We present methods for combining time-dependent density functional theory and the Hubbard U potential in the framework of the real-time propagation of Kohn-Sham orbitals to describe electron-atom coupled dynamics beyond the Born-Oppenheimer approximation. The time evolution of the noncommuting nonlocal operators were realized through Crank-Nicolson's inversion method and Suzuki-Trotter's split exponentiation. The electron dynamics related to the high speed motion of an alkali atom on a conjugated carbon plane is presented. The nonequilibrium charge oscillation between a metal surface and a localized atomic orbital, as modeled with graphene and Ca, is discussed.