Molecular Simulation Studies of Chromonic
Mesogens in Aqueous Solution

Abstract

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.