(a) Structure of the photoswitchable Aib peptide used in the studies of Hamm and co-workers (Refs. 33–35). To initiate energy flow along the peptide -helix, either UV excitation via photoisomerization of the azobenzene photoswitch or IR pumping of a localized mode was considered. In the MD simulations, moreover, we employed a temperature jump and a stationary heating excitation of the atom, which connects the photoswitch to the peptide. (b) Simple kinetic scheme of the energy flow in the system, which describes the energy transport along the peptide by the transport rate constant and the energy loss to the solvent by the cooling rate constant .
Time evolution of the mean kinetic energy per atom of the first (black), third (red), and fifth (green) residues of the Aib peptide obtained from nonequilibrium MD simulations. Shown are results for excitation via (a) a UV pulse, (b) an IR pulse, (c) a T-jump, and (d) stationary heating. The smooth lines are fits using the kinetic scheme shown in Fig. 1(b).
Time evolution of the energy correlation between the heated atom and (a) unit 1, (b) unit 3, and (c) unit 5 of the Aib peptide.
Mean kinetic energy of units 1, 3, 5, and 8, obtained for various modifications of the MD interaction energy of the Aib peptide. Panels (a) and (b) present simulations using the standard force field in solvent and in vacuo, respectively. The remaining panels show in vacuo simulations where (c) the nonbonded Coulomb and Lennard-Jones interactions within the peptide are switched off, (d) all bonds and bonding angles of the peptide are constrained, (e) all bonds and bonding angles are softened (using 10% and 30% of the original force constant of the bonds and angles, respectively), and (f) the atom masses of the peptide were increased by a factor of 4.
Density of states, specific heat (in ), and mean free path (in nm) of the Aib peptide, obtained for the standard force field (black lines) and a modification (red lines) with considerably softened bonds. Employing instantaneous normal mode calculations, these quantities are presented as a function of the normal mode frequency . Modes with imaginary frequency (Ref. 54) are not shown.
Time evolution of the mean kinetic energy of the local vibrational mode of the first (black), third (red), and fifth (green) residues, respectively.
Transferred vibrational energy to (a) peptide residues 1 (black) and 3 (red) shown as a function of temperature (for better visibility, was multiplied by a factor of 2). Standard deviations are given with respect to the statistical average. Panel (b) shows the corresponding energy transfer to the modes of these residues.
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