A resonance-assisted intra­molecular hydrogen bond in compounds containing 2-hy­droxy-35-di­nitro­benzoic acid and its various deprotonated forms: redetermination of several related structures

摘要

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. B>72, 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.