Different molecular conformations in the crystal structures of three 5-nitroimidazolyl derivatives

Abstract

The crystal structures of (E)-1-methyl-5-nitro-1H-imidazole-2-carbaldehyde O-benzyloxime, C12H12N4O3, (I), (E)-1-methyl-5-nitro-1H-imidazole-2-carbaldehyde O-(4-fluorobenzyl) oxime, C12H11FN4O3, (II), and (E)-1-methyl-5-nitro-1H-imidazole-2-carbaldehyde O-(4-bromobenzyl) oxime, C12H11BrN4O3, (III), are described. The dihedral angle between the ring systems in (I) is 49.66 (5)° and the linking Nm—C—C=N (m = methylated) bond shows an anti conformation [torsion angle = 175.00 (15)°]. Compounds (II) and (III) are isostructural [dihedral angle between the aromatic rings = 8.31 (5)° in (II) and 5.34 (15)° in (III)] and differ from (I) in showing a near-syn conformation for the Nm—C—C=N linker [torsion angles for (II) and (III) = 17.64 (18) and 8.7 (5)°, respectively], which allows for the occurrence of a short intramolecular C—H...N contact. In the crystal of (I), C—H...N hydrogen bonds link the molecules into [010] chains, which are cross-linked by very weak C—H...O bonds into (100) sheets. Weak aromatic π–π stacking interactions occur between the sheets. The extended structures of (II) and (III) feature several C—H...N and C—H...O hydrogen bonds, which link the molecules into three-dimensional networks, which are consolidated by aromatic π–π stacking interactions. Conformational energy calculations and Hirshfeld fingerprint analyses for (I), (II) and (III) are presented and discussed.

Keywords

• benzoxathiol-2-one
• hydrogen bonds
• Hirshfeld surface
• crystal structure