Cation tautomerism, twinning and disorder in the triclinic and monoclinic forms of 4-amino-5-chloro-2,6-dimethylpyrimidinium 5-chloro-2-hydroxybenzoate and a new disordered refinement of 2-amino-4,6-dimethoxypyrimidin-1-ium thiophene-2-carboxylate

Abstract

Pyrimidines are important compounds in biology and medicine, and the aminopyrimidine fragment can be identified in three of the four bases in DNA. The targeted drug action of pharmaceuticals containing this functionality is likely to depend heavily on molecular recognition processes involving hydrogen bonding. Crystallization of an equimolar mixture of 4-amino-5-chloro-2,6-dimethylpyrimidine and 5-chloro-2-hydroxybenzoic acid yielded two forms of the 1:1 salt, C₆H₉ClN₃ ⁺·C₇H₄ClO₃ ⁻, each containing a different tautomeric form of the cation. 6-Amino-5-chloro-2,4-dimethylpyrimidin-1-ium 5-chloro-2-hydroxybenzoate, (I), crystallizes in the space group P\overline{1}, with Z′ = 2, and all of the component ions are fully ordered. 4-Amino-5-chloro-2,6-dimethylpyrimidin-1-ium 5-chloro-2-hydroxybenzoate, (II), also crystallizes with Z′ = 2, but in the space group P2₁/c and as a merohedral twin which closely mimics an orthorhombic unit cell. In (II), one of the cations and one of the anions is disordered, each over two sets of atomic sites having occupancies of 0.836 (2) and 0.164 (2), and 0.834 (2) and 0.166 (2). The bond lengths in the cations of (I) and (II) provide evidence for o-quinonoid and p-quinonoid bond fixation, respectively. A combination of six N—H...O hydrogen bonds links the component ions of (I) into two independent four-ion aggregates, but the ions in (II) are linked by a combination of four N—H...O and two N—H...N hydrogen bonds to form a three-dimensional framework structure. The recently reported structure of 2-amino-4,6-dimethoxypyrimidin-1-ium thiophene-2-carboxylate, C₆H₁₀N₃O₂ ⁺·C₅H₃O₂S⁻, (III), has been rerefined, using the original data set, to show that the anion is disordered over two sets of atomic sites, approximately related by a 180° rotation about the exocyclic C—C bond, and having occupancies of 0.8687 (19) and 0.1313 (19).