Synopsis We have developed a theoretical model of ion-atom collisions, which is based on the time-dependent density functional theory combined with the molecular dynamics (TDDFT-MD).Employing real-time and realspace method, the coordinate space translation (CST) technique was introduced to allow one to focus on the region of the target or the projectile.The benchmark calculations were given for the collision of He2+ + Ne.The processes of electron capture have been investigated.The calculated cross sections showed a good agreement with available experimental data over a wide range of impact energies.