The self-assembly of PdX2 (X- = CIO4- and PF6-)1 with C-3-symmetric l- and d-L [L = (2S,2'S,2 '' S)- and (2R,2'R,2 '' R)-[benzenetricarbonyltris(azanediyl)]tris(3-phenylpropane-2,1-diyOtriisonicotinate] produces the chiral nanocube pair [Pd-6(l-L)(8)](X)(12) and [Pd-6(d-L)(8)](X)(12) (X- = CIO4- and PF6-, respectively) with an inner cavity of 12.3 X 12.3 X 12.3 angstrom(3). These chiral nanocubes are effective for the enantiorecognition of various chiral amino acids via the square-wave-voltammetry technique. In the present study, the site of enantiorecognition was confirmed by density functional theory calculated interactions between each nanocube and the chiral amino acids, and the calculated interactions were coincident with the shifts of the electrochemical oxidation potentials.