The charge transfer of slow atoms colliding with a surface is studied by means of a LCAO-method supplemented with a LD many-body contribution. Atomic levels and the parameters controlling the atom-surface interaction are obtained for H and He on Al(100). The method is well suited for analyzing short ion-surface distances, where the strong coupling promotes molecular orbitals. Charge transfer processes are finally calculated by solving Keldysh-Green function equations that describe the full quantum process associated with the ion-surface interactions. These equations give a specific prescription for calculating velocity and three-dimensional crystal effects, taking into account the two-dimensional surface periodicity. Calculations for some specific cases are presented.