Ab initiostudies of structural features not easily amenable to experiment. 23. Molecular structures and conformational analysis of the dipeptideN-acetyl-N′-methyl glycyl amide and the significance of local geometries for peptide structures

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Abstract
The molecular structures of four conformations of N-acetyl–N′-methyl glycyl amide were refined by geometrically unconstrained ab initio gradient relaxation on the 4–21G level. The most stable form I contains a seven-membered ring closed by hydrogen bonding. A second local minimum II is less than 1 kcal/mol above I and represents the fully extended form with a five-membered hydrogen bonded ring. The two other minima refined, III and IV, are open forms which are 4–5 kcal/mol less stable than I. The refined geometries make it possible to estimate the significance of local geometries, in contrast to standard geometry, in the various conformations. It is found that bond distances in different conformations can vary by up to 0.02 Å, and important backbone bond angles can vary by up to 7°. Except for the symmetrical form II, small deviations from amide planarity (H–N–C = 0 angles of 3–10°) are the rule, even though the equilibrium structure of the unperturbed amide group in 4–21G space is planar. It can be concluded that local geometry relaxations at different points of the potential energy surface of a peptide system can amount to several Kcal/mol per residue and should be an important aspect of protein conformational analysis.