Quantitative investigation of the nature of non-covalent interactions in 2-((benzo[d][1,3]dioxol-5-ylmethyl)amino)-N-phenyl-2-thioxoacetamide: insights from crystallographic, DFT analysis, molecular docking, and molecular dynamics simulation

Lohith T., Ravi Singh K., FEIZI DEH NAYEBI M., Santhosh C., Kishorkumar S., Sridhar M., ...Daha Fazla

Molecular Physics, cilt.123, sa.15, 2025 (SCI-Expanded, Scopus)

  • Yayın Türü: Makale / Tam Makale
  • Cilt numarası: 123 Sayı: 15
  • Basım Tarihi: 2025
  • Doi Numarası: 10.1080/00268976.2024.2444467
  • Dergi Adı: Molecular Physics
  • Derginin Tarandığı İndeksler: Science Citation Index Expanded (SCI-EXPANDED), Scopus, Chemical Abstracts Core, Chimica, Compendex, INSPEC
  • Anahtar Kelimeler: COVID-19, DFT, molecular docking, QTAIM, XRD
  • Süleyman Demirel Üniversitesi Adresli: Evet

Özet

The aim of this work was to synthesise the novel compound 2-((benzo[d][1,3]dioxol-5-ylmethyl)amino)-N-phenyl-2-thioxoacetamide (P1) using the reflux method with ethanol as the solvent. The obtained product is characterised by single-crystal XRD analysis. All various contacts like intra and intermolecular found in P1 were determined by the X-ray diffraction technique performed on single crystals. On the other hand, the optimisation of P1 was accomplished by the DFT/ωB97XD method at the 6–311 + G(d, p) level. Furthermore, the electrostatic potential of the molecule (MEP), and global reactivity descriptors were analysed to gain a better understanding of the electronic properties and the active sites of P1. The Quantum Theory of Atoms in Molecules (QTAIM) and non-covalent interactions-based density of regional indicator (DORI) analyses were utilised to examine the intermolecular interaction energies and strength and nature of van der Waal's interactions. A computational analysis employing molecular docking simulations was conducted to explore the potential binding interactions between the synthesised compound P1 and the target proteins, specifically SARS-CoV-2 receptor protein (PDB ID: 6LU7) and breast cancer protein (PDB ID: 3HB5). In addition, molecular docking studies are validated by the molecular dynamics simulation studies.