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Molecular simulation studies of self-assembly for a chromonic perylene dye: all-atom studies and new approaches to coarse-graining

Gary, Yu; Wilson, Mark Richard

Molecular simulation studies of self-assembly for a chromonic perylene dye: all-atom studies and new approaches to coarse-graining Thumbnail


Yu Gary


Perylene tetracarboxylic acid bisimides are compounds that show intense visible light absorption and exhibit excellent chemical, photochemical and thermal stability. As such, they have been widely used as dyes and have a range of industrial applications. These dyes have also been investigated for various applications in aqueous media as chromonic liquid crystals: lyotropic systems characterised by the association of aromatic mesogenic cores into stacked structures. In this study, we focus on one perylene dye bis-(N,N-diethylaminoethyl) perylene-3,4,9,10-tetracarboxylic diimide dihydrochloride, PER, and study its self-assembly in aqueous solution through both atomistic and coarse-grained molecular models. All-atom molecular dynamics simulations demonstrate spontaneous self-assembly into chromonic H-aggregate stacks with an interparticle twist between molecules. The coarse-graining of complex chromonic mesogens introduces a wealth of subtle complexities that presents a significant challenge to overcome. Consequently, we developed coarse-grained (CG) models using both bottom-up and top-down approaches: the multiscale coarse-graining method (MS-CG) in the form of hybrid force matching (FM) and the MARTINI 3 force field, respectively. We discuss the successes/deficiencies of these approaches and introduce changes to improve upon their performance and representability. For the MARTINI 3 model, careful optimisation of parameters allows it to exactly reproduce the atomistic self-assembly behaviour including the relevant thermodynamic properties in solution. The bottom-up CG model, produced using a conventional MS-CG treatment, fails to reproduce most of the target properties, but the implementation of the potentials into a combined FM-MARTINI 3 framework allows the recovery of the correct self-assembly behaviour in solution.

Journal Article Type Article
Acceptance Date Nov 23, 2021
Online Publication Date Nov 27, 2021
Publication Date Jan 1, 2022
Deposit Date Aug 10, 2021
Publicly Available Date Jan 7, 2022
Journal Journal of Molecular Liquids
Print ISSN 0167-7322
Publisher Elsevier
Peer Reviewed Peer Reviewed
Volume 345
Article Number 118210
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Copyright Statement
This is an open access article distributed under the terms of the Creative Commons CC-BY license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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