In proteins, the peptide bond is known to prefer dominantly the trans conformation. The analyses of X-ray protein structures showed that the cis populations are ～0.04% for the nonprolyl peptide bond and ～6% for the prolyl peptide bond . It has been reported that the cis-trans isomerization of the X-Pro bond is often involved in the rate-determining steps for folding and refolding of various proteins . Although nonprolyl cis peptide bonds are rare in proteins, they often occur in regions near the active sites of proteins, and contribute to regulate the biochemical properties and binding modes . There are only a limited number of works reported on the kinetics and thermodynamics of the nonprolyl cis-trans isomerization for peptides. The conformational study on the alanine and proline dipeptides is carried out to explore the differences in the backbone conformational preference and the cis-trans isomerization for the nonprolyl and prolyl residues. All ab initio HF and density functional B3LYP calculations were carried out using the Gaussian 03 package . The computational methods are described elsewhere in detail.
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