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Updated: Feb 10, 2026

Spatial Separation of Molecular Conformers and Clusters
Published on: January 9, 2014
Different mol-ecular conformations in the crystal structures of three 5-nitro-imidazolyl derivatives
Luis F B Osorio1, Samir A Carvalho1, Edson F da Silva1
1Instituto de Tecnologia em Fármacos e Farmanguinhos, Fundação Oswaldo Cruz, 21041-250 Rio de Janeiro, RJ, Brazil.
Abstract:
The crystal structures of (E)-1-methyl-5-nitro-1H-imidazole-2-carbaldehyde O-benzyl-oxime, C12H12N4O3, (I), (E)-1-methyl-5-nitro-1H-imidazole-2-carb-alde-hyde O-(4-fluoro-benz-yl) oxime, C12H11FN4O3, (II), and (E)-1-methyl-5-nitro-1H-imidazole-2-carbaldehyde O-(4-bromo-benz-yl) 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 = methyl-ated) 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 intra-molecular C-H⋯N contact. In the crystal of (I), C-H⋯N hydrogen bonds link the mol-ecules into [010] chains, which are cross-linked by very weak C-H⋯O bonds into (100) sheets. Weak aromatic π-π stacking inter-actions 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 mol-ecules into three-dimensional networks, which are consolidated by aromatic π-π stacking inter-actions. Conformational energy calculations and Hirshfeld fingerprint analyses for (I), (II) and (III) are presented and discussed.
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