Classical, many-body molecular dynamics simulations are used to study polyatomic ion beam deposition on carbon nanopeapods (C-60-filled, single-walled carbon nanotubes). The results confirm the effectiveness of ion bombardment in inducing chemical modifications of nanopeapods. The simulations show how the coalescence of C-60 molecules starts with the damage of fullerenes and intermolecular bridging. In addition, the cross-linking of C-60 molecules to the tube wall is also predicted. This cross-linking results in changes in the electronic band structure as compared to the unmodified nanopeapod, which is investigated using first principles density functional theory. (c) 2006 Elsevier B.V. All rights reserved.