Structure analysis of dipeptides in water by exploring and utilizing the structural sensitivity of amide III by polarized visible Raman, FTIR-spectroscopy and DFT based normal coordinate analysis

A series of dipeptides AX and XA (X = G, K, L, S, and V) were investigated by polarized visible Raman and FTIR-spectroscopy to examine the conformational determinants of the amide III band. A spectral decomposition combined with density functional calculations revealed that the an-tide III band has a multicomponent structure in that three different modes contribute to amide III vibrations. One of them (amide III2) dominates the Raman spectra particularly of the cationic species. Its normal mode displays an in-phase combination of NH and Calpha1H in plane bending vibrations, which makes it sensitive to changes of the dihedral angle psi. Indeed, our Raman data show that amide III, varies with psi but remains practically unaffected by variation of phi in the region between -95degrees and -75degrees. which is sampled by the investigated AX peptides. Our data support the Lord hypothesis that amide III depends solely on V (Lord, R. Appl. Spectrosc. 1977, 31, 187) but specifies to which of the amide III modes this statement applies. Our data further reveal that all an-tide III modes can interact with side chains vibrations. For some residues this causes a mode delocalization which yields a reduction of the Raman cross section. Amide S, which is a structure sensitive band resonance enhanced with UV-excitation, disappears for V-values outside of the beta-sheet region due to changes of the normal mode compositions of several modes between 1300 and 1420 cm(-1). This explains its absence in the UV-Raman spectra of a-helical structures. Our data suggest that all AX peptides exhibit V, angles around 150degrees.