Local amide I mode frequencies and coupling constants in polypeptides

Ab initio calculations of the amide I modes of right-handed α-helical, 3₁₀-helical, left-handed α-helical, π-helical, parallel β-sheet, antiparallel β-sheet, and fully extended β-sheet polypeptide conformations with two to five peptide bonds were performed to investigate the site dependencies of the local amide I mode frequencies and vibrational coupling constants between neighboring peptides. A Hessian matrix reconstruction method is used to obtain these quantities from the ab initio-calculated amide I normal modes. The local amide I mode frequencies of the peptides in the inner region of a given helical polypeptide are significantly larger than those of terminal peptides, whereas the local amide I mode frequencies of β-sheet polypeptides are not site-dependent. The amide I vibrational coupling constants are not sensitive to the length of the polypeptide, but they are found to be strongly dependent on the three-dimensional conformation of the polypeptides. An empirical model for predicting diagonal amide I mode frequency shift is used to theoretically describe the site dependence of the local amide I mode frequency.