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

Yu, Gary; Walker, Martin; Wilson, Mark R.

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


Gary Yu

Martin Walker


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.

Journal Article Type Article
Acceptance Date Mar 3, 2021
Online Publication Date Mar 5, 2021
Publication Date Mar 21, 2021
Deposit Date Mar 4, 2021
Publicly Available Date Sep 7, 2021
Journal Physical Chemistry Chemical Physics
Print ISSN 1463-9076
Electronic ISSN 1463-9084
Publisher Royal Society of Chemistry
Peer Reviewed Peer Reviewed
Volume 23
Issue 11
Pages 6408-6421
Public URL


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