  A mixed quantum-classical approach to simulate the coupled dynamics of
electrons and nuclei in nanoscale molecular systems is presented. The method
relies on a second order expansion of the Lagrangian in time-dependent density
functional theory (TDDFT) around a suitable reference density. We show that the
inclusion of the second order term renders the method a self-consistent scheme
and improves the calculated optical spectra of molecules by a proper treatment
of the coupled response. In the application to ion-fullerene collisions, the
inclusion of self-consistency is found to be crucial for a correct description
of the charge transfer between projectile and target. For a model of the
photoreceptor in retinal proteins, nonadiabatic molecular dynamics simulations
are performed and reveal problems of TDDFT in the prediction of intra-molecular
charge transfer excitations.
