Non-equilibrium Green's function theory for non-adiabatic effects in quantum transport [Kershaw and Kosov, J. Chem. Phys. 147, 224109 (2017) and J. Chem. Phys. 149, 044121 (2018)] is extended to the case of interacting electrons. We consider a general problem of quantum transport of interacting electrons through a central region with dynamically changing geometry. The approach is based on the separation of time scales in the non-equilibrium Green's functions and the use of the Wigner transformation to solve the Kadanoff-Baym equations. The Green's functions and correlation self-energy are non-adiabatically expanded up to the second order central time derivatives. We produce expressions for Green's functions with non-adiabatic corrections and a modified formula for electric current; both depend not only on instantaneous molecular junction geometry but also on nuclear velocities and accelerations. The theory is illustrated by the study of electron transport through a model single-resonant level molecular junction with local electron-electron repulsion and a dynamically changing geometry.
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