A resonance-assisted intramolecular hydrogen bond in compounds containing 2-hydroxy-3,5-dinitrobenzoic acid and its various deprotonated forms: Redetermination of several related structures

Abstract

A large number of structural determinations of compounds containing 2-hydroxy-3,5-dinitrobenzoic acid (I) and its various deprotonated forms, 2-hydroxy-3,5-dinitrobenzoate (II) or 2-carboxy-4,6-dinitrophenolate (III), are biased. The reason for the bias follows from incorrectly applied constraints or restraints on the bridging hydrogen, which is involved in the intramolecular hydrogen bond between the neighbouring carboxylic/carboxylate and oxo/hydroxy groups. This hydrogen bond belongs to the category of resonance-assisted hydrogen bonds. The present article suggests corrections for the following structure determinations that have been published in Acta Crystallographica: DUJZAK, JEVNAA, LUDFUL, NUQVEB, QIQJAD, SAFGUD, SEDKET, TIYZIM, TUJPEV, VABZIJ, WADXOR, YAXPOE [refcodes are taken from the Cambridge Structural Database [CSD; Groom et al. (2016). Acta Cryst. B72, 171-179]. The structural features of the title molecules in all the retrieved structures, together with structures that contain 3,5-dinitro-2-oxidobenzoate (IV), are discussed. Attention is paid to the localization of the above-mentioned bridging hydrogen, which can be situated closer to the O atom of the carboxylate/carboxylic group or that of the hydroxy/oxo group. In some cases, it is disordered between the two O atoms. The position of the bridging hydrogen seems to be dependent on the pK a (base) although with exceptions. A stronger basicity enhances the probability of the presence of a phenolate (III). The present article examines the problem of the refinement of such a bridging hydrogen as well as that of the hydrogen atoms involved in the hydroxy and primary and secondary amine groups. It appears that the best model, in many cases, is obtained by fixing the hydrogen-atom position found in the difference electron-density map while refining its isotropic displacement parameter.