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

Yana, Janchai and Chiangraeng, Natthiti and Nimmanpipug, Piyarat and Lee, Vannajan Sanghiran (2021) A theoretical study of supramolecular aggregation of polydopamine tetramer subunits in aqueous solution. Journal of Molecular Graphics & Modelling, 107. ISSN 1093-3263, DOI https://doi.org/10.1016/j.jmgm.2021.107946.

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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 pi-pi 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 in both gas phase and aqueous solution pointed out that there are high possibilities of aggregations of the 16 kinds of tetramer subunits although the conformations of each tetramer subunit are not flat. In summary, this work brings an insight into the controversial structure of PDA tetramer units and explains some of the important structural features found in the aqueous phase in comparison to the gas phase.

Item Type: Article
Funders: Chiang Mai Rajabhat University, Program Management Unit for Human Resources & Institutional Development, Research and Innovation, Office of National Higher Education Science Research and Innovation Policy Council (NXPO)[B16F640001], Chiang Mai University[R000026614]
Uncontrolled Keywords: Polydopamine; Aggregation; MD simulation; Binding energy; Kratky plot
Subjects: Q Science > QC Physics
Q Science > QD Chemistry
T Technology > TK Electrical engineering. Electronics Nuclear engineering
Divisions: Faculty of Science
Depositing User: Ms. Juhaida Abd Rahim
Date Deposited: 18 Apr 2022 01:33
Last Modified: 18 Apr 2022 01:33
URI: http://eprints.um.edu.my/id/eprint/26754

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