Structural and dynamical characteristics of peptoid oligomers with achiral aliphatic side chains studied by molecular dynamics simulation.

All-atom molecular dynamics simulations of N-substituted glycine peptoid oligomers with methyl and methoxyethyl side chains have been carried out for chain lengths of 5, 10, 20, and 50 residues in aqueous phase at room temperature. The (ϕ, ψ) backbone dihedral angle distributions in the Ramachandran plots show that helical structures, similar to polyproline type I and type II helices, are the most favorable conformations in most peptoid oligomers studied. The left-handed helical structures are shown to be increasingly favored as the oligomer chain length grows. A significant population of cis amide bond configurations has been identified in the peptoid oligomers. By combining the analysis of ϕ and ω backbone dihedral angles, we determined the relative composition of the four major conformations favored by the backbone dihedral angles. The trans α(D) conformation is found to be most favored for all peptoid oligomers studies. The time correlation functions of the end-to-end distance highlight a rigid backbone structure relative to side chains for peptoid oligomers. The transition between right-handed and left-handed helical conformations is found to be very rare and between cis and trans isomerism in the amide bond completely absent in the simulation time scale. The radii of gyration for all peptoid oligomers have been found to be consistently larger in comparison to the peptide counterparts, suggesting slightly open structures for peptoids relative to peptides, whereas the fluctuations in the radius of gyration support a rigid backbone structure of peptoids.