The IR vibrational spectra of isolated alanine as well as its hydrated and crystalline forms were investigated based on classical MD simulations using the AMOEBA polarizable force field . In the gas phase, we studied both zwitterioinc and neutral forms, which are shown in Fig. , even though, when isolated, alanine is most stable in the neutral form. In contrast, once alanine is hydrated or in a crystal, the zwitterionic form becomes more stable. In the following, we will present the theoretical and technical background at the basis of our methodology, with the aim to characterize the vibrational modes of alanine in different environments in the spectral region 1000-2000 cm -1 (Section II A) based on the calculation of the IR spectra of the molecule in the various phases introduced above (Section II B).