Multicomponent synthesis, structural and molecular dynamics simulation studies of a novel spirooxindole derivative
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...
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| Format: | Article |
| Language: | English |
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Elsevier
2024-06-01
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| Series: | Chemical Physics Impact |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2667022424000112 |
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| author | Mahesha Majal Sapnakumari B.S. Chethan Thomas Jinkle M.V. Deepa Urs N.S. Lingegowda N.K. Lokanath S. Naveen |
| author_facet | Mahesha Majal Sapnakumari B.S. Chethan Thomas Jinkle M.V. Deepa Urs N.S. Lingegowda N.K. Lokanath S. Naveen |
| author_sort | Mahesha |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-08T09:00:27Z |
| format | Article |
| id | doaj.art-5a5cb6018f094583918d7140552be9fa |
| institution | Directory Open Access Journal |
| issn | 2667-0224 |
| language | English |
| last_indexed | 2024-03-08T09:00:27Z |
| publishDate | 2024-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Chemical Physics Impact |
| spelling | doaj.art-5a5cb6018f094583918d7140552be9fa2024-02-01T06:35:37ZengElsevierChemical Physics Impact2667-02242024-06-018100467Multicomponent synthesis, structural and molecular dynamics simulation studies of a novel spirooxindole derivative Mahesha0Majal Sapnakumari1B.S. Chethan2Thomas Jinkle3M.V. Deepa Urs4N.S. Lingegowda5N.K. Lokanath6S. Naveen7Department of Physics, SJCE, JSS Science & Technology University, Mysuru 570 006, IndiaDepartment of Chemistry, St. Agnes Centre for Post Graduate Studies and Research, Mangaluru 575 002, IndiaDepartment of Studies in Physics, University of Mysore, Manasagangotri, Mysuru 570 006, India; Department of Basic Sciences, Amruta Institute of Engineering & Management Sciences, Bangalore 562109, IndiaDepartment of Chemistry, St. Agnes Centre for Post Graduate Studies and Research, Mangaluru 575 002, IndiaDepartment of Physics, The National Institute of Engineering, Mysore 570008, IndiaDepartment of Chemistry, Vidya Vardhaka College of Engineering, Mysuru 570 002, IndiaDepartment of Studies in Physics, University of Mysore, Manasagangotri, Mysuru 570 006, IndiaDepartment of Physics, Faculty of Engineering & Technology, JAIN (Deemed-to-be University), Bangalore 562 112, India; Corresponding author.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.http://www.sciencedirect.com/science/article/pii/S2667022424000112SpirooxindoleDynamics simulationSingle crystalHirshfeld surfaceXRDDFT |
| spellingShingle | Mahesha Majal Sapnakumari B.S. Chethan Thomas Jinkle M.V. Deepa Urs N.S. Lingegowda N.K. Lokanath S. Naveen Multicomponent synthesis, structural and molecular dynamics simulation studies of a novel spirooxindole derivative Chemical Physics Impact Spirooxindole Dynamics simulation Single crystal Hirshfeld surface XRD DFT |
| title | Multicomponent synthesis, structural and molecular dynamics simulation studies of a novel spirooxindole derivative |
| title_full | Multicomponent synthesis, structural and molecular dynamics simulation studies of a novel spirooxindole derivative |
| title_fullStr | Multicomponent synthesis, structural and molecular dynamics simulation studies of a novel spirooxindole derivative |
| title_full_unstemmed | Multicomponent synthesis, structural and molecular dynamics simulation studies of a novel spirooxindole derivative |
| title_short | Multicomponent synthesis, structural and molecular dynamics simulation studies of a novel spirooxindole derivative |
| title_sort | multicomponent synthesis structural and molecular dynamics simulation studies of a novel spirooxindole derivative |
| topic | Spirooxindole Dynamics simulation Single crystal Hirshfeld surface XRD DFT |
| url | http://www.sciencedirect.com/science/article/pii/S2667022424000112 |
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