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Issue 36, 2018
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Towards a coarse-grained model of the peptoid backbone: the case of N,N-dimethylacetamide

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Abstract

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.

Graphical abstract: Towards a coarse-grained model of the peptoid backbone: the case of N,N-dimethylacetamide

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Publication details

The article was received on 23 May 2018, accepted on 25 Aug 2018 and first published on 27 Aug 2018


Article type: Paper
DOI: 10.1039/C8CP03283A
Citation: Phys. Chem. Chem. Phys., 2018,20, 23386-23396
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    Towards a coarse-grained model of the peptoid backbone: the case of N,N-dimethylacetamide

    P. Du, S. W. Rick and R. Kumar, Phys. Chem. Chem. Phys., 2018, 20, 23386
    DOI: 10.1039/C8CP03283A

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