A quantum-classical description of the amide I vibrational spectrum of trialanine cation in D2O is given that combines (i) a classical molecular dynamics simulation of the conformational distribution of the system, (ii) comprehensive density functional theory calculations of the conformation-dependent and solvent-induced frequency fluctuations, and (iii) a semiclassical description of the vibrational line shapes which includes nonadiabatic transitions between vibrational eigenstates. Various assumptions that are usually employed in the calculation of condensed-phase vibrational spectra are tested, including the adiabatic, the Franck-Condon, and the second-order cumulant approximations, respectively. All three parts of the theoretical formulation are shown to have a significant impact on the simulated spectrum, suggesting that the interpretation of peptide amide I spectra may require substantial theoretical support.

Recent two-dimensional infrared (2D-IR) experiments on a short peptide 3(10)-helix in chloroform solvent [E. H. G. Backus et al., J. Phys. Chem. B 113, 13405 (2009)] revealed an intriguing temperature dependence of the homogeneous line width, which was interpreted in terms of a dynamical transition of the peptide. To explain these findings, extensive molecular dynamics simulations at various temperatures were performed in order to construct the free energy landscape of the system. The study recovers the familiar picture of a glass-forming system, which below the glass transition temperature T(g) is trapped in various energy basins, while it diffuses freely between these basins above T(g). In fact, one finds at T(g) approximately 270 K a sharp rise of the fluctuations of the backbone dihedral angles, which reflects conformational transitions of the peptide. The corresponding C=O frequency fluctuations are found to be a sensitive probe of the peptide conformational dynamics from femtosecond to nanosecond time scales and lead to 2D-IR spectra that qualitatively match the experiment. The calculated homogeneous line width, however, does not show the biphasic temperature dependence observed in experiment.

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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.

Local structures and energies were calculated for the interaction of acetone molecules with ice I h at the (0001) surface, in the bulk and at small-angle grain boundaries. Force-field methods were used; for the surface additionally ab initio calculations were done. An ordered crystal-structure model of ice I h in space group P112 1 (Z ¼ 8) was used. The small-angle grain boundary was set up as a series of line defects with Burgers vectors of [2/3 1/3 1/2] (in the hexagonal lattice of ice I h ). All calculations were carried out with one or two acetone molecules in a sufficiently large simulation box containing up to 4608 water molecules, representing the low concentration of acetone in the atmosphere. The adsorption on the surface is energetically preferred. The acetone molecule is bound to the surface by two hydrogen bonds. This result is in contrast to earlier works with high acetone concentrations where only one hydrogen bond is formed. With two hydrogen bonds the adsorption enthalpy is calculated as À41.5 kJ mol À1 , which is in agreement with experimental results. The interaction at small-angle grain boundaries is energetically less favourable than at the surface but much more favourable than in the bulk ice. In bulk ice and at small-angle grain boundaries the acetone molecule is bound by two hydrogen bonds like at the surface. The incorporation of acetone in bulk ice distorts the crystal structure significantly, whereas an incorporation at a small-angle grain boundary leads only to a minor distortion.