Crystal structure, Hirshfeld surface analysis and DFT study of N-(2-nitrophenyl)maleimide
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SUBMITTER: Montoya-Garcia M
PROVIDER: S-EPMC10915672 | biostudies-literature | 2024 Feb
REPOSITORIES: biostudies-literature
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Project description:The supramolecular assemblies of the two title structures are one-dimensional: the chain-of-rings motifs are supported by aromatic π–π interactions. The synthesis and crystal structures of the molecular salts of 4-(4-nitrophenyl)piperazine with trifluoroacetate, namely, 4-(4-nitrophenyl)piperazin-1-ium trifluoroacetate, C10H14N3O2+·C2F3O2− (I), and with trichloroacetate, namely, 4-(4-nitrophenyl)piperazin-1-ium trichloroacetate, C10H14N3O2+·C2Cl3O2−, (II), are reported and compared. A partial positional disorder of the anions was found. In both structures, the piperazine rings adopt a chair conformation, whereas the positions of the nitrophenyl group on the piperazine ring differ from bisectional in (I) to equatorial in (II). In both structures, the supramolecular assemblies are mono-periodic on the basis of the chain-of-rings motifs supported by aromatic π–π interactions. Hirshfeld surface analysis was used to explore the intermolecular close contacts in both crystals. The most dominant contacts of the Hirshfeld surface of the cation–anion pairs of the asymmetric units are O⋯H/H⋯O, and those with a contribution of halogen atoms: F⋯H/H⋯F in (I) and Cl⋯H/H⋯Cl in (II), respectively.
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Project description:The title compound, C34H58O2, consists of cholesteryl and hepta-noate units, in which the six-membered rings adopt chair and twisted-boat conformations while the five-membered ring adopts an envelope conformation. In the crystal, the mol-ecules are aligned along the a-axis direction and stacked along the b-axis direction. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (92.4%) and H⋯O/O⋯H (6.1%) inter-actions. van der Waals inter-actions are the dominant inter-actions in the crystal packing. Density functional theory (DFT) optimized structures at the B3LYP/ 6-31 G(d) level are compared with the experimentally determined mol-ecular structure in the solid state. The HOMO-LUMO behaviour was elucidated to determine the energy gap, and the mol-ecular electrostatic potential (MEP) of the compound was investigated.
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Project description:In the title quinoline derivative, C14H14ClNO3, there is an intra-molecular C-H⋯O hydrogen bond forming an S(6) graph-set motif. The mol-ecule is essentially planar with the mean plane of the ethyl acetate group making a dihedral angle of 5.02 (3)° with the ethyl 6-chloro-2-eth-oxy-quinoline mean plane. In the crystal, offset π-π inter-actions with a centroid-to-centroid distance of 3.4731 (14) Å link inversion-related mol-ecules into columns along the c-axis direction. Hirshfeld surface analysis indicates that H⋯H contacts make the largest contribution (50.8%) to the Hirshfeld surface.
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Project description:In the title mol-ecule, C16H14N2O, the di-hydro-quinoxaline moiety is not planar as there is a dihedral angle of 4.51 (5)° between the constituent rings. In the crystal, C-H⋯O hydrogen bonds form helical chains about the crystallographic 21 screw axis in the b-axis direction. Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H⋯H (51.7%), H⋯C/C⋯H (26%) and H⋯O/O⋯H (8.5%) inter-actions. The optimized structure calculated using density functional theory (DFT) at the B3LYP/6-311 G(d,p) level is compared with the experimentally determined structure in the solid state. The calculated HOMO-LUMO energy gap is 3.8918 eV.
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Project description:The two crystallographically non-equivalent molecules in the title compound have C2 and Ci symmetries. The crystal structure features strong intermolecular O—H⋯O hydrogen bonds, which form eight-membered rings with The title compound, C16H22O2, was synthesized in order to obtain its guest-free form because ‘wheel-and-axle’-shaped molecules tend to crystallize from solutions as solvates or host–guest molecules. It crystallizes in the monoclinic space group P2/c with two crystallographically non-equivalent molecules, one situated on an inversion center and the other on a twofold axis. The rod-like 1,3-diyne fragments have the usual linear geometry. In the crystal, O—H ⋯ O bonds form eight-membered rings of the R44(8) type, linking molecules into layers. The Hirshfeld surface analysis indicates that the largest contributions are from intermolecular H⋯H (ca 71%) and H⋯C/C⋯H (ca 19%) contacts. The energies of the frontier molecular orbitals were determined by DFT calculations at the B3LYP/def2-TZVP level of theory.
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Project description:In the title mol-ecule, C17H23NO2, the di-hydro-indole portion is planar (r.m.s. deviation = 0.0157 Å) and the nonyl substituent is in an 'extended' conformation. In the crystal, the nonyl chains inter-calate and the di-hydro-indole-dione units are associated through C-H⋯O hydrogen bonds to form micellar blocks. Based on the Hirshfeld surface analysis, the most important inter-molecular inter-action is the H⋯H inter-action.
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Project description:In the title compound, C8H9BrN2O2, the C-O-C-C torsion angle between isonicotine and the ethyl group is 180.0 (2)°. Intra-molecular N-H⋯O and C-H⋯O inter-actions consolidate the mol-ecular structure. In the crystal, N-H⋯N inter-action form S(5) zigzag chains along [010]. The most significant contributions to the Hirshfeld surface arise from H⋯H (33.2%), Br⋯H/H⋯Br (20.9%), O⋯H/H⋯O (11.2%), C⋯H/H⋯C (11.1%) and N⋯H/H⋯N (10%) contacts. The topology of the three-dimensional energy frameworks was generated using the B3LYP/6-31 G(d,p) model to calculate the total inter-action energy. The net inter-action energies for the title compound are E ele = 59.2 kJ mol-1, E pol = 15.5 kJ mol-1, E dis = 140.3 kJ mol-1 and E rep = 107.2 kJ mol-1 with a total inter-action energy E tot of 128.8 kJ mol-1. The mol-ecular structure was optimized by density functional theory (DFT) at the B3LYP/6-311+G(d,p) level and the theoretical and experimentally obtained parameters were compared. The frontier mol-ecular orbitals HOMO and LUMO were generated, giving an energy gap ΔE of 4.0931 eV. The MEP was generated to identify active sites in the mol-ecule and mol-ecular docking studies carried out with the title compound (ligand) and the covid-19 main protease PDB ID: 6LU7, revealing a moderate binding affinity of -5.4 kcal mol-1.
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Project description:The asymmetric unit of the title compound, C14H11N3O3, consists of two independent mol-ecules having very similar conformations in which the indazole moieties are planar. The independent mol-ecules are distinguished by small differences in the rotational orientations of the nitro groups. In the crystal, N-H⋯O and C-H⋯O hydrogen bonds form zigzag chains along the b-axis direction. Additional C-H⋯O hydrogen bonds link the chains into layers parallel to (10). These are connected by slipped π-stacking and C-H⋯π(ring) inter-actions.
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Project description:The title compound, C29H36O4 [systematic name (4aR,5R,6aS,7R,11aS,11bR)-4a-hydroxy-4,4,7,11b-tetramethyl-1,2,3,4,4a,5,6,6a,7,11,11a,11b-dodecahydrophen-anthro[3,2-b]furan-5-yl cinnamate], a natural diterpene known as pulcherrin J, was isolated from stem barks of medicinally important Caesalpinia pulcherrima (L.). The crystal structure of pulcherrin J shows it to be composed of a central core of three trans-fused cyclo-hexane rings and a near planar five-membered furan ring, along with an axially oriented cinnamate moiety and an -hydroxy substituent attached at positions 4a and 5 of the steroid ring system, respectively. The absolute structure was established with the use of Cu Kα radiation. In the crystal, mol-ecules are linked by O-H⋯O hydrogen bonds to generate [100] C(8) chains. Hirshfeld surface analysis indicates that the most significant contacts in packing are H⋯H (67.5%), followed by C⋯H (19.6%) and H⋯O (12.9%).
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Project description:The title compound, C14H16, exhibits exceptionally weak inter-molecular C-H⋯π hydrogen bonding of the ethynyl groups, with the corresponding H⋯π separations [2.91 (2) and 3.12 (2) Å] exceeding normal vdW distances. This bonding complements distal contacts of the CH (aliphatic)⋯π type [H⋯π = 3.12 (2)-3.14 (2) Å] to sustain supra-molecular layers. Hirshfeld surface analysis of the title compound suggests a relatively limited significance of the C⋯H/H⋯C contacts to the crystal packing (24.6%) and a major contribution from H⋯H contacts accounting 74.9% to the entire surface.
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