Exploring the Structural Dynamics in aqueous medium of a novel Pentafluorophenyl-Ureido Derivative: A Molecular Dynamics Study

The synthesis and characterization of organic molecules with specialized structural and electronic features are crucial for applications in materials science, catalysis, and molecular electronics. This study introduces PDPF, a pentafluorophenyl-ureido derivative of 2,6-diaminopyridine, recognized for its unique crystal architecture and intermolecular interactions. Single-crystal X-ray diffraction reveals that PDPF crystallizes in a triclinic system (Pī space group), with a densely packed lattice stabilized by N—H···O and C—H···F hydrogen bonds. The pentafluorophenyl rings and urea moieties contribute electron-withdrawing effects, enhancing stability and unique steric properties. To investigate PDPF’s stability and conformational dynamics, molecular dynamics (MD) simulations were conducted under thermal fluctuations and solvent interactions. Principal component analysis (PCA) of MD trajectories identified localized flexibility in carbon and nitrogen atoms, with rapid stabilization along principal components. Radial distribution function (RDF) profiles indicate limited solubility and hydrophobic tendencies, with minimal hydrogen bonding in aqueous environments. Further analyses of temperature, pressure, density, and energy fluctuations confirm structural integrity, with stable kinetic and potential energy profiles across conditions. This comprehensive study provides insights into PDPF’s intermolecular interactions and stability while demonstrating the effectiveness of computational methods in characterizing complex organic molecules with intricate packing arrangements.