Abstract
A large number of structural determinations of compounds containing 2-hy-droxy-3,5-di-nitro-benzoic acid (I) and its various deprotonated forms, 2-hy-droxy-3,5-di-nitro-benzoate (II) or 2-carb-oxy-4,6-di-nitro-phenolate (III), are biased. The reason for the bias follows from incorrectly applied constraints or restraints on the bridging hydrogen, which is involved in the intra-molecular hydrogen bond between the neighbouring carb-oxy-lic/carboxyl-ate and oxo/hy-droxy 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 mol-ecules in all the retrieved structures, together with structures that contain 3,5-di-nitro-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 carboxyl-ate/carb-oxy-lic group or that of the hy-droxy/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 pKa (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 hy-droxy 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.
Highlights
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
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)
Summary
2-Hydroxy-3,5-dinitrobenzoic acid (I; alternatively 3,5-dinitrosalicylic acid, DNSA), 2-hydroxy-3,5-dinitrobenzoate (II; alternatively 3,5-dinitrosalicylate), 2-carboxy-4,6-dinitrophenolate (III) and 3,5-dinitro-2-oxidobenzoate (IV), are molecules that have interesting structural and chemical features. The data for the suspect structures published in Acta Crystallographica were retrieved from the journal’s web page Some of the retrieved structures were difficult or impossible to recalculate with sufficient accuracy: HILPOI (trimethoprimium 3,5-dinitrosalicylate; Subashini et al, 2007) because of an abnormally low proportion of observed reflections ( the bridging hydrogen H6a is situated out of the plane between the carboxylate and hydroxy oxygen atoms, which seems to indicate an error) and VUZNEK (3,4-diaminopyridinium 2-carboxy-4,6-dinitrophenolate; Hemamalini & Fun, 2010b) because of the disorder present in the structure
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