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

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

Abstract

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.

Citation

Yu, G., Walker, M., & Wilson, M. R. (2021). Atomistic simulation studies of ionic cyanine dyes: self-assembly and aggregate formation in aqueous solution. Physical Chemistry Chemical Physics, 23(11), 6408-6421. https://doi.org/10.1039/d0cp06205g

• 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
• DOI: https://doi.org/10.1039/d0cp06205g
• Public URL: https://durham-repository.worktribe.com/output/1245855