Coherent vibrational energy transfer along a peptide helix

Abstract

To measure the transport of vibrational energy along a peptide helix, Hamm and co-workers [J. Phys. Chem. B 112, 9091 (2008)] performed time-resolved vibrational experiments, which showed that the energy transport rate increases by at least a factor of 4, when a localized C=O mode of the peptide instead of an attached chromophore is excited. This finding raises the question if coherent excitonic energy transfer between the C=O modes may be of importance for the overall energy transport in peptides. With this idea in mind, nonequilibrium molecular dynamics simulations as well as quantum-classical calculations are performed, which qualitatively reproduce the experimental findings. Moreover, the latter model (an exciton Hamiltonian whose matrix elements depend on the instantaneous positions of the peptide and solvent atoms) indeed exhibits the signatures of coherent quantum energy transport, at least within the first few picoseconds and at low temperatures. The origin of the observed decoherence, the absence of vibrational self-trapping, and the possibility of quantum interference between various transport paths are discussed in some detail.

Energy transfer in finite-size exciton-phonon systems: Confinement-enhanced quantum decoherence

“…For instance, recent experiments revealed that the coherent nature of the exciton may explain the remarkable efficiency of light-harvesting complexes [21,22]. Similarly, in a peptide helix, it has been shown that when a localized amide-I mode is selectively excited, the energy transport rate drastically increases [23] suggesting that a coherent energy flow takes place * Electronic address: vincent.pouthier@univ-fcomte.fr between amide-I modes [24].…”

Two-dimensional infrared spectral signature and hydration of the oxalate dianion

“…The coefficients provide the instantaneous populations of the sites and the instantaneous interstate coherences. 24 To compute observables, the statistical density matrix must be computed by averaging the instantaneous values c * m (t)c n (t) over trajectories describing the ensemble. Such a procedure yields the statistical density matrix…”

A method for analyzing the vibrational energy flow in biomolecules in solution

“…From a theoretical point of view, the intramolecular vibrational energy flow in biomolecules has also received a great deal of attention 2, 28 through different approaches including harmonic theories, 8,26,[29][30][31][32][33] molecular dynamics (MD) simulations, 28,[34][35][36][37][38][39][40][41][42][43][44][45][46] coarse-grained models, 33,47 and quantum methods. 21,[48][49][50][51][52][53] Despite this diversity of theoretical treatments, comparison between experimental and theoretical studies is still unsatisfactory because it faces the major difficulty that whereas experiments provide information on the energy transport spectroscopically from the vibrational modes which are active in the technique employed, most of the theoretical treatments discuss the energy flow in terms of residuebased models which, although shown to be quite useful in describing the spatial evolution of the energy, 38,39,41,44 are not well suited for direct comparison with observed data since the residues are not the experimentally active units.…”