It has become apparent that molecular modeling is a powerful approach to examining the properties of biomolecular systems like nucleic acids and their noncovalent interactions with other substances. Theoretical studies dealing with the dynamics of such extended molecules are based on the molecular mechanics simulations exhibiting very low computational requirements without sacrificing accuracy. This advantage is balanced by a limitation that the electronic structure of the biomolecules is treated as being unaltered throughout the entire simulations. Hence, it is impossible to observe formation or break up of intra- and intermolecular interactions in order to describe the process of charge transfer. Consequently, it is indispensable to employ quantum-chemical methods, which would allow the change of electronic structure in a certain region of the biomolecular system under investigation. This article reviews advances over the last few years in which quantum-chemical wave function-based calculations have been applied to this problem.