Molecular structure and conformational analysis of two 2-oxo(thioxo)-1,2,3,4-tetrahydropyrimidine-5-esters

X-ray crystal structure analysis and quantum chemical calculations based on density functional theory (DFT) were used for structural and electronic characterizations of two 1,2,3,4-tetrahydropyrimidine derivatives (THPMs), namely, ethyl 6-methyl-4-phenyl-2-thioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate (1) and methyl 4-(4-bromophenyl)-1,6-dimethyl-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate (2). The results of these studies revealed that the heterocyclic ring adopts a quasi-boat conformation, in which the 4-aryl group occupies the pseudo-axial position. The occurrence of the C4-stereocenter in the heterocyclic ring causes the formation of both R- and S-enantiomers. X-ray diffraction technique indicates that both compounds exist as a racemic mixture in the crystal structure and the enantiomers are orientated to each other via hydrogen bonding between N3H as donor and the C2S or C2O groups as acceptor species, in each layer under formation of an enantio-syndio packing. Most computational bond lengths and angles are well in agreement with experimental data, and support the pseudo-axial orientation of the C4-aryl substitution.