Semi-empirical methods vibrational spectroscopy

A critical pre-requisite to using Raman and resonance Raman spectroscopy to examine the excited-state structural dynamics of nucleic acids and their components, is the determination of the normal modes of vibration for the molecule of interest. The most definitive method for determining the normal modes is exhaustive isotopic substitution, subsequent measurement of the IR and Raman spectra, and computational analysis with the FG method of Wilson, Decius, and Cross [77], Such an analysis is rarely performed presently because of the improvements in accuracy of ab initio and semi-empirical calculations. Ab initio computations have been applied to most of the nucleobases, which will be described in more detail below, resulting in relatively consistent descriptions of the normal modes for the nucleobases. 

The use of gas-phase biomolecule spectroscopy for structural characterization rehes strongly on the interplay between experiment and theory. Structural properties can usually only be extracted from experimental spectra with the use of high-level quantum-chemical calculatirms. The chapter Theoretical Methods for Vibrational Spectroscopy and CoIUsirai Induced Dissociation in the Gas Phase reviews some recent advances in the theoretical methods applied to predict vibrational spectra, including molecular-dynamics-based methods to model photo-dissociation spectra and DFT-based molecular dynamics to predict spectra in the far-infrared region. The use of trajectory calculations on a semi-empirical potential is investigated as an alternative to transition-state calculations for the modeling of collision-induced dissociation of protonated peptides. 

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