The new single crystal, bis(2-chloro-4,6-diaminopyrimidine)-copper(II)-dichloride [CDPCD] compound was synthesized. The crystal structure of the compound was solved by the single crystal X-ray diffraction method. CDPCD has a=6.3334(9) Å, b=6.9914 (10)Å, c=8.9901(12)Å, α=78.127(11)°, β=86.853(11)°, γ=67.307(10)° and Z=1 parameters and is crystallized in the space group P-1 in the triclinic crystal system. Complete vibration assignments of CDPCD in gas phase and experimental frequencies are reported together with the scaled force constants. The optimized geometric parameters and frequency values were theoretically calculated using DFT/B3LYP method with LANL2DZ basis set. The XRD single crystal measurement parameters are good agreed with the optimized parameters. Molecular orbital surfaces and molecular electrostatic potential properties were measured at B3LYP/LANL2DZ level. Hirshfeld surface and fingerprint drawings were obtained to explain the intermolecular interactions of the crystal structure. The most important contributions for the crystal packing are from Cl…H/H…Cl (38.7%), H…H (17.9%) and N…H/H…N (14.8%) interactions. In addition, the molecule was tested by MTT test to determine the apoptosis and necrosis by cytotoxicity and double staining method. For the MTT test [MTT: (3,4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide], the tetrazolium salt was used. In different percentages of the compound, apoptotic necrotic index ratios of L929 fibroblasts and MCF-7 cells decreased. Bilateral staining method was used to evaluate the cells that had undergone apoptosis and necrosis of FITC (480-520nm wavelength). Apoptotic and necrotic index results of L929 fibroblasts and MCF-7 cells decreased as the amount of concentration decreased.