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We describe single electron tunneling through molecular structures under the influence of nano-mechanical excitations. We develop a full quantum mechanical model, which includes charging effects and dissipation, and apply it to the vibrating C single electron transistor experiment by Park {\em et al.} {[Nature {\bf 407}, 57 (2000)].} We find good agreement and argue vibrations to be essential to molecular electronic systems. We propose a mechanism to realize negative differential conductance using local bosonic excitations.

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