Molecular Simulation Studies of Chromonic Mesogens in Aqueous Solution

This thesis focuses on understanding the aggregation behaviour of lyotropic chromonic liquid crystals in aqueous solution. Molecular simulation methods are used to provide structural and thermodynamic information on the self-assembly of chromonic mesogens, and the results used to re-interpret data from previous experimental studies of these systems. Extensive atomistic level molecular dynamic simulations have been performed on three chromonic dyes in solution: 5,5'-dimethyoxy-bis-(3,3'-di-sulphopropyl)- thiacyanine triethylammonium salt (Dye A), 5,5'-dichloro-bis-(3,3'-di-sulphopropyl)- thiacyanine triethylammonium salt (Dye B), and Bordeaux dye. The results are compared to key experimental data, such as X-ray scattering and cross-sectional areas and aggregation free energies. Previously suggested chromonic aggregation models, such as a double-width column and a brickwork layer structure, have been discounted based on the simulation results. Instead the simulations of dyes A and B demonstrate an anti-parallel stacking arrangement providing columns in which solubilizing sulphonate groups lie on alternate sides of the column as the column is traversed. In addition, a new type of chromonic smectic layered phase is predicted for these molecules. For dye A, a novel chiral column structure is seen within isolated columns in isotropic solution. For Bordeaux dye a stable single-molecule column is seen, along with a number of meta-stable structures including a double-width column in which two single-molecule columns are linked via a salt bridge. In an attempt to simulate larger time and length scales, two bottom-up coarsegraining techniques, iterative Boltzmann inversion (IBI) and force matching (FM), were tested on simple hexane/water systems and then applied to Dye A. Both of these methods proved to be largely unsuccessful in reproducing the same aggregation behaviour seen in the atomistic simulation work.