Optical nuclear electric resonance (ONER), a recently proposed protocol for nuclear spin manipulation in atomic systems via short laser pulses with MHz repetition rate, exploits the coupling between the nuclear quadrupole moment of a suitable atom and the periodic modulations of the electric field gradient generated by an optically stimulated electronic excitation. In this theory paper, we extend the scope of ONER from atomic to molecular systems and show that molecular vibrations do not interfere with our protocol. Exploring the diatomic molecule LiNa as a first benchmark system, our investigation showcases the robustness with respect to molecular vibration, and the ability to address and manipulate each of the two nuclear spins independently, simply by adjusting the repetition rate of a pulsed laser. Our findings suggest that it might be possible to shift complicated spin manipulation tasks required for quantum computing into the time domain by pulse-duration encoded laser signals.