Can we trust the experiment? Anisotropic displacement parameters in 1-(halomethyl)-3-nitrobenzene (halogen = Cl or Br).

Damian Mroz,Richard Dronskowski,Ruimin Wang,Ulli Englert

doi:10.1107/s2053229620006221

Damian Mroz, Richard Dronskowski + Show 2 more

Open Access

https://doi.org/10.1107/s2053229620006221

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Abstract

1-(Chloromethyl)-3-nitrobenzene, C7H6NClO2, and 1-(bromomethyl)-3-nitrobenzene, C7H6NBrO2, were chosen as test compounds for benchmarking anisotropic displacement parameters (ADPs) calculated from first principles in the harmonic approximation. Crystals of these compounds are isomorphous, and theory predicted similar ADPs for both. In-house diffraction experiments with Mo Kα radiation were in apparent contradiction to this theoretical result, with experimentally observed ADPs significantly larger for the bromo derivative. In contrast, the experimental and theoretical ADPs for the lighter congener matched reasonably well. As all usual quality indicators for both sets of experimental data were satisfactory, complementary diffraction experiments were performed at a synchrotron beamline with shorter wavelength. Refinements based on these intensity data gave very similar ADPs for both compounds and were thus in agreement with the earlier in-house results for the chloro derivative and the predictions of theory. We speculate that strong absorption by the heavy halogen may be the reason for the observed discrepancy.

Highlights

Careful diffraction experiments on crystals of reasonable quality provide reliable intensity data from which atomic positions and anisotropic displacement parameters (ADPs) can be derived almost routinely
Lattice parameters of the minimum energy structures match those observed experimentally well for 1 and 2, but a different picture is obtained when displacement parameters are considered. At low temperatures, such as 100 or 150 K, theoretical ADPs from first principles based on the harmonic approximation can be expected to match experiments reasonably well (George et al, 2015a,b; Deringer et al, 2016; Mroz et al, 2019)
If one wants to establish to what extent either absorption or variable illumination are responsible for apparent ADP problems, diffraction data on the same crystal should be collected as a function of beam size and wavelength, and multi-scan corrections should be tested as a function of multiplicity of observations

Summary

Introduction

Careful diffraction experiments on crystals of reasonable quality provide reliable intensity data from which atomic positions and anisotropic displacement parameters (ADPs) can be derived almost routinely. The alternative route towards ADPs, namely, their calculation from first principles, has made good progress (George et al, 2015a,b, 2016, 2017; Deringer et al, 2014, 2016, 2017; Baima et al, 2016; Lane et al, 2012; Madsen et al, 2013; Pozzi et al, 2013; Dittrich et al, 2012) This progress has been benchmarked by comparison with the results from single-crystal X-ray or neutron diffraction. In this context, a ‘heavy atom problem’ with ADPs from theory was suspected (Deringer et al, 2016) but not conclusively proven. More relevant in the context of this work is the previous report on 2 (CSD refcode INEFIS; Maris, 2016) because it was based on diffraction data collected at 100 K, the same temperature as in our case; we will come back to this CSD communication in more detail below

Experimental

Results and discussion

Conclusions

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