We present results on the identification and molecular characterization of conformers with secondary cis amide peptide bonds for a number of oligopeptides containing tyrosine and phenylalanine in aqueous solution. Employing H-1 NMR techniques, peptide bonds adjacent to the aromatic amino acid were found to generate a cis isomer population ranging from 0.1% to 1% in dependence on the chain length and the ionization slate of the peptide. The rate constant of the trans --> cis interconversion for zwitterionic Ala-Tyr was 2.4 x 10(-3) s(-1) at 298 K and thus in a range typical of imidic prolyl peptide bonds. However, the rate constant k(cis)-->(trans)= 0.6 s(-1) of the reverse isomerization revealed a much faster process in Ala-Tyr. Extending the peptide chain in both directions of the Ala-Tyr moiety led to a decrease of both the cis content and the barrier to rotation in the cis --> trans direction. The linear Arrhenius plots gave E-a values of 76.7 +/- 1.5 and 64.6 +/- 1.5 kJ mol(-1) for the dipeptide Ala-Tyr and the corresponding bond in the pentapeptide Ala-Ala-Tyr-Ala-Ala, respectively. Isomerization rates were affected by both the position and the nature of amino acids flanking the isomerizing bond as could be proved by comparison of peptides containing Gly, Tyr, and Phe residues. These studies provide data that permit the extraction of kinetic events originating from the isomerization of "normal" peptide bonds in protein backbone structuring.