Crystal structure of 2-amino-4,6-dimethoxypyrimidinium thiophene-2-carboxylate

Abstract

In the title salt, C6H10N3O2 +·C5H3O2S−, the 2-amino-4,6-di­meth­oxy­pyrimidinium cation inter­acts with the carboxyl­ate group of the thio­phene-2-carboxyl­ate anion through a pair of N—H⋯O hydrogen bonds, forming an R 2 2(8) ring motif. These motifs are centrosymmetrically paired via N—H⋯O hydrogen bonds, forming a complementary DDAA array. The separate DDAA arrays are linked by π–π stacking inter­actions between the pyrimidine rings, as well as by a number of weak C—H⋯O and N—H⋯O inter­actions. In the anion, the dihedral angle between the ring plane and the CO2 group is 11.60 (3)°. In the cation, the C atoms of methoxy groups deviate from the ring plane by 0.433 (10) Å.

Supramolecular architectures in CoIIand CuIIcomplexes with thiophene-2-carboxylate and 2-amino-4,6-dimethoxypyrimidine ligands

“…. Similar values were also observed for aminopyrimidine-thiophenecarboxylate interactions (Rajam et al, 2015).…”

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

“…Subject to these conditions, the refined twin fractions are 0.551 (2) and 0.449 (2), and the occupancies of the disordered cation and anion are 0.836 2and 0.164 (2) for the cation, and 0.834 (2) and 0.166 (2) for the anion. The new refinement of (III) used the original data set and started with the published atomic coordinates (Rajam et al, 2015). The constraints and restraints applied in the disorder model were the same as those employed for the disordered components of (II), and the H atoms were handled in like manner, giving final occupancies for the major and minor forms of the anion of 0.8687 (19) and 0.1313 (19).…”

“…It is of interest briefly to compare the structures of (I) and (II) reported here with those of some related compounds. In the structure of 2-amino-4,6-dimethoxypyrimidin-1-ium thiophene-2-carboxylate, (III), three independent N-HÁ Á ÁO hydrogen bonds link the component ions into a centrosymmetric four-ion aggregate in which a central R 2 4 (8) ring is flanked by two inversion-related R 2 2 (8) rings (Rajam et al, 2015). The bond lengths in the cation provide clear evidence of o-quinonoid bond fixation, just as found here for (I), but the bond lengths in the thiophene ring show some unusual values, suggesting the possibility of unmodelled disorder.…”

“…The ionic components in compound (III), showing the orientational disorder in the anion, where the major component is drawn with full lines and the minor component is drawn with broken lines. The atom labelling follows that in the original report (Rajam et al, 2015) and, for the sake of clarity, displacement ellipsoids are drawn at the 30% probability level.…”

Four closely related N-(3-benzoyl-4,5,6,7-tetrahydrobenzo[b]thiophen-2-yl)benzamides: order versus disorder, and similar molecular conformations but different modes of supramolecular aggregation, with a new disordered refinement of 2-amino-3-benzoyl-4,5,6,7-tetrahydrobenzo[b]thiophene

“…In this connection, we have recently noted (Rajam et al, 2017) an example of unmodelled conformational disorder involving a simple thiophene group (Rajam et al, 2015). While enantiomeric and positional disorder are usually easy to detect, although not always straightforward to unravel in cases of multiple disorder across special positions (Zakaria et al, 2003;Cobo et al, 2009), the detection of conformational disorder usually requires careful inspection of the refined bond distances and anisotropic displacement parameters, as well as attention to any unexpected features in the difference maps.…”