Effects of Local Interactions on the Structural Features of Dipeptides: A Theoretical Study

Structural features of small amino acid sequences are known to determine the dynamic properties and functional specificity of proteins and polypeptides. In this study, the effects of solvation and identity of the varying C-terminal residue on the energetics, structural features of the peptide planes, values of the ψ and ф dihedrals, geometry around the α-carbon atoms and theoretically predicted vibrational spectra of a series of dipeptides are analyzed. The dipeptide geometries, constructed by considering Phe, Trp, Met, Gly, Cys or Tyr as varying C-terminal residue and pyrrolysine as the fixed N-terminal residue, are subjected to full geometry optimization and vibrational frequency calculations at B3LYP/6-31++G(d,p) level in gas and simulated aqueous phase using a polarizable continuum model (PCM). The identity of the varying C-terminal residue influences the values of ф, planarity of the peptide planes and geometry around the C17 α-carbon atoms while the solvation effects are evident on the values of bond lengths and bond angles of the amide planes. The interplay of intramolecular H-bonds influences the planarity of the peptide planes, geometry around the αcarbon atoms and determines the energetics of the dipeptides.