The importance of careful refinement
A large number of structural determinations of compounds containing 2-hydroxy-3,5-dinitrobenzoic acid and its various deprotonated forms, 2-hydroxy-3,5-dinitrobenzoate or 2-carboxy-4,6-dinitrophenolate, are biased. The reason for this follows from incorrectly applied constraints or restraints on the bridging hydrogen, which is involved in an intramolecular hydrogen bond between neighbouring carboxylic/carboxylate and oxo/hydroxy groups. This hydrogen bond belongs to the category of resonance-assisted hydrogen bonds. The position of the bridging hydrogen seems to be dependent on the pKa(base), though with some exceptions. A stronger basicity enhances the probability of the presence of a phenolate. The problem of the location and refinement of such a bridging hydrogen, as well as that of the hydrogen atoms involved in the hydroxy group, and primary and secondary amine groups, is discussed in a recent article by Fábry [Acta Cryst. (2018). E74, 1344-1357]. It appears that the best model, in many cases, is obtained by fixing the hydrogen-atom positions found in a difference electron-density map while refining its isotropic displacement parameter.
"It is almost futile to state that modern automated diffractometers have enabled single-crystal X-ray structure analysis to become widely applied even by non-experts," commented Dr Fábry. "At the same time, however, it is important to emphasize that a large number of structure determinations of even simple molecules suffer from defects that are caused by inappropriately applied constraints or restraints. These defects bias not only the structure determinations themselves but also - more importantly - the overall information contained in the crystallographic databases. The present study of a whole family of the title molecules demonstrates the importance of careful refinement as well as of inspection of difference electron-density maps. I hope that this experience will reach especially those scientists for whom crystallography is not their specialization but nevertheless use it in their studies."
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