Towards a coarse-grained model of the peptoid backbone: The case of N, N -dimethylacetamide
© 2018 the Owner Societies. In this study, a coarse-grained (CG) model for N,N-dimethylacetamide (DMA), which represents the polypeptoid backbone, is developed as a step towards establishing a CG model of the complex polypeptoid system. Polypeptoids or poly N-substituted glycines are a type of peptidomimetic polymers that are highly tunable, and hence an ideal model system to study self-assembly as a function of chemical groups in aqueous soft matter systems. The DMA CG model is parameterized to reproduce the structural properties of DMA liquid as well as a dilute aqueous solution of DMA using a reference all atom model, namely the OPLS-AA force-field. The intermolecular forces are represented by the Stillinger-Weber potential, that consists of both two- and three-body terms that are very short-ranged. The model is validated on thermodynamic properties of liquid and aqueous DMA, as well as the vapor-liquid interface of liquid DMA and the structure of a concentrated aqueous solution of DMA in water as well as a simple peptoid in water. Without long-ranged interactions and the absence of interaction sites on hydrogen atoms, the CG DMA model is an order of magnitude faster than the higher resolution all-atom (AA) model.
Publication Source (Journal or Book title)
Physical Chemistry Chemical Physics
Du, P., Rick, S., & Kumar, R. (2018). Towards a coarse-grained model of the peptoid backbone: The case of N, N -dimethylacetamide. Physical Chemistry Chemical Physics, 20 (36), 23386-23396. https://doi.org/10.1039/c8cp03283a