•The new analytical copper(II) based ara-C analog (an anticancer drug) was synthesized according to different analytical conditions and characterized by analytical and spectroscopic methods.•All chemical activity analyses of the molecules were performed on the basis of by DFT method B3LYP functional and LANL2DZ (Cu(II) atom), 6-311G(d,p) mixed basis sets (carbon, oxygen, nitrogen, chlorine and hydrogen atoms).•The interactions between the molecule with DNA bases such as adenine, cytosine, guanine, and thymine were investigated by using the ECT (electrophilicity-based charge transfer) method for ara-C and Cu2(ara-C)2Cl4.•Molecular docking and DNA binding analysis were performed for ara-C and Cu2(ara-C)2Cl4.•The hyperconjugation interaction energy and electron densities of donor and acceptor bonds were calculated by using natural bond orbital (NBO) analysis for Cu2(ara-C)2Cl4. In this study, the new copper(II) based cytosine arabinoside (ara-C) analog was synthesized and characterized by analytical and spectroscopic methods. Especially the data obtained from FT-IR spectroscopy showed that ara-C coordinated with copper(II) ions through –C=O and -Nring groups and formed a complex compound in a tetrahedral structure. The proposed structure of this dimeric copper(II) complex was defined as Cu2(ara-C)2Cl4. Also, the ability of both compounds to bind to double helix fish sperm DNA (dsDNA) and the damage to the HeLa cell line was investigated. All theoretical chemical activity analyses (hardness and softness parameters, Fukui functions, net charges) of the ara-C and Cu2(ara-C)2Cl4 molecules were performed with DFT with mixed basis set including LANL2DZ for Cu atom and 6-311G(d,p) for carbon, oxygen, nitrogen, chlorine and hydrogen atoms with B3LYP functional was applied. The stability of the molecule arising from hyperconjugative interactions, charge delocalization was analyzed by using natural bond orbital analysis (NBO) for optimized structure of Cu2(ara-C)2Cl4. Also, the interactions between the studied molecules (ara-C and Cu2(ara-C)2Cl4 with DNA bases such as adenine, cytosine, guanine, and thymine were investigated by using the ECT (electrophilicity-based charge transfer) method. Furthermore, the best binding sites of the DNA (PDB:1BNA) protein to the ligands (ara-C and Cu2(ara-C)2Cl4 were examined and the binding energies and interaction states were determined by molecular docking study.