A theoretical study of supramolecular aggregation of polydopamine tetramer subunits in aqueous solution.

Journal of Molecular Graphics & Modelling
Janchai YanaVannajan Sanghiran Lee

Abstract

Conformational search for the most stable geometry connection of 16 sets of polydopamine (PDA) tetramer subunits has been systematically investigated using density functional theory (DFT) calculations. Our results indicated that the more planar subunits are, the more stable they are. This finding is in good agreement with recent experimental observations, which have suggested that PDA are composed of the nearly planar subunits that appear to be stacked together via the π-π interactions to form graphite-like layered aggregates associated with the balance of the intramolecular hydrogen bonds and steric effects from the indole and catechol moieties. Molecular dynamics (MD) simulations of 16 spherical clusters of the tetramer subunits of PDA in the gas and aqueous phase were performed at 298 K and confirmed the stability of supramolecular tetramer aggregates. The complex formation and binding energy of all 16 clusters are very strong although the shapes of the clusters in aqueous solution are not spherical and are very much different from those in the gas phase. The aggregations of all 16 clusters in aqueous solution were also confirmed from the profiles of the Kratky plot and the radius of gyration of all clusters. Our MD results ...Continue Reading

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