An analysis of the charge transfer mechanism in the collision of multiply charged ions with molecular and biomolecular targets is performed, considering the non-adiabatic interactions between the molecular states involved. Collisions of doubly charged C
2+ ions on small molecular targets, CO and OH, have been investigated, together with the analysis of charge transfer between C
4+ ions on uracil and halouracil biomolecular targets. The process is studied theoretically by means of ab-initio molecular calculations followed by a semi-classical treatment of the collision dynamics. The influence of rotational couplings is discussed with regard to the collision energy. Strong anisotropic and vibration effects are pointed out.