Peptide Bond Vibrational Coupling

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Abstract

Neutral trialanine (Ala3), which is geometrically constrained to have its peptide bond at Φ and Ψ angles of α-helix and PPII-like conformers, are studied at the B3LYP/6-31+G(d,p) level of theory to examine vibrational interactions between adjacent peptide units. Delocalization of the amide I, amide II, and amide III3 vibrations are analyzed by calculating their potential energy distributions (PED). The vibrational coupling strengths are estimated from the frequency shifts between the amide vibrations of Ala3 and the local amide bond vibrations of isotopically substituted Ala3 derivatives. Our calculations show the absence of vibrational coupling of the amide I and amide II bands in the PPII conformations. In contrast, the α-helical conformation shows strong coupling between the amide I vibrations due to the favorable orientation of the CO bonds and the strong transitional dipole coupling. The amide III3 vibration shows weak coupling in both the α-helix and PPII conformations; this band can be treated as a local independent vibration. Our calculated results in general agree with our previous experimental UV Raman studies of a 21-residue mainly alanine-based peptide (AP).

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