DASTAN, Alireza (2017). Free self-assembly of spontaneously chiral, supramolecular structures. Doctoral, Sheffield Hallam University.
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ADastan_2017_PhD_FreeSelf-Assemblyof.pdf - Accepted Version
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ADastan_2017_PhD_FreeSelf-Assemblyof.pdf - Accepted Version
Available under License Creative Commons Attribution Non-commercial No Derivatives.
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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.
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