Infrared spectroscopy in the gas and liquid phase from first principle molecular dynamics simulations: application to small peptides

We discuss the applicability of finite temperature Car-Parrinello molecular dynamics simulations for the calculation of infrared spectra of complex molecular systems, either in the gas phase or in the condensed phase, taking examples from the infrared spectroscopy of N-methylacetamide and small peptides. Band assignments for the simulation is still challenging and we introduce here a general method for obtaining effective normal modes of molecular systems from Molecular Dynamics simulations. The effective normal modes are defined as a linear combination of internal coordinates such that the power spectra of these modes are as localized as possible in frequency. We further define band intensities for these modes from different levels of approximation of the infrared spectrum. Applications of this approach for assigning infrared bands from first-principle molecular dynamics simulations are presented for N-methylacetamide in gas phase and in solution, for the gas phase alanine dipeptide and the gas phase octa-alanine peptide.