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 R22(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.