Undergrad_Book_16-18_Pge_View_Print_no print marks_compressed

Selected Projects 2016-18
Computing Center (MGHPCC), a statewide computing
cluster with high computing capabilities.
The basic theorized mechanism of nanotube
self-assembly is that monomers form small aggregates,
which then form rings, which stack to form
tubes. So far, I have used a bottom-up approach to
model these initial steps of nanotube self-assembly
to provide a fundamental molecular understanding
of the process. Progress so far can be broken down
into three basic stages: a study of each of the four
dipeptides, a study of their dimers, and a study of
their hexamers (Figure 1).
In the first stage of the study, conformer analyses of
the four dipeptides were performed using the MMFF
implemented in Spartan14 software to determine all
energetically and geometrically possible configurations
of the dipeptides. More accurate calculations
were then carried out with density functional theory,
specifically DFT-M05/6-31G*, on a few lowest
stable conformers using GAMESS (General Atomic
Molecular and Electronic Structure) to determine
more accurately the lowest-energy conformer of
each dipeptide, representing their most stable
forms (Figure 2). Structural analysis revealed that
the most stable conformers of the linear YY and WY
dipeptides both featured intramolecular hydrogen
bonding within their backbones. The most stable
conformers of the cyclic YY and WY dipeptides
both feature slightly puckered boat structures in
their diketone-backbone rings. The orbital analysis
suggested that π-π stacking, XH-π interactions, and
charge-transfer interactions likely participate in
the aggregation and self-assembly of these dipeptides.
These findings have recently been published
in Computational and Theoretical Chemistry (DOI:
10.1016/j.comptc.2018.03.031).
In the second stage of the study, dimers of each of
the four dipeptides were studied, using the density
functional tight binding (DFTB) method. The lowest
energy conformers from stage one were dimerized
in three orientations: “side by side,” parallel, and
perpendicular “T.” Analysis of structural and spectroscopic
properties showed that the side-by-side
and parallel orientation were found to be the most
favorable for linear and cyclic dipeptides, respectively.
This suggests that linear dipeptides mainly
Figure 2. The optimized structures of the lowest-energy
conformers of each of the dipeptides studied
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