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

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

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...

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Main Authors:	Yana, Janchai, Chiangraeng, Natthiti, Nimmanpipug, Piyarat, Lee, Vannajan Sanghiran
Format:	Article
Published:	Elsevier Sceince Inc 2021
Subjects:	QC Physics QD Chemistry TK Electrical engineering. Electronics Nuclear engineering
Online Access:	http://eprints.um.edu.my/26754/
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spelling	my.um.eprints.267542022-04-18T01:33:28Z http://eprints.um.edu.my/26754/ A theoretical study of supramolecular aggregation of polydopamine tetramer subunits in aqueous solution Yana, Janchai Chiangraeng, Natthiti Nimmanpipug, Piyarat Lee, Vannajan Sanghiran QC Physics QD Chemistry TK Electrical engineering. Electronics Nuclear engineering 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. Elsevier Sceince Inc 2021-09 Article PeerReviewed 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 <https://doi.org/10.1016/j.jmgm.2021.107946>. 10.1016/j.jmgm.2021.107946
institution	Universiti Malaya
building	UM Library
collection	Institutional Repository
continent	Asia
country	Malaysia
content_provider	Universiti Malaya
content_source	UM Research Repository
url_provider	http://eprints.um.edu.my/
topic	QC Physics QD Chemistry TK Electrical engineering. Electronics Nuclear engineering
spellingShingle	QC Physics QD Chemistry TK Electrical engineering. Electronics Nuclear engineering Yana, Janchai Chiangraeng, Natthiti Nimmanpipug, Piyarat Lee, Vannajan Sanghiran A theoretical study of supramolecular aggregation of polydopamine tetramer subunits in aqueous solution
description	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.
format	Article
author	Yana, Janchai Chiangraeng, Natthiti Nimmanpipug, Piyarat Lee, Vannajan Sanghiran
author_facet	Yana, Janchai Chiangraeng, Natthiti Nimmanpipug, Piyarat Lee, Vannajan Sanghiran
author_sort	Yana, Janchai
title	A theoretical study of supramolecular aggregation of polydopamine tetramer subunits in aqueous solution
title_short	A theoretical study of supramolecular aggregation of polydopamine tetramer subunits in aqueous solution
title_full	A theoretical study of supramolecular aggregation of polydopamine tetramer subunits in aqueous solution
title_fullStr	A theoretical study of supramolecular aggregation of polydopamine tetramer subunits in aqueous solution
title_full_unstemmed	A theoretical study of supramolecular aggregation of polydopamine tetramer subunits in aqueous solution
title_sort	theoretical study of supramolecular aggregation of polydopamine tetramer subunits in aqueous solution
publisher	Elsevier Sceince Inc
publishDate	2021
url	http://eprints.um.edu.my/26754/
_version_	1735409453672431616
score	13.211869

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

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