In this study, three different organic molecules containing piperazine were synthesized and characterized by FT-IR and NMR spectroscopic methods. GaussView 5.0 and Gaussian 09 molecular structures of all compounds. With these programs, three-dimensional (3D) shapes of molecules were created and conformation structures were obtained by PES (Potential Energy Surface) analysis to calculate base condition energies. All conformations of the molecules studied were obtained by using the Density Function Theory Becke-3-Lee-Yang-Parr (DFT/B3LYP) and AM1(Semi Empirical Method). Vibration frequencies magnetic properties (Nuclear Magnetic Resonance spectrum) were examined. The microbiological bacteria (three Gram-positive and two Gram-negative strains) and three fungal by using micro dilution (as MICs) and disc diffusion (as mm zone) methods.