Contribution of transition dipole coupling to amide coupling in IR spectra of peptide secondary structures

Abstract

Transition dipole coupling (TDC) is often regarded as a principal mechanism for vibrational coupling that is the basis for the conformational sensitivity of amide vibrations in peptides and proteins. We have computationally tested the relative contribution of TDC to coupling of amide I bands in model peptides. First, the amide I IR spectra were calculated for sizable peptides (up to 12 amides) in both α-helical and β-sheet conformations at the density functional theory (DFT) level. Second, the spectra were calculated using TDC to approximate long-range vibrational coupling between the local (diagonal) vibrational parameters, which were transferred from DFT calculations on smaller fragments. The TDC contribution was obtained using classical representations, but employed DFT-determined transition dipole moments of the fragments. Full DFT simulations of the peptide vibrational spectra have greater dispersion than those obtained by TDC corrections, which reflects an underestimate of amide coupling in the TDC, although this difference does decrease at long distances. If DFT computations are used for in-strand coupling, then TDC does give reasonable interstrand coupling magnitudes for β-sheet models. These systematic analyses show that TDC alone cannot account for the vibrational interactions that give rises to the characteristic amide I band-shapes.