Relation between calculated amide frequencies and solution structure in Ala‐X peptides

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Abstract
Computational techniques have been used to aid interpretation of observed systematic shifts in the amide III frequencies of Ala‐X peptides. Optimized structures and frequencies have been calculated for Ala‐X peptides using GAUSSIAN86/88 with the 4‐31G basis, MOPAC, and normal mode methods based on empirical force fields. We observe the following: (1) Frequencies calculated using scaled GAUSSIAN86 force constants correlate well with the experimental results. (2) Structures of the Ala‐X peptides optimized by GAUSSIAN show a clear trend toward lower values of the dihedral angle ϕ as the X side chain becomes larger, while structures optimized here using semiempirical and empirical force fields do not show trends. (3) Computational changes in peptide conformations from β‐sheet to α‐helix produce large changes in both amide I and amide III frequencies that are inconsistent with the experimental results. (4) Computational changes in the dihedral angle ϕ of Ala‐Ala produce a change in the amide III frequency consistent with the experimental results. (5) The experimental frequency shifts cannot be attributed directly to the effects of changing mass.