Multicomponent synthesis, structural and molecular dynamics simulation studies of a novel spirooxindole derivative

Abstract

The 4′-(4-chlorobenzoyl)-3,-(2,6-dichlorophenyl)-1′-methylspiro(indole-3,2′-pyrrolidin)-2(1H)-one (SOD1) compound has been synthesized and the single crystals are grown by the slow evaporation method using ethanol. Initially, FT-IR and NMR (1H and 13C NMR) spectroscopic studies were used to confirm the structure of the compound. Single crystal X-ray diffraction data were used to determine the solid state structure of the grown single crystals. The title compound SOD1 crystallizes in the orthorhombic space group Pbca. The crystal packing analysis of the compound shows that distinct hydrogen bonding intermolecular interactions construct the R22(12), R22(8), and R12(8), supramolecular synthons to stabilize the packing modes. The propensity of intermolecular interactions is quantified by the Hirshfeld surface analysis, 2-D fingerprint plots and enrichment ratio analysis. Further, the 3-D packing topology of the molecular fragments is visualized through energy frameworks, which reveal the predominance of dispersion energy over other interaction energies. The optimized structure's geometric parameters were computed using DFT calculations using B3LYP/6–311+G(d,p) basis set and compared with the crystal structure parameters obtained by the X-ray diffraction studies. To explore the anticancer activity of the spiro compound, molecular docking with the 6FS1 protein was performed and the binding score of -7.7 kcal/mol was observed. Further, the binding interaction was explored by the dynamics simulation studies.

Keywords

• Spirooxindole
• Dynamics simulation
• Single crystal
• Hirshfeld surface
• XRD
• DFT