We have calculated the energy loss of swift O{sub 2}{sup +}, N{sub 2}{sup +}, and C{sub n}{sup +} (n=2-60) molecular ions moving through an amorphous carbon target. The dielectric formalism is used to evaluate the vicinage effects in the energy loss of the atomic ions that form the molecular projectile, but we take into account that the charge state of these atomic ions is affected by their correlated motion through the target and by the screened Coulomb potential between them. When vicinage effects in the charge state are taken into account, the Coulomb repulsion is weakened, leading to a reduction in the interatomic separations ({approx}3% for N{sub 2}{sup +} and {approx}9% for C{sub 60}{sup +}, both having similar velocities). These charge state effects can be neglected for diatomic molecular ions, but they give rise to a reduction of {approx}8% in the vicinage effects in the energy loss of larger molecular ions with cage like geometrical structures, like C{sub n}{sup +} (n=20,60) projectiles.