We formulate a time-dependent density functional theory for the coupled dynamics of electrons and nuclei that goes beyond the Born-Oppenheimer (BO) approximation. We prove that the time-dependent marginal nuclear probability density , the conditional electronic density , and the current density are sufficient to uniquely determine the full time-evolving electron-nuclear wave function, and thus the dynamics of all observables. Moreover, we propose a time-dependent Kohn-Sham scheme which reproduces the exact conditional electronic density and current density and the exact N-body nuclear density. The remaining task is to look for functional approximations for the Kohn-Sham exchange-correlation scalar and vector potentials. Using a model driven proton transfer system, we numerically demonstrate that the adiabatic extension of a beyond-BO ground state functional captures the dominant nonadiabatic effects in the regime of slow driving.

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