Theoretical analyses of L-alanine (L-Ala)− and L-homocysteine (L-Hcy)−Cu(II) complexes in basic, neutral, and acidic solutions were carried out using density functional theory to investigate the pH dependence of the formation mechanism of amino acid−Cu(II) complexes. The calculated complex formation energies indicate that the amino acid−Cu(II) complexes were expected to form in basic and neutral solutions but not in acidic solutions. The factors that determine the stability of these complexes are the coordination ability of each amino acid and the significance of intramolecular interactions among ligands within the complexes. As predicted from the molecular structure, in neutral solutions, the coordination ability of amino acid becomes lower than that in basic solutions because of the inert structure of the protonated amino group, −NH 3 + ; however, the coordination ability originating from the −COO − group is estimated to be sufficient for stabilizing the entire complex system. Moreover, two H 2 O molecules coordinate with the central Cu 2+ ion from the equatorial direction and interact with the coordinating amino acids, providing additional stability within the complex. In contrast, in acidic solutions, the complex does not have either sufficient coordination ability of amino acids or effective intramolecular interactions within the complex.