A concise and efficient synthesis of amino‐substituted (1H‐benzo[d]imidazol‐1‐yl)pyrimidine hybrids: synthetic sequence and the molecular and supramolecular structures of six examples

A concise and efficient synthesis of a series of amino‐substituted benzimidazole–pyrimidine hybrids has been developed, starting from the readily available N⁴‐(2‐aminophenyl)‐6‐methoxy‐5‐nitrosopyrimidine‐2,4‐diamine. In each of N⁵‐benzyl‐6‐methoxy‐4‐(2‐phenyl‐1H‐benzod]imidazol‐1‐yl)pyrimidine‐2,5‐diamine, C₂₅H₂₂N₆O, (I), 6‐methoxy‐N⁵‐(4‐methoxybenzyl)‐4‐2‐(4‐methoxyphenyl)‐1H‐benzod]imidazol‐1‐yl]pyrimidine‐2,5‐diamine, C₂₇H₂₆N₆O₃, (III), 6‐methoxy‐N⁵‐(4‐nitrobenzyl)‐4‐2‐(4‐nitrophenyl)‐1H‐benzod]imidazol‐1‐yl]pyrimidine‐2,5‐diamine, C₂₅H₂₀N₈O₅, (IV), the molecules are linked into three‐dimensional framework structures, using different combinations of N—H…N, N—H…O, C—H…O, C—H…N and C—H…π hydrogen bonds in each case. Oxidative cleavage of 6‐methoxy‐N⁵‐(4‐methylbenzyl)‐4‐2‐(4‐methylphenyl)‐1H‐benzod]imidazol‐1‐yl]pyrimidine‐2,5‐diamine, (II), with diiodine gave 6‐methoxy‐4‐2‐(4‐methylphenyl)‐1H‐benzod]imidazol‐1‐yl]pyrimidine‐2,5‐diamine, which crystallized as a monohydrate, C₁₉H₁₈N₆O·H₂O, (V), and reaction of (V) with trifluoroacetic acid gave two isomeric products, namely N‐{5‐amino‐6‐methoxy‐6‐2‐(4‐methylphenyl)‐1H‐benzod]imidazol‐1‐yl]pyrimidin‐2‐yl}‐2,2,2‐trifluoroacetamide, which crystallized as an ethyl acetate monosolvate, C₂₁H₁₇F₃N₆O₂·C₄H₈O₂, (VI), and N‐{2‐amino‐6‐methoxy‐4‐2‐(4‐methylphenyl)‐1H‐benzod]imidazol‐1‐yl]pyrimidin‐5‐yl}‐2,2,2‐trifluoroacetamide, which crystallized as a methanol monosolvate, C₂₁H₁₇F₃N₆O₂·CH₄O, (VIIa). For each of (V), (VI) and (VIIa), the supramolecular assembly is two‐dimensional, based on different combinations of O—H…N, N—H…O, N—H…N, C—H…O and C—H…π hydrogen bonds in each case. Comparisons are made with some related structures.