The aggregation of amyloid beta-peptide (A beta peptide) has been associated with the pathogenesis of Alzheimer's disease (AD). In the present study, we aimed to disclose how Zn2+ affects the A beta aggregation in detail. Thus, molecular dynamics simulation was implemented to elucidate the changes of structure and residual hydrophobicity upon Zn2+ coordination. Our results show that Zn2+ can strongly influence the structural properties of A beta 40 and A beta 42 by reducing helical formation and increasing turn formation to expose the hydrophobic regions. Furthermore, hydrophobicity of Zn2+-A beta 40 and Zn2+-A beta 42 was much higher than that of each monomer, since Zn2+ binding can significantly influence the hydrophilic domains of A beta. The further analyses indicate that not only four residues (H6, E11, H13, and H14) but also R5, D7, K16, K28, and terminal residues influence hydrophobicity upon Zn2+ coordination. Importantly, R5, K16, and K28 play a crucial role to regulate solvation-free energies. This work is helpful to understand the fundamental role of Zn2+ in aggregation, which could be useful for further development of new drugs to inhibit Zn2+-A beta aggregation.