The supramolecular assemblies of N-phthalimide protected (E)- and (Z)-4-amino-2-butenyl 5-substituted pyrimidine derivatives:: from dimers to two-dimensional and three-dimensional networks

The supramolecular structures of three (E)-N-phthalimide protected 4-amino-2-butenyl 5-substituted pyrimidine derivatives, uracil derivative (1), 5-fluorouracil derivative (2), and 5-(trifluoromethyl)uracil derivative (3), were analyzed in order to understand how variations in their molecular structure influence their supramolecular aggregation. The structure of 5-fluorouracil derivative (2) is compared also with its (Z)-isomer (4). The molecules of 1-3 are assembled by self-complementary N-H center dot center dot center dot O hydrogen bonds into centrosymmetric dimers. Compound 4 crystallized with two independent molecules in the asymmetric unit that are linked also by two N-H center dot center dot center dot O hydrogen bonds into dimers. In supramolecular assembling of 1-4 C-H center dot center dot center dot O hydrogen bonds participate also, while supramolecular structures of 2, 3, and 4 additionally contain C-H center dot center dot center dot F interactions. The C-H center dot center dot center dot O hydrogen bonds in 1 and C-H center dot center dot center dot O hydrogen bonds and C-H center dot center dot center dot F interactions in 3 and 4 complete a three-dimensional network. The structure of 2 is built of dimers that generate a two-dimensional network.