Phonon spectra and thermodynamic properties of the infinite polyalanine alpha helix: a density-functional-theory-based harmonic vibrational analysis.

We have performed a density-functional theory harmonic vibrational analysis of the infinite polyalanine alpha helix. The calculated phonon dispersion spectrum shows excellent agreement to available experimental data, except for the high frequency hydrogen stretching modes which show characteristic shifts due to anharmonic effects. A major advantage compared to previously performed empirical force field studies is that long range effects such as electrostatic interaction and polarization are intrinsically taken into account for characterizing hydrogen bond formation in the helix. Our results indicate that these effects are crucial to accurately describe the low frequency acoustical branches and lead to a significantly better agreement with experiment for the specific heat in the low temperature range.