Linear and nonlinear infrared signatures of local α- and 310-helical structures in alanine polypeptides

Vibrational exciton Hamiltonians for the amide I and amide A modes of both the α- and 310-helical conformations of a fifteen unit polyalanine oligomer CH3–CO(Ala)15–NHCH3 are constructed using density-functional calculations for smaller model peptides. Energy levels as well as the transition dipoles of all singly and doubly excited-state manifolds are calculated. A variety of C13-substituted isotopic derivatives are examined with respect to their ability to reveal differences in local secondary structures in two-dimensional infrared spectra in the amide I region. Amide mode anharmonicities are predicted to be valid indicators of secondary helical structures.