Molecular Dynamics Study of the Effect of l-Alanine Chiral Dopants on Diluted Chromonic Solutions

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

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 15k_BT for dimerisation, concordant with typical values for ionic chromonics (7 to 14k_BT), 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.

Lyotropic Chromonic Liquid Crystals and Their Impurities Reveal the Importance of the Position of Functional Groups in Self-Assembly

We study the effect of purification and impurities on the self-assembly and phase behavior of lyotropic chromonic liquid crystals (LCLCs). LCLC molecules in water stack to form aggregates; then, the elongated nanoaggregates align to make liquid crystalline phases. Utilizing multiple experimental techniques, we unveil impurities in commercial Sunset Yellow FCF (SSY), a representative LCLC, and how the precipitation-based purification promotes the formation of the aggregates and mesophase. We further explore the roles of intrinsic impurities, i.e., byproducts of the SSY synthesis, whose molecular structures are almost identical to that of SSY but differ only in the number and position of sulfonate groups. Combining quantum chemical calculations of molecular structures and experimental investigation of aggregate structures and phase behavior, we propose that the impurities of the planar shapes behave as planar SSY, i.e., participating in aggregate formation, whereas the nonplanar one disrupts the nematic phase. These results highlight the critical roles of the impurities and deepen our understanding of self-assembled aggregates and their aligned mesophases.