Conformations of Thioamide-Containing Dipeptides: A Computational Study

Four model dipeptides, Ac-ψ[CSNH]-Gly-NHMe, Ac-Gly-ψ[CSNH]-NHMe, Ac-ψ[CSNH]-Ala-NHMe, and Ac-Ala-ψ[CSNH]-NHMe, each containing a thioamide bond, were studied by high-level ab initio calculations. For each model compound, a conformational potential energy surface was generated by constrained optimization at the HF/6-31G*//HF/6-31G* level of 144 starting geometries, resulting from the systematic variation of the two flexible backbone torsions φ and ψ. Selected regions of each potential energy surface were used as starting points for full geometry optimization at the HF/6-31G*//HF/6-31G* and MP2/6-31G*//MP2/6-31G* levels. The structures and energies of the resulting minima were used to examine the conformational behavior of the model compounds. Whereas the conformations of the C-terminal thioamides were generally close to those of the corresponding peptides, the N-terminal thioamides displayed markedly different conformational behavior. The changes in the conformational profile of thioamide-containing peptides appear to result from a combination of the decreased hydrogen bonding-accepting ability and increased size of sulfur versus oxygen and lengthening of the C S bond in the thioamide as compared to the C O bond in an amide. Insertion of a thioamide linkage into a peptide structure is thus not conformationally neutral and can produce substantial changes in peptide structure, primarily in the residues on the C-terminal side of the thioamide. In addition to the effects on the proteolysis of peptides, the results indicate that this substitution may demonstrate utility as a probe of local peptide secondary structure.