Peptides and Peptoids - A Systematic Structure Comparison

Abstract

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_7ß, 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.