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Atomistic simulation studies of ionic cyanine dyes: self-assembly and aggregate formation in aqueous solution

Yu, Gary and Walker, Martin and Wilson, Mark R. (2021) 'Atomistic simulation studies of ionic cyanine dyes: self-assembly and aggregate formation in aqueous solution.', Physical chemistry chemical physics., 23 (11). pp. 6408-6421.


Cyanine dyes are known to form large-scale aggregates of various morphologies via spontaneous self-assembly in aqueous solution, akin to chromonic liquid crystals. Atomistic molecular dynamics simulations have been performed on four cyanine dyes: pseudoisocyanine chloride (PIC), pinacyanol chloride (PCYN), 5,5’,6,6’-tetrachloro-1,1’,3,3’- tetraethylbenzimidazolylcarbocyanine chloride (TTBC) and 1,1’-disulfopropyl-3,3’-diethyl-5,5’,6,6’- tetrachloro-benzimidazolylcarbocyanine sodium salt (BIC). Simulations employed an optimised general AMBER force field and demonstrate the organisation of the dyes into stacked structures at dilute concentrations. The thermodynamics of self-assembly was studied by calculating potentials of mean force for n-mers (n = 2, 3 or 4), from which the free energies of association are determined. We report binding free energies in the range of 8 to 15 kBT for dimerisation, concordant with typical values for ionic chromonics (7 to 14 kBT), and examine the enthalpic and entropic contributions to the aggregation process. The self-assembly of these dyes yields two distinct classes of structures. We observe the formation of H-aggregate stacks for PCYN, with further complexity in these assemblies for PIC; where the aggregates contain shift and Y junction defects. TTBC and BIC associate into a J-aggregate sheet structure of unimolecular thickness, and is composed of a brickwork arrangement between molecules. These sheet structures are characteristic of the smectic chromonic mesophase, and such assemblies provide a route to the emergence of nanoscale tubular architectures.

Item Type:Article
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Publisher statement:This article is licensed under a Creative Commons Attribution 3.0 Unported Licence.
Date accepted:03 March 2021
Date deposited:08 March 2021
Date of first online publication:05 March 2021
Date first made open access:07 September 2021

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