structural and computational analysis of a triclinic pentafluorophenylurea based pyridine derivative: a dft-based approach

In this study, we report the structural and electronic properties of a newly synthesized compound, n, n’-pyridine-2,6-diylbis-[3-(pentafluorophenyl) urea], alternatively named 1-(perfluorophenyl)-3-(6-(3-(2,3,4,5,6-pentafluorophenyl) ureido) pyridin-2-yl) urea, referred to as pdpf. this novel pentafluorophenyl-substituted 2,6-diaminopyridine-urea derivative was comprehensively characterized using both experimental and theoretical methods. the compound crystallizes in a triclinic system, with detailed structural features determined via x-ray diffraction (xrd) analysis. to complement experimental findings, we employed density functional theory (dft) calculations with the b3lyp/6-311++g(d,p) basis set to explore the molecular geometry, electronic structure, and vibrational frequencies. select vibrational modes, such as n-h stretching and c=o bending, were compared with experimental data to validate the computational results. the calculated homo-lumo gap of 3.0785 ev suggests potential applications in optoelectronic devices. charge distribution within the molecule was analyzed through natural bond orbital (nbo) and mulliken population analyses, supported by a molecular electrostatic potential (mep) map to identify regions of electrophilicity and nucleophilicity. in addition, statistical analysis of charge variations across atomic sites was conducted using principal component analysis (pca) and k-means clustering, highlighting patterns in electron density and bond interactions. to further understand molecular stability and interactions, radial distribution function (rdf) analysis and reciprocal space structure factor analysis were performed using atomes software. spherical harmonics analysis quantified atomic order and local symmetries, offering insights into the compound’s structural properties. this multi-faceted approach combining crystallographic, spectroscopic, and computational analyses provides a thorough understanding of the structural and electronic properties of pdpf, highlighting its potential for advanced material science applications.