The new piperazine-based Schiff base hydrazone with N, O donor set of atoms, LPE, has been prepared by the condensation reaction of new piperazine-based diamine, APE, with salicylaldehyde. The structure of newly prepared compounds was characterized by using FT-IR, UV-Vis, 1H NMR, and 13C{1H]-spectroscopic methods as well as elemental analysis data. Furthermore, the structure of piperazine-based compounds, APE and LPE, has been optimized and the geometrical structures of a diamine compound, APE, and Calcium atom have been investigated at the level of density functional theory (DFT). The 6-311++G(d,p) basis set was utilized for ligands in the gas phase. The optimized structures contain N…Ca interactions and piperazine rings have boat structure in most of them. The chelating structures of piperazine rings show most stabilization among other interactions, the stabilization energy is -1493.9667 kJ mol-1. Also, the prepared compounds were evaluated for preventive effect on apoptotic motor neurons in adult mouse spinal cord slices. The APE inhibited apoptosis in the motor neurons and significantly increased viability in these neurons.