Modeling quantum vibrational excitations in condensed-phase systems

In this paper, we present an extension of the theoretical–computational methodology based on the per- turbed matrix method and molecular dynamics simulations that we introduced in a recent paper (Daidone et al., Chem Phys Lett 488:213–218, 2010). This methodology models quantum vibrational states of polyatomic systems (i.e. beyond the one-dimensional vibrational mode case) embedded in a complex atomic-molecular environment such as liquid-state conditions. In the extended model, we now include the anharmonic correction to the excitation fre- quency of each mode and the excitonic coupling effects, providing a detailed description of the theoretical basis and an explicit scheme to achieve a very efficient implementa- tion of the method. Application of the proposed procedure to study the amide I band of the infrared spectra of a b-hairpin peptide shows that a quantitative and accurate reproduction of the experimental spectral variations due to folding– unfolding transition can be achieved.