  We present a theoretical approach to include dynamical aspects of molecular
structural fluctuations, such as, for example, forming and breaking hydrogen
bonds, isomerizations, and dynamical supramolecular structures, in
nonequilibrium Green's functions electron transport calculations. Structural
transitions are treated as a stochastic telegraph process, and the primary
quantity of interest is a retarded Green's function averaged over realizations
of a stochastic process. Using the Novikov-Furutsu functional stochastic
calculus method, we derive equations of motion for stochastically averaged
retarded Green's function in closed form. Consequently, we obtain the
expression for electric current averaged over transitions, which depends not
only on probabilities of observing particular molecular structures but also on
the dynamics. However, the proposed method has a significant limitation - we
have to assume that the imaginary parts of retarded self-energies produced by
left and right electrodes are proportional to each other; this significantly
restricts possible applications of the theory. Several examples illustrate the
proposed approach.
