The presented investigation aims to establish a foundation for the study of ion beam cancertherapy employing time-dependent density functional theory for calculating collision cross-sections and energies of secondary electrons produced by a charged ion impacting on a biological target of arbitrary size and shape. The obtained collision cross-sections compare well to values obtained using the popular PASS code, which relies on the modified Bohr theory. Furthermore, we demonstrate that the differential cross-sections obtained in this study seem to be affected by post-collision electron recapture processes occurring inside the target.