General treatment of vibrations of helical molecules and application to transition dipole coupling in amide I and amide II modes of α-helical poly(l-alanine) Original Research Article

We have developed a general formalism for the vibrational dynamics of a helical macromolecule that avoids the assumption of weak coupling between groups along the helix as well as the use of perturbation theory to calculate the frequencies. We have applied the concepts of this theory to the calculation of the amide I and amide II frequencies of α-helical poly (l-alanine). Although intergroup dipole derivatives required by the theory are not presently available, we have been able to show that they are important in accounting for the observations, particularly the E2-species amide I frequency. An optimized set of intergroup force constants, which implies a non-weak-coupling-non-perturbation treatment, gives excellent reproduction of the observed frequencies.