Abstract

Conformations of achiral and chiral aromatic homo-polypeptoids of Nphe, Nspe and Nrpe were studied by quantum mechanics and molecular dynamics approaches. The amide bond geometry in model peptoids Ac-X-NMe2 could be both cis and trans and the Nphe peptoids adopted degenerate conformations of opposite handedness with Φ, Ψ values of ~ ± 120º, ± 150º with trans amide bond geometry. This degeneracy was lifted with increase in chain length; in favor of the structure with Φ = -120º, Ψ = -150º. Polypeptoids of Nspe and Nrpe with and without protecting groups populated states with Φ, Ψ values of ~ 110º, 155º & -110º, -165º respectively with trans amide bond geometry. Simulation studies in water revealed that with protecting groups peptoid Ac-(Nspe/Nrpe)5-NMe2 populated with cis amide bond geometry in PP type I and inverse PP type I helices respectively due to interactions between the solvent molecules and carbonyl oxygens of the backbone. Without protecting groups these polypeptoids populated poly-L-proline type II conformations. In DMSO these peptoids were shown to populate in PP type-I and inverse PP type-I helices and without protecting groups they could be realized in PP type-I as well as inverse PP type-I conformation whereas the peptoid -Nrpe6-NH2 could be realized in inverse PP type-I conformation. Analysis of simulation results as a function of time ruled out amide bond inter-conversions between cis and trans geometry. Hence, like polyproline peptoids can also be exploited as molecular spacers.

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