A molecular dynamics simulation of N-(fluorenyl-9-methoxycarbonyl)-dipeptides supramolecular hydrogel

Fmoc protected D-Ala-D-Ala dipeptides were known to self-assemble into supramolecular hydrogel with interesting properties. However their molecular mechanisms were not well understood. In this study, a series of coarse grained molecular dynamics simulation were conducted to investigate the formation of this hydrogel at different concentrations. The three dimensional network of hydrogel and the stacking of the Fmoc planes were observed intuitively from the snapshots of the trajectory. Importantly, by analyzing the RDF of Fmoc planes’ centriods and the distribution of neighboring Fmocs, we confirmed the π–π interaction as the mainly driving force for the gelation process.

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► Simulation of gelation was expanded to large scale and long time by using CG-MD.
► We got the gel’s configuration on molecular level (π stacking, entanglement).
► We confirmed the π–π stacking as the mainly gelation driven force.