Nonequilibrium molecular dynamics simulation of the energy transport through a peptide helix

Recent progress in transient infrared spectroscopy has made it possible to monitor the transient flow of vibrational energy along a peptide helix [V. Botan et al., Proc. Natl. Acad. Sci. U.S.A. 104, 12749 (2007)]. To provide a theoretical description of these experiments, extensive nonequilibrium molecular dynamics simulations of the photoinduced energy transport in a photoswitchable Aib peptide are performed. By calculating the response of the molecule caused by its excitation via optical and infrared pulses as well as temperature jump and stationary heating, it is shown that these methods are equivalent in that they provide approximately the same molecular energy transfer times. The resulting thermal diffusivity of 10 A(2) ps(-1) qualitatively agrees with the results of previous normal mode calculations for proteins and with experimental bulk values (e.g., 14 A(2) ps(-1) for water). To compare to experiment, a new way of approximating the measured signals is suggested which leads to an improved agreement with the experimental results and explains previous discrepancies. To elucidate the mechanism of energy transfer, modifications to the molecular dynamics force field are introduced, which reveal that the energy transfer occurs mainly through the peptide backbone and depends surprisingly little on the force field parametrization. Employing a harmonic model, quantum-mechanical effects are estimated to moderately (about a factor of 2) speed up the energy transport along the peptide.