Synthesis, crystal structure, Hirshfeld surface, DFT calculations, Z-scan and nonlinear optical studies of novel flourinated hexahydropyrimidine

Abstract A new fluorinated hexahydropyrimidine was synthesized and its crystal structure was elucidated using single crystal X-ray diffraction technique. This compound, C15H17F3N2O6 crystallizes in monoclinic space group P21/c with cell parameters a = 10.6345(3) A, b = 14.7074(4) A, c = 10.6677(4) A, β= 101.453(2)° and V= 1635.27 (9) A3. In this compound the hexahydropyrimidine ring (C7/C8/C12/N1/C14/N2) adopts sofa conformation. The puckering parameters are Q = 0.5117A, Ɵ = 129.59° and φ =304.0802°. The analysis of Hirshfeld surface indicates the presence of hydrogen bonds C‒H•••F, C‒H•••O, O‒H•••O, N‒H•••O and π•••π stacking stabilizes the system. The energy optimized structure was calculated using Density Functional Theory (DFT) and were employed by hybrid functional theory (B3LYP) at 6-311++G(d,p) basis set in the Gaussian09_revision C0.1 program package. The natural bond orbital analysis results state that the highest energy transfer of 604.21 kJ/mol occur between the donor σ(O4‒H43) to acceptor σ*(C34‒H36) through carboxylate chain. Moreover, the vibrational assignments, global reactivity descriptors, energy gap and molecular electrostatic potential (MEP) also gives clear insight about chemical and biological activity of the molecule. The first hyperpolarizability value 7.2987 × 10−30 esu of the synthesized compound is twenty times greater than that of urea (0.3728 × 10−30 esu). The one electron excitation of the synthesized crystal calculated by the time dependent-density functional theory (TD-DFT) calculation and comparatively studied using recorded UV spectrum. The single beam Z-scan unit equipped with 532 nm continuous Nd:YAG wave laser with 5ns pulse width was used to measure third order nonlinear optical property reveal that the investigated molecule possess effective two photon absorption with higher effective absorption coefficient. The imaginary and real parts of the third-order susceptibility values determined as Im χ3 = 2.31 × 10−6 cm W−1 and Re χ3 = 8.74 × 10−8 cm2 W−1 respectively.