Ab initio molecular orbital study of the amide I vibrational interactions between the peptide groups in di- and tripeptides and considerations on the conformation of the extended helix

Abstract

Interrelationships among the coupling between the amide I vibrations of peptide groups, the A–E1 wavenumber difference of the amide I mode and the conformation of helical polypeptide chains were examined theoretically. Ab initio molecular orbital (MO) calculations were performed for a glycine dipeptide and a glycine tripeptide with various ϕ and ψ angles to obtain the coupling constants between the amide I vibrations of the nearest peptide groups and between those of the second nearest peptide groups. It was found that the coupling constants between the second nearest peptide groups were reasonably well explained by the transition dipole coupling mechanism, whereas the coupling constants between the nearest peptide groups contained other factors that mainly depended on ψ. The wavenumbers of the A and E1 components of the amide I mode were calculated for various helices on the basis of these coupling constants. The A component is strong in the infrared (IR) spectrum when the transition dipole of the amide I vibration is nearly parallel to the helix axis, whereas the E1 component has a strong IR intensity when they are nearly perpendicular to each other. The A component has a strong Raman intensity in both cases. Therefore, the Raman–infrared wavenumber difference of 10–20 cm-1 observed for the amide I bands of poly(L-glutamate) and poly(L-lysine) with charged side chains indicates that these polypeptides, in that so-called ‘extended helix’ state, have conformations giving rise to strong IR bands of the E1 component which are lower in wavenumber than the Raman bands of the A component by 10–20 cm-1. The ranges of the ϕ and ψ angles that are consistent with such spectral features are discussed on the basis of the calculated structures and amide I wavenumbers. © 1998 John Wiley & Sons, Ltd.