Exploring the Conformation of Mixed Cis- Trans α,β-Oligopeptoids: A Joint Experimental and Computational Study

The synthesis and conformational preferences of a set of new synthetic foldamers that combine both the α,β-peptoid backbone and side chains that alternately promote cis- and trans-amide bond geometries have been achieved and addressed jointly by experiment and molecular modeling. Four sequence patterns were thus designed and referred to as cis-β-trans-α, cis-α-trans-β, trans-β-cis-α, and trans-α-cis-β. α- and βNtBu monomers were used to enforce cis-amide bond geometries and α- and βNPh monomers to promote trans-amides. NOESY and molecular modeling reveal that the trans-α-cis-β and cis-β-trans-α tetramers show a similar pattern of intramolecular weak interactions. The same holds for the cis-α-trans-β and trans-β-cis-α tetramers, but the interactions are different in nature than those identified in the trans-α-cis-β-based oligomers. Interestingly, the trans-α-cis-β peptoid architecture allows establishment of a larger amount of structure-stabilizing intramolecular interactions.