Molecular dynamics simulations were performed to investigate H2+ and SiH3+ ion bombardment of hydrogen terminated Si(001)2×1 surfaces. Normal incidence ion bombardment effects on dangling bond generation, adatom diffusion, and nucleation were studied as a function of incident energy between 10 and 40 eV. The dangling bond generation rate due to H2+ impacts at 20 and 40 eV was about twice that of SiH3+. However these effects appeared to be insignificant compared to probable neutral radical effects under typical plasma-enhanced chemical vapor deposition conditions. The enhanced diffusion of Si adatoms due to ion bombardment was observed to be minor in comparison with thermal diffusion and the disruption of ledge sites due to SiH3+ ion bombardment is not significant, with ion incident energies up to 40 eV. Ion bombardment in the incident energy range between 10 and 20 eV can contribute the modification of surface kinetics without bulk damage. © 2003 American Vacuum Society.