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Updated: Jul 11, 2025
10:37
Spatial Separation of Molecular Conformers and Clusters
Published on: January 9, 2014
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Using Enhanced Sampling Simulations to Study the Conformational Space of Chiral Aromatic Peptoid Monomers
Rakshit Kumar Jain1, Carol K Hall1, Erik E Santiso1
1Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27606, United States.
Journal of Chemical Theory and Computation
|November 8, 2023
Summary
This study enhances the CGenFF-NTOID forcefield for peptoids (N-substituted glycines) by adding new parameters. Optimized simulations accurately model peptoid cis-trans isomerism, aiding computational material design.
Area of Science:
- Computational chemistry
- Materials science
- Biomolecular modeling
Background:
- Peptoids (N-substituted glycines) exhibit complex conformational landscapes due to cis-trans isomerism.
- Conventional molecular dynamics struggles to fully sample peptoid energy landscapes.
- Accurate force fields are crucial for simulating peptoid behavior.
Purpose of the Study:
- To extend the CGenFF-NTOID peptoid forcefield with parameters for four additional side chains.
- To accurately model the cis-trans isomerism of specific peptoid monomers (s1pe and s1ne).
- To advance the computational design of novel peptoid-based materials.
Main Methods:
- Developed an extended CGenFF-NTOID peptoid forcefield.
- Employed explicit solvent well-tempered metadynamics for parameter optimization.
- Utilized parallel bias metadynamics to study cis-trans isomerism.
- Validated simulation results with experimental data and ab initio calculations.
Main Results:
- Successfully parameterized four new side chains for the CGenFF-NTOID forcefield.
- Accurately modeled the cis-trans isomerism of S1-phenylethyl (s1pe) and S1-naphthylethyl (s1ne) peptoid monomers.
- Generated free energy minima consistent with experimental data where available.
- Provided reliable simulation data for cases lacking experimental validation.
Conclusions:
- The extended CGenFF-NTOID forcefield improves the simulation of peptoid conformational dynamics.
- This work facilitates more accurate computational studies of peptoid materials.
- Represents a significant advancement towards the rational design of peptoid-based functional materials.
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