Amide-I lifetime-limited vibrational energy flow in a one-dimensional lattice of hydrogen-bonded peptide units

A time-convolutionless master equation is established for describing the amide-I vibrational energy flow in a lattice of H-bonded peptide units. The dynamics is addressed within the small polaron formalism to account for the strong coupling between the amide-I vibron and the phonons describing the H-bond vibrations. Therefore, special attention is paid to characterize the influence of the amide-I relaxation on the polaron transport properties. This relaxation is modeled by assuming that each amide-I mode interacts with a bath of intramolecular normal modes whose displacements are strongly localized on the C=O groups. It has been shown that the energy relaxation occurs over a very short time scale which prevents any significant delocalization of the polaron. At biological temperature, the polaron explores a finite region around the excited site whose size is about one or two lattice parameters. However, two regimes occur depending on whether the vibron-phonon coupling is weak or strong. For a weak coupling, the energy propagates coherently along the lattice until the polaron disappears. By contrast, for a strong coupling, a diffusive regime occurs so that the polaron explores a finite size region incoherently. In both cases, the finite polaron lifetime favors the localization of the vibron density whose amplitude decreases exponentially.