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Protocol publication

[…] CG water-soluble fibres (1) and (2) with the BTA-C6 oligomers, soluble in organic solvent, we also created an analogous CG model for this system. The CG model for a BTA-C6 fibre was built starting from initially extended CG-fibre (1), cutting the PEG terminal units and leaving two of the four hydrophobic CG beads of the alkyl chains (Supplementary Fig. ). As previously done in the development of the CG models for BTA water-soluble monomers, the ±q charges in the CG amide beads of CG BTA-C6 have been opportunely adjusted to reproduce the correct monomer-monomer dimerization free-energy (). As the organic solvent in this CG model we used octane (C8), which is a well validated standard in the MARTINI environment. All AA and CG simulations and analyses conducted in this work used the GROMACS 5.1.2 software and the PLUMED 2 plugin (see  for details). The equilibrated configurations for the AA and CG-fibre models served as the input for the WT-MetaD study of monomer exchange., Taking our CG model for fibre (1) as a reference, we used this as a toy model to understand the effect of tuning determined interactions between the monomers (i.e., core-core interaction against monomer hydrophobicity) in these supramolecular polymers. In our CG-fibre model, this was done by progressively strengthening/weakening the interaction between the BTA cores (Fig. ) without modifying any other solute-solute or solute-solvent interaction (monomer hydrophobicity is unchanged). To this end, we multiplied per 1.5, 3, or 0.75 t […]

Pipeline specifications

Software tools MARTINI, GROMACS, PLUMED