Chain conformation in polyretropeptides: Quantum mechanical and empirical force field calculations on 2,6,8-trioxo-3,5,9-triazadecane,a model compound for poly(retro-glycine)

We report here our results on semiempirical AM1 calculations for the conformational preferences of 2,6,8-trioxo-3,5,9-triazadecane, a model compound for polymers made of retropeptide units. We have evaluated the effect of applying symmetry constraints between chemically equivalent torsion angles. These results suggest that preferred conformations around the ? NH? CH₂? NH? group are quite independent from those on the ? CO? CH₂? CO? unit, so all possible combinations generate the complete set of energy minima for the model compound. We have analyzed the implications of the different minimum energy conformation in an infinite chain model and we have explored the conformational space of regular polyretropeptides. This shows a close relation to that of regular polypeptides but with significant differences arising from the change of orientation of the peptide units along the polymer molecule. The energy calculations also support previously proposed models for the crystal structure of the simplest polyretropeptide, poly(retro-glycine). Finally, we discuss the consequences of retropeptide-peptide copolymerization as well as the expected conformations for regular alternate terpolymers. © 1995 John Wiley & Sons, Inc.