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Selected Projects 2016-18
were arranged into six-membered hexamers. The
binding energies were found to be moderately large,
suggesting that the dipeptides have high affinity
for each other in this hexamer arrangement. The
binding energies of linear WY and cyclic WY, were almost
identical, suggesting that both forms of WY are
equally likely to self-assemble. However, the binding
energy of cyclic YY was almost twice as much as the
binding energy of linear YY, suggesting that the cyclic
form of YY will self-assemble much more readily. In
fact, the cyclic YY hexamer was found to have the
largest binding energy of all the dipeptides studied,
suggesting it is the most likely to form nanotubes.
The calculated inner and outer diameters of each
hexamer were compared against experimental data
for the highly studied diphenylalanine nanotube,
revealing that these four nanotubes will be slightly
larger, due to large side chains and higher polarity.
An interaction energy decomposition was also
carried out on the hexamers at HF/6-31G* and
shows that the same forces that drive the interaction
between the dimers are at play on a larger scale
also, and therefore likely drive the self-assembling
of the whole nanotube as well.
This project can take several directions from here.
One next step could be to use molecular dynamics
simulations to study the self-assembly of
dipeptides by simulating their behavior over time.
Another next step could be to apply the techniques
used thus far to tripeptides and tetrapeptides to
learn about their fundamental properties, as these
oligopeptides are also commonly used as building
blocks for peptide nanostructures.
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