Peptide-inspired N-substituted glycine oligomers have been used as biomarkers for a number of biological applications (e.g., antibody specific detection probes, pharmacological profiling, etc). These synthetic biomimetics in which their sidechains are attached to the backbone nitrogen atoms, rather than α-carbons, have been named peptoids. This difference confers upon peptoids structural properties very different to peptides. For instance, peptoids lack the inter- and intrachain hydrogen bonding in the backbone, which also eliminates the main-chain chirality and results in a polymer family whose properties are dominated by the side-chain identity and monomer sequence. It also results in proteolysis resistance, inexpensive synthesis, good solubility in many common solvents, accessible thermal processability and overall increased flexibility. The latter is due stereoelectronic effects that allow isomerism over the amide bond. In contrast to peptides, both cis and trans amide configurations can be significantly populated at room temperature. Previous force fields have been developed for the simulation of peptoids, but enhanced sampling techniques are often needed to achieve amide isomerism. In this work, we have empirically developed new torsional potentials and van der Waals parameters, within the GROMOS force field scope, that allow the appropriate description of relative cis/trans configurations in peptoids at room temperature. This work has been supported by CNPq, CAPES, FACEPE and NIH. Partial computational resources were provided by the Swiss National Supercomputing Centre (CSCS).

On the cis/trans isomerization of amide bonds for classical simulation of peptoids

251st National Meeting (2016)

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