Methyl 1-[(6-meth-oxy-5-methyl-pyrimidin-4-yl)meth-yl]-1 H-benzo[ d]imidazole-7-carboxyl-ate: a combined X-ray and DFT study

Abstract

The title compound, C₁₆H₁₆N₄O₃, was obtained as a side product during the synthesis of the previously reported anti-tubercular agent N-(2-fluoro-eth-yl)-1-[(6-meth-oxy-5-methyl-pyrimidin-4-yl)meth-yl]-1H-benzo[d]imidazole-4-carboxamide and structurally characterized by X-ray crystallography and computational methods. In the crystal (space group P2₁/n, Z = 4), the title compound adopts a twisted conformation with a dihedral angle between the benzimidazole and pyrimidine mean planes of 84.11 (3)°. The carboxyl-ate group and the 5-methyl group on the pyrimidine ring exhibit partial disorder. The DFT-optimized mol-ecular structure resembles the structure of the minor component in the crystal.

Keywords: DFT calculations; benzimidazole; crystal structure; pyrimidine; tuberculosis.

Figure 1

N-Alkyl­ation of 1 with 4-(chloro­meth­yl)-6-meth­oxy-5-methyl­pyrimidine to yield structural isomers 2 and 3.

Figure 2

Displacement ellipsoid plot of 3 (50% probability level). Hydrogen atoms are represented by small spheres of arbitrary radius. Disordered parts with minor occupancy are drawn with empty bonds.

Figure 3

Structure overlay plot of the mol­ecular structure of 3 in the crystal (green; displacement ellipsoids with 50% probability) and the DFT-optimized mol­ecular structure (orange). The respective benzimidazole moieties were superimposed (r.m.s deviation for non-hydrogen atoms: 0.024 Å).

Figure 4

Section of the crystal structure of 3. Colour scheme: carbon, grey; nitro­gen, blue; oxygen, red. Hydrogen atoms and O2′ are omitted for clarity.