Chiral salen ligand with quaternary ammonium groups, (R,R)-1,2-bis{4-[2-(trimethylammonium)-ethoxy]-2-hydroxy-salicylideneamino}cyclohexane perchlorate (L) and ML complexes [M=Zn(II), Cu(II), Ni(II), Co(II), Fe(III), Mn(III)] were synthesized and characterized. The electronic spectra and circular dichroism spectra were discussed. By UV-Vis and CD spectrophotometry, the molecular recognition of the host ZnL toward amino acid was studied. The coordination number (n), equilibrium constants (K) and thermodynamic parameters (Delta H-r(m)circle minus, Delta S-r(m)circle minus) between the complex ZnL and a series of chiral amino acid ligands were measured. The results show that the equilibrium constants decrease in the order of K-Phe>K-Val>K-Thr. The reaction is an exothermic process with entropy decrease. The cleavage reaction of DNA with the chiral salen metal complexes in the presence of H2O2 was studied by means of gelatin electrophoresis.