Conformation dependence of the CalphaDalpha stretch mode in peptides. 1. Isolated alanine peptide structures.

Ab initio normal mode calculations have been performed on isolated alanine di- through octa-(i.e., blocked) peptides in uniform alphaR, beta, and polyproline II conformations to determine how the CalphaDalpha stretch mode, which has been proposed as a possible determinant of the varphi,psi conformation at the Calpha atom (Mirkin, N. G.; Krimm, S. J. Phys. Chem. A 2004, 108, 10923), depends on conformation and sequence length. This set of frequencies, including results on some kinked structures, demonstrates that such a discrimination is likely to be possible through experimental observations of peptides synthesized with successive deuteration at the Halpha sites, on the basis of at least three properties: the values of the frequency at the first residue, the pattern of successive frequency differences, and the frequency differences between the first and last residues.