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

Area of Science:

• Physical Chemistry
• Materials Science
• Supramolecular Chemistry

Background:

• Cyanine dyes self-assemble in aqueous solutions, forming structures analogous to chromonic liquid crystals.
• Understanding the morphology and thermodynamics of these aggregates is crucial for materials science applications.

Purpose of the Study:

• To investigate the self-assembly of four cyanine dyes using atomistic molecular dynamics simulations.
• To determine the thermodynamic driving forces and structural characteristics of cyanine dye aggregation.

Main Methods:

• Atomistic molecular dynamics simulations with an optimized general AMBER force field.
• Calculation of potentials of mean force to determine free energies of association for n-mers.
• Analysis of aggregate morphology, including H-aggregates and J-aggregate sheets.

Main Results:

• Simulations revealed the organization of cyanine dyes into stacked structures at dilute concentrations.
• Binding free energies for dimerisation ranged from 8 to 15 k_BT, consistent with ionic chromonics.
• Two distinct aggregate structures were observed: H-aggregates (PIC, PCYN) and J-aggregate sheets (TTBC, BIC).

Conclusions:

• The self-assembly of cyanine dyes leads to diverse structures, including H-aggregates with defects and unimolecular J-aggregate sheets.
• J-aggregate sheets exhibit a brickwork arrangement and are characteristic of the smectic chromonic mesophase.
• These self-assembled structures offer a pathway for the formation of nanoscale tubular architectures.