Martinoid: the peptoid martini force field.
Hamish W A Swanson1, Alexander van Teijlingen1, King Hang Aaron Lau1
1Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, UK. aaron.lau@strath.ac.uk.
Physical Chemistry Chemical Physics : PCCP
|January 26, 2024
Summary
Researchers developed a new Martini forcefield model for peptoid simulations. This model accurately predicts peptoid assembly and secondary structures, enabling efficient discovery of novel peptoid materials.
Area of Science:
- Materials Science
- Computational Chemistry
- Biophysics
Background:
- Peptoid assembly is crucial for developing novel materials.
- Existing coarse-grained models for peptoids are limited.
- Minimal peptoid assemblers are feasible and expected.
Purpose of the Study:
- Develop a Martini forcefield compatible peptoid model.
- Enable accurate simulation of peptoid assembly and structure.
- Facilitate the discovery of minimal peptoid assemblers.
Main Methods:
- Dual bottom-up and top-down parameterization approach.
- Targeted reproduction of atomistic molecular dynamics (MD) dynamics.
- Validation against experimental log D7.4 partition coefficients and assembly systems.
Main Results:
- Developed a novel Martini forcefield model for peptoids.
- Successfully reproduced experimental peptoid nanosheet and tripeptoid assembly.
- Demonstrated simulation of peptoid helix secondary structure for antimicrobial sequences.
- Provided freely available code for Gromacs MD software.
Conclusions:
- The new model accurately simulates peptoid behavior.
- Facilitates in silico screening for minimal peptoid assemblers.
- Accelerates the design and discovery of functional peptoid materials.
Related Concept Videos
01:20¹³C NMR: Distortionless Enhancement by Polarization Transfer (DEPT)
1.1K
When proton-coupled carbon-13 spectra are simplified by a broadband proton decoupling technique, structural information about the coupled protons is lost. Distortionless enhancement by polarization transfer (DEPT) is a technique that provides information on the number of hydrogens attached to each carbon in a molecule. While the DEPT experiment utilizes complex pulse sequences, the pulse delay and flip angle are specifically manipulated. The resulting signals have different phases depending on...
1.1K
02:28Intermolecular Forces in Solutions
33.7K
The formation of a solution is an example of a spontaneous process, a process that occurs under specified conditions without energy from some external source.
When the strengths of the intermolecular forces of attraction between solute and solvent species in a solution are no different than those present in the separated components, the solution is formed with no accompanying energy change. Such a solution is called an ideal solution. A mixture of ideal gases (or gases such as helium and argon,...
When the strengths of the intermolecular forces of attraction between solute and solvent species in a solution are no different than those present in the separated components, the solution is formed with no accompanying energy change. Such a solution is called an ideal solution. A mixture of ideal gases (or gases such as helium and argon,...
33.7K
03:37Molecular Shape and Polarity
60.5K
Dipole Moment of a Molecule
60.5K
01:27π Electron Effects on Chemical Shift: Overview
1.1K
An applied magnetic field causes loosely bound π-electrons in organic molecules to circulate, producing a local or induced diamagnetic field over a large spatial volume. As the molecules tumble in solution, the field generated by π-electrons in spherical substituents results in a zero net field. However, the net field generated by π-electrons in non-spherical substituents is not zero. The effect of this induced field depends on the orientation of the molecule with respect to B0,...
1.1K