Polydopamine and eumelanin molecular structures investigated with ab initio calculations
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Buehler_Polydopamine and eumelanin.pdf
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Author(s)
Chen, Chun-Teh
Martinez, Francisco
Jung, Gang Seob
Buehler, Markus J
Date Issued
November 2016
Journal
Chemical Science
Publisher
Royal Society of Chemistry
Citation
Chen, Chun-Teh et al. “Polydopamine and Eumelanin Molecular Structures Investigated with Ab Initio Calculations.” Chem. Sci. 8.2 (2017): 1631–1641. © The Royal Society of Chemistry 2017
Version
Final published version
Abstract
A set of computational methods that contains a brute-force algorithmic generation of chemical isomers, molecular dynamics (MD) simulations, and density functional theory (DFT) calculations is reported and applied to investigate nearly 3000 probable molecular structures of polydopamine (PDA) and eumelanin. All probable early-polymerized 5,6-dihydroxyindole (DHI) oligomers, ranging from dimers to tetramers, have been systematically analyzed to find the most stable geometry connections as well as to propose a set of molecular models that represents the chemically diverse nature of PDA and eumelanin. Our results indicate that more planar oligomers have a tendency to be more stable. This finding is in good agreement with recent experimental observations, which suggested that PDA and eumelanin are composed of nearly planar oligomers that appear to be stacked together via π–π interactions to form graphite-like layered aggregates. We also show that there is a group of tetramers notably more stable than the others, implying that even though there is an inherent chemical diversity in PDA and eumelanin, the molecular structures of the majority of the species are quite repetitive. Our results also suggest that larger oligomers are less likely to form. This observation is also consistent with experimental measurements, supporting the existence of small oligomers instead of large polymers as main components of PDA and eumelanin. In summary, this work brings an insight into the controversial structure of PDA and eumelanin, explaining some of the most important structural features, and providing a set of molecular models for more accurate modeling of eumelanin-like materials.
MIT Department
Massachusetts Institute of Technology. Department of Civil and Environmental Engineering
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DOI of Published Version
https://doi.org/10.1039/c6sc04692d
