R-free factor and experimental charge-density analysis of 1-(2′-aminophenyl)-2-methyl-4-nitroimidazole: a crystal structure with Z′ = 2

Abstract

The experimental charge-density distribution was determined for 1-(2′-aminophenyl)-2-methyl-4-nitro-1H-imidazole crystals. An anharmonic model was applied to the N atoms of both amino groups and to one nitro group in order to account for high residual peaks after harmonic multipole refinement and to obtain a better charge-density model. Free R-factor calculations [Brünger (1992). Nature, 355, 472–475] with restrained models implemented in MoPro were used to determine the degree of similarity of the two symmetry-independent molecules in the unit cell. The results are compared with 1-phenyl-4-nitroimidazole in order to analyze the influence of the amine and methyl functional groups. The asymmetric unit contains two symmetry-independent molecules giving rise to a dimer connected via strong N—H...N hydrogen bonds; these dimers are the building blocks of the crystal. In the crystal structure there are also weaker interactions and many short directional contacts (C—H...O, C—H...N and C—H...π), for which the Koch–Popelier topological criteria were applied. This analysis revealed that the C—H...π interactions lie at the border between weak hydrogen bonds and van der Waals interactions. Special attention was also paid to stabilizing H...H interactions. It turned out that the electron density, Laplacian and density energies at the critical points show an exponential dependence on the contact distance, similar to the relation found for other interactions.