Effects of helical distortions on the optical properties of amide NH infrared absorption in short peptides in solution

The secondary structure of ordered peptides in solution usually exhibits helical distortions that are enhanced by the shortness of the backbone chain. These distortions are reflected in the optical proper-ties of amide NH infrared absorption and in the shape of the CD spectra. These effects are exemplified here in a series of short, intramolecularly H-bonded peptides of the general formula F[(alphaMe)Val](r)-T-[(alphaMe)Val](2)NHt-Bu where T = Toac and F = Fmoc, a nitroxide-based alpha-amino acid quencher and a fluorophoric N-alpha protecting group. respectively, where r = 0-3. Their structural features in methanol were determined by a combined approach of time-resolved fluorescence resonance energy transfer measurements and molecular mechanics calculations. They show a rather compact arrangement of the probes around the distorted, 3(10)-helical backbone chain, which accounts for the slow interconversion between conformational substates on the nanosecond time scale.