Free self-assembly of spontaneously chiral, supramolecular structures

Abstract

In this thesis, Molecular Dynamics simulations are used to investigate the free selfassembly of supramolecular, chiral structures. The main coarse-grained model used for this is the disc-shaped variant of the Gay-Berne potential. This is parameterised to favour face-face configurations, consistent with chromonic molecules which tend to stack due to their π − π interactions. Additionally, assemblies formed by mixtures of these discs and a second species, modelled as Lennard-Jones spheres, are investigated. Here, hot-spot zones on the rims of the discs are used to provide strong interactions with the spheres. Simulations of disc-only systems lead to self-assembly of multi-thread, chiral fibres. Depending on the choice of particle shape and face-face interaction strength, the formed fibres are reproducibly either straight or, for reasons of packing efficiency, spontaneously chiral. As they grow radially, increasing stresses cause chiral fibres to untwist either continuously or via morphological rearrangement. It is also found that, due to the kinetics of fibre initiation, the isotropic solution has to be significantly supercooled before aggregation takes place. As a result, the thermal hysteresis of the formed fibres extends to 10-20% of their formation temperatures. The kinetic barriers to the early stages of growth are investigated by the introduction of a small permanent seed. Depending on the size of the seed, monotonic fibre growth is then observed 5-10% above the normal formation temperatures. On introducing Lennard-Jones spheres and hot-spot zones at the rims of discs, twisted bilayer ribbons, sandwiching a helicoidal sphere layer, are obtained. Systematic investigation of the effects of hot-spot size on the formation and structural properties of these twisted bilayers is then performed. This shows that lateral growth of these bilayers, and the associated increases in bend stresses, lead to the development of defect lines. For relatively small hot-spot sizes, rope structures with five helical threads of discs wrapped around a sphere core self-assemble. Where such ropes aggregate, geometrical frustration leads to multi-rope structures undergoing morphological rearrangement into double-bilayers. Extending the model by giving the discs double hot-spots leads to the formation of a multi-layer twisted bundle with three different directions of growth and three modes of twist. If the sizes of the interacting particles are changed, then, further new arrangements result. For thinner discs, a different class of bilayer is found in which the threads in the two leaflets are mutually orthogonal. This is shown to provide a new pathway for formation of tubes by a rolling-up mechanism involving intermediate saddle bilayer and half-pipe structures. The dimensions of such tubes are found to be very sensitive to the extent of the hot-spot. Double-helix structures, involving two helices of discs wrapped around a central thread of sphere, are the other major class of supramolecular assembly adopted by systems involving thinner discs. Finally, the interaction of self-assembled objects, leading to behaviours such as the formation of multi-bilayer structures, is shown to be accessed on the time- and length-scales of this class of computer simulation.