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

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 C(18)H(15)ClN(5)O·H(2)O and C(18)H(15)BrN(5)O·H(2)O, 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, C(25)H(18)N(8)O(5)·C(2)H(6)OS, (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, C(27)H(24)N(6)O, (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, C(26)H(21)ClN(6)O, (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.