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We present a theoretical approach to include dynamical aspects of molecularstructural fluctuations, such as, for example, forming and breaking hydrogenbonds, isomerizations, and dynamical supramolecular structures, innonequilibrium Green's functions electron transport calculations. Structuraltransitions are treated as a stochastic telegraph process, and the primaryquantity of interest is a retarded Green's function averaged over realizationsof a stochastic process. Using the Novikov-Furutsu functional stochasticcalculus method, we derive equations of motion for stochastically averagedretarded Green's function in closed form. Consequently, we obtain theexpression for electric current averaged over transitions, which depends notonly on probabilities of observing particular molecular structures but also onthe dynamics. However, the proposed method has a significant limitation - wehave to assume that the imaginary parts of retarded self-energies produced byleft and right electrodes are proportional to each other; this significantlyrestricts possible applications of the theory. Several examples illustrate theproposed approach.

Molecular electronic junctions with stochastic structural transitions