Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Crystal structure, Hirshfeld surface analysis and density functional theory study of 6-methyl-2-[(5-methyl-isoxazol-3-yl)meth-yl]-1H-benzimidazole.

ABSTRACT: In the title mol-ecule, C₁₃H₁₃N₃O, the isoxazole ring is inclined to the benzimidazole ring at a dihedral angle of 69.28 (14)°. In the crystal, N-H⋯N hydrogen bonds between neighboring benzimidazole rings form chains along the a-axis direction. Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H⋯H (48.8%), H⋯C/C⋯H (20.9%) and H⋯N/N⋯H (19.3%) inter-actions. The optimized structure calculated using density functional theory at the B3LYP/6-311 G(d,p) level is compared with the experimentally determined structure in the solid state. The calculated highest occupied mol-ecular orbital (HOMO) and lowest unoccupied mol-ecular orbital (LUMO) energy gap is 4.9266 eV.

SUBMITTER: Idrissi A

PROVIDER: S-EPMC8025869 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Crystal structure, Hirshfeld surface analysis and density functional theory study of 6-methyl-2-[(5-methyl-isoxazol-3-yl)meth-yl]-1H-benzimidazole.

Idrissi Ahlam A Chkirate Karim K Abad Nadeem N Djerrari Bahia B Achour Redouane R Essassi El Mokhtar EM Van Meervelt Luc L

Acta crystallographica. Section E, Crystallographic communications 20210319 Pt 4

In the title mol-ecule, C13H13N3O, the isoxazole ring is inclined to the benzimidazole ring at a dihedral angle of 69.28 (14)°. In the crystal, N-H⋯N hydrogen bonds between neighboring benzimidazole rings form chains along the a-axis direction. Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H⋯H (48.8%), H⋯C/C⋯H (20.9%) and H⋯N/N⋯H (19.3%) inter-actions. The optimized structure calculated using den ...[more]

PMID: 33936764

Similar Datasets

Zwitterionic 4-bromo-6-meth-oxy-2-{[tris-(hy-droxy-meth-yl)methyl]-iminiumyl-meth-yl}phenolate: crystal structure and Hirshfeld surface analysis.

Project description:In the solid state, the title compound, C12H16BrNO5 [systematic name: 4-bromo-2-((1E)-{[1,3-dihy-droxy-2-(hy-droxy-meth-yl)propan-2-yl]iminium-yl}meth-yl)-6-meth-oxy-benzen-1-olate], C12H16BrNO5, is found in the keto-amine tautomeric form, with an intra-molecular iminium-N-H⋯O(phenolate) hydrogen bond and an E conformation about the C=N bond. Both gauche (two) and anti relationships are found for the methyl-hydroxy groups. In the crystal, a supra-molecular layer in the bc plane is formed via hy-droxy-O-H⋯O(hy-droxy) and charge-assisted hy-droxy-O-H⋯O(phenolate) hydrogen-bonding inter-actions; various C-H⋯O inter-actions provide additional cohesion to the layers, which stack along the a axis with no directional inter-actions between them. A Hirshfeld surface analysis confirms the lack of specific inter-actions in the inter-layer region.

| S-EPMC4971878 | biostudies-literature

Crystal structure, Hirshfeld surface analysis and DFT studies of 4-methyl-2-({[4-(tri-fluoro-meth-yl)phen-yl]imino}-meth-yl)phenol.

Project description:The title compound, C15H12F3NO, crystallizes with one mol-ecule in the asymmetric unit. The configuration of the C=N bond is E and there is an intra-molecular O-H⋯N hydrogen bond present, forming an S(6) ring motif. The dihedral angle between the mean planes of the phenol and the 4-tri-fluoro-methyl-phenyl rings is 44.77 (3)°. In the crystal, mol-ecules are linked by C-H⋯O inter-actions, forming polymeric chains extending along the a-axis direction. The Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from C⋯H/H⋯C (29.2%), H⋯H (28.6%), F⋯H/H⋯F (25.6%), O⋯H/H⋯O (5.7%) and F⋯F (4.6%) inter-actions. The density functional theory (DFT) optimized structure at the B3LYP/6-311 G(d,p) level is compared with the experimentally determined mol-ecular structure in the solid state. The HOMO-LUMO behaviour was elucidated to determine the energy gap. The crystal studied was refined as an inversion twin.

| S-EPMC7405564 | biostudies-literature

Crystal structure and Hirshfeld surface analysis of (Z)-2-{[(2,4-di-methyl-phen-yl)imino]-meth-yl}-4-methyl-phenol.

Project description:The title compound, C16H17NO, is a Schiff base that exists in the enol-imine tautomeric form and adopts a Z configuration. The mol-ecule is non-planar, with the twisted rings making a dihedral angle of 39.92 (4)°. The intra-molecular O-H⋯N hydrogen bond forms an S(6) ring motif. In the crystal, mol-ecules are linked by C-H⋯π inter-actions and very weak π-π stacking inter-actions also help to consolidate the crystal packing. A Hirshfeld surface analysis was performed to investigate the contributions of different inter-molecular contacts within the supra-molecular structure. The major contributions are from H⋯H (65%), C⋯H (19.2%) and O⋯H (6.6%) inter-actions.

| S-EPMC8587990 | biostudies-literature

Crystal structure and Hirshfeld surface analysis of 4-{[(anthracen-9-yl)meth-yl]amino}-benzoic acid di-methyl-formamide monosolvate.

Project description:The title compound, C22H17NO2·C3H7NO, was synthesized by condensation of an aromatic aldehyde with a secondary amine and subsequent reduction. It was crystallized from a di-methyl-formamide solution as a monosolvate, C22H17NO2·C3H7NO. The aromatic mol-ecule is non-planar with a dihedral angle between the mean planes of the aniline moiety and the methyl anthracene moiety of 81.36 (8)°. The torsion angle of the Car-yl-CH2-NH-Car-yl backbone is 175.9 (2)°. The crystal structure exhibits a three-dimensional supra-molecular network, resulting from hydrogen-bonding inter-actions between the carb-oxy-lic OH group and the solvent O atom as well as between the amine functionality and the O atom of the carb-oxy-lic group and additional C-H⋯π inter-actions. Hirshfeld surface analysis was performed to qu-antify the inter-molecular inter-actions.

| S-EPMC7199275 | biostudies-literature

Crystal structure, Hirshfeld surface analysis and DFT studies of (E)-4-methyl-2-{[(4-methyl-phen-yl)imino]-meth-yl}phenol.

Project description:In the title compound, C15H15NO, the configuration of the C=N bond of the Schiff base is E, and an intra-molecular O-H⋯N hydrogen bond is observed, forming an intra-molecular S(6) ring motif. The phenol ring is inclined by 45.73 (2)° from the plane of the aniline ring. In the crystal, mol-ecules are linked along the b axis by O-H⋯N and C-H⋯O hydrogen bonds, forming polymeric chains. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the packing arrangement are from H⋯H (56.9%) and H⋯C/C⋯H (31.2%) inter-actions. The density functional theory (DFT) optimized structure at the B3LYP/ 6-311 G(d,p) level is compared with the experimentally determined mol-ecular structure, and the HOMO-LUMO energy gap is provided. The crystal studied was refined as an inversion twin.

| S-EPMC7336782 | biostudies-literature

(E)-2-Meth-oxy-6-[(5-methyl-isoxazol-3-yl)imino-meth-yl]phenol.

Project description:In the title mol-ecule, C(12)H(12)N(2)O(3), the benzene and isoxazole rings form a dihedral angle of 5.9 (6)°. The hydr-oxy group is involved in an intra-molecular O-H⋯N hydrogen bond [O⋯N = 2.616 (5) Å], resulting in approximate planarity of the mol-ecular skeleton. In the crystal structure, mol-ecules related by translation along the c axis are stacked into columns, the shortest inter-molecular C⋯C distance being 3.298 (6) Å.

| S-EPMC2960214 | biostudies-literature

Crystal structure and Hirshfeld surface analysis of (Z)-3-methyl-4-(thio-phen-2-yl-methyl-idene)isoxazol-5(4H)-one.

Project description:The title compound, C9H7NO2S crystallizes with two independent mol-ecules (A and B) in the asymmetric unit with Z = 8. Both mol-ecules are almost planar with a dihedral angle between the isoxazole and thio-phen rings of 3.67 (2)° in mol-ecule A and 10.00 (1) ° in mol-ecule B. The packing of mol-ecules A and B is of an ABAB⋯ type along the b-axis direction, the configuration about the C=C bond is Z. In the crystal, the presence of C-H⋯O, C-H⋯ N and π-π inter-actions [centroid-centroid distances of 3.701 (2) and 3.766 (2) Å] link the mol-ecules into a three-dimensional architecture. An analysis of Hirshfeld surfaces shows the importance of C-H⋯O and C-H⋯N hydrogen bonds in the packing mechanism of the crystalline structure.

| S-EPMC8025857 | biostudies-literature

Crystal structure and Hirshfeld surface analysis of (E)-2-{[(2-iodo-phen-yl)imino]-meth-yl}-6-methyl-phenol.

Project description:The title compound, C14H12INO, was synthesized by condensation of 2-hy-droxy-3-methyl-benzaldehyde and 2-iodo-aniline, and crystallizes in the ortho-rhom-bic space group P212121. The 2-iodo-phenyl and benzene rings are twisted with respect to each other, making a dihedral angle of 31.38 (2)°. The mol-ecular structure is stabilized by an O-H⋯N hydrogen bond, forming an S(6) ring motif. In the crystal, mol-ecules are linked by C-H⋯π inter-actions, resulting in the formation of sheets along the a-axis direction. Within the sheets, very weak π-π stacking inter-actions lead to additional stabilization. The Hirshfeld surface analysis and fingerprint plots reveal that the crystal structure is dominated by H⋯H (37.1%) and C⋯H (30.1%) contacts. Hydrogen bonding and van der Waals inter-actions are the dominant inter-actions in the crystal packing. The crystal studied was refined as a two-component inversion twin.

| S-EPMC7534256 | biostudies-literature

Crystal structure and Hirshfeld surface analysis of 4-(4-chloro-phen-yl)-5-methyl-3-{4-[(2-methyl-phen-yl)meth-oxy]phen-yl}-1,2-oxazole.

Project description:In the title compound, C24H20ClNO2, the mean planes of 4-chloro-phenyl, 2-methyl-phenyl and phenyl-ene rings make dihedral angles of 62.8 (2), 65.1 (3) and 15.1 (2)°, respectively, with the 5-methyl-1,2-oxazole ring. In the crystal, mol-ecules are linked by inter-molecular C-H⋯N, C-H⋯Cl, C-H⋯π contacts and π-π stacking inter-actions between the phenyl-ene groups. Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H⋯H (48.7%), H⋯C/C⋯H (22.2%), Cl⋯H/H⋯Cl (8.8%), H⋯O/O⋯H (8.2%) and H⋯N/N⋯H (5.1%) inter-actions.

| S-EPMC8025860 | biostudies-literature

Crystal structure and Hirshfeld surface analysis of N-[(2-hy-droxy-naphthalen-1-yl)(3-methyl-phen-yl)meth-yl]acetamide.

Project description:The title compound, C20H19NO2, is of inter-est as a precursor to biologically active substituted quinolines and related compounds. This compound crystallizes with two independent mol-ecules (A and B) in the asymmetric unit. The dihedral angles between mean planes of the methyl-phenyl ring and the naphthalene ring system are 78.32 (6) and 84.70 (6)° in mol-ecules A and B, respectively. In the crystal, the anti-ferroelectric packing of mol-ecules A and B is of an ABBAABB type along the b-axis direction. The crystal structure features N-H⋯O, O-H⋯O and weak C-H⋯O hydrogen bonds, which link the mol-ecules into infinite chains propagating along the b-axis direction.

| S-EPMC6038626 | biostudies-literature