Peptides and peptoids - A systematic structure comparison

A systematic analysis of the conformational space of the basic structure unit of peptoids in comparison to the corresponding peptide unit was performed based on ab initio MO theory and complemented by molecular mechanics (MM) and molecular dynamics (MD) calculations both in the gas phase and in aqueous solution. The calculations show three minimum conformations denoted as C-7 beta, a(D) and a that do not correspond to conformers on the gas phase peptide potential energy hypersurface. The influence of aqueous solvation was estimated by means of continuum models. The MD simulations indicate the a(D) form as the preferred conformation in solution both in cis and trans peptide bond orientations.