Gas-Phase IR Spectroscopy and Structure of Biological Molecules

Marie-Pierre Gaigeot, Riccardo Spezia, Gaigeot, Marie-Pierre, Spezia, Riccardo

In this chapter we review recent advances in theoretical methods to understand and rationalize anharmonic vibrational spectroscopy (IR-MPD and IR-PD) and collision induced dissociations (CID) in the gas phase. We focused our attention on the application of molecular dynamics-based methods. DFT-based molecular dynamics was shown to be able to reproduce InfraRed Multi-Photon Dissociation (IR-MPD) and InfraRed Pre-Dissociation (IR-PD) action spectroscopy experiments, and help assign the vibrational bands, taking into account finite temperature, conformational dynamics, and various anharmonicities. Crucial examples of dynamical vibrational spectroscopy are given on the protonated Ala n H(+) series (related to IR-MPD in the 800-4,000 cm(-1) domain), ionic clusters (related to IR-PD in the 3,000-4,000 cm(-1) region), and neutral peptides (related to IR-MPD in the far-IR). We give examples from simple (e.g., cationized urea) to more complex (e.g., peptides and carbohydrates) molecular systems where molecular dynamics was particularly suited to understanding CID experiments.