Hydrogen bonding patterns in salts of derivatives of aminopyrimidine and thiobarbituric acid

Abstract

Three salts, namely 2-amino-4,6-dimethylpyrimidin-1-ium thiobarbiturate trihydrate (I), 2-amino-4,6-dimethoxypyrimidin-1-ium thiobarbiturate dihydrate (II) and 2,4-diamino-5-(3′,4′,5′-trimethoxybenzyl)pyrimidin-1-ium thiobarbiturate (III), were synthesized and characterized by IR and X-ray diffraction techniques. The primary interaction between the acid and base happensviaN—H...O hydrogen bonds in (II) and (III), andviawater-mediated N—H...OWand OW—HW...S in (I). The water molecules present in compound (I) form a (H2O)12water clusterviawater–water interactions. In all three compounds (I)–(III), thiobarbiturate anions form self-complementary pairs with a robustR22(8) motifviaa pair of N—H...O/N—H...S hydrogen bonds. They mimic the nucleobase base pairs by utilizing the same groups (thymine/uracil uses N3—H and C4=O8 groups during the formation of Watson–Crick and Hoogsteen base pairs with adenine). Compound (I) forms a water-mediated base pair through N—H...OWhydrogen bonds and forms anR42(12) motif. The formation of N—H...S hydrogen bonds, water-mediated base pairs and water–water interactions in these crystal systems offers scope for these systems to be considered as a model in the study of hydration of nucleobases and water-mediated nucleobase base pairs in macromolecules.