe method, as well as the influence of the source of radiation (with the same resolution).…”

Hirshfeld atom like refinement with alternative electron density partitions

“…HAR was applied to refinement of anharmonic thermal motions (Woinska et al, 2019;Orben & Dittrich, 2014), refinement of compounds that contain transition metals (Woiń ska et al, 2016;Bučinský et al, 2016Bučinský et al, , 2019Malaspina et al, 2019) and refinements including relativistic effects (Bučinský et al, 2016(Bučinský et al, , 2019Malaspina et al, 2019). Initial work aimed at optimizing HAR for the refinement of macromolecules is also available: HAR-ELMO (Malaspina et al, 2019) and fragHAR (Bergmann et al, 2020).…”