Synthesis of 5-(arylmethylideneamino)-4-(1H-benzo[d]imidazol-1-yl)pyrimidine hybrids: synthetic sequence and the molecular and supramolecular structures of two intermediates and three final products

Abstract

A concise and versatile synthesis of 5-(arylmethylideneamino)-4-(1H-benzo[d]imidazol-1-yl)pyrimidines has been developed, starting from 4-(1H-benzo[d]imidazol-1-yl)pyrimidines, and we report here the synthesis and spectroscopic and structural characterization of three such products, along with those of two intermediates in the reaction pathway. The intermediates 4-[2-(4-chlorophenyl)-1H-benzo[d]imidazol-1-yl]-6-methoxypyrimidine-2,5-diamine, (II), and 4-[2-(4-bromophenyl)-1H-benzo[d]imidazol-1-yl]-6-methoxypyrimidine-2,5-diamine, (III), crystallize as the isostructural monohydrates C18H15ClN5O·H2O and C18H15BrN5O·H2O, respectively, in which the components are linked into complex sheets by O—H...N and N—H...O hydrogen bonds. In the product (E)-4-methoxy-5-[(4-nitrobenzylidene)amino]-6-[2-(4-nitrophenyl)-1H-benzo[d]imidazol-1-yl]pyrimidin-2-amine, which crystallizes as a 1:1 solvate with dimethyl sulfoxide, C25H18N8O5·C2H6OS, (IV), inversion-related pairs of the pyrimidine component are linked by N—H...N hydrogen bonds to form cyclic centrosymmetric R 2 2(8) dimers to which pairs of solvent molecules are linked by N—H...O hydrogen bonds. (E)-4-Methoxy-5-[(4-methylbenzylidene)amino]-6-[2-(4-methylphenyl)-1H-benzo[d]imidazol-1-yl]pyrimidin-2-amine, C27H24N6O, (V), crystallizes with Z′ = 2 and the molecules are linked into a three-dimensional framework structure by a combination of N—H...N, C—H...N and C—H...π(arene) hydrogen bonds. The analogous product (E)-4-methoxy-5-[(4-chlorobenzylidene)amino]-6-[2-(4-methylphenyl)-1H-benzo[d]imidazol-1-yl]pyrimidin-2-amine, C26H21ClN6O, (VI), crystallizes from dimethyl sulfoxide in two forms: one, denoted (VIa), is isostructural with (V), and the other, denoted (VIb), crystallizes with Z′ = 1, but as an unknown solvate in which the pyrimidine molecules are linked by N—H...N hydrogen bonds to form a ribbon containing two types of centrosymmetric ring.