MARTINI-Compatible Coarse-Grained Model for the Mesoscale Simulation of Peptoids

Area of Science:

• Polymer Chemistry
• Computational Chemistry
• Materials Science

Background:

• Peptoids are synthetic polymers, regioisomers of peptides, with diverse applications.
• Computational modeling aids in understanding and designing peptoid-based nanomaterials.
• Accurate force fields are crucial for simulating peptoid behavior at larger scales.

Purpose of the Study:

• To parameterize coarse-grained peptoid force fields using the MARTINI framework.
• To enable efficient and accurate simulations of peptoid nanomaterials.
• To facilitate the design and understanding of novel peptoid-based materials.

Main Methods:

• Bottom-up parameterization of coarse-grained force fields against all-atom simulation data.
• Iterative Boltzmann inversion for bonded interactions and potential of mean force matching for nonbonded interactions.
• Parallel bias metadynamics to ensure sampling of amide bond isomerizations.

Main Results:

• Developed coarse-grained models for polysarcosine and poly(N-((4-bromophenyl)ethyl)glycine).
• Achieved excellent agreement between coarse-grained and all-atom simulation results.
• Demonstrated up to 25-fold efficiency increase with coarse-grained models, compatible with MARTINI force fields.

Conclusions:

• Established a rigorously parameterized coarse-grained peptoid force field.
• Enabled simulations of peptoid nanomaterials at previously inaccessible length and time scales.
• Provided a valuable tool for the future design and understanding of peptoid-based materials.