Peptoids are structural isomers of natural peptides,
with side
chain attachment at the amide nitrogen, conferring this class of compounds
with the ability to access both
cis
and
trans
ω torsions as well as an increased diversity of ψ/φ
states with respect to peptides. Sampling within these dimensions
is controlled through side chain selection, and an expansive set of
viable peptoid residues exists. It has been shown recently that “minimal”
di- and tripeptoids with aromatic side chains can self-assemble into
highly ordered structures, with size and morphological definition
varying as a function of sequence pattern (e.g., XFF and FXF, where
X = a nonaromatic peptoid monomer). Aromatic groups, such as phenylalanine,
are regularly used in the design of minimal peptide assemblers. In
recognition of this, and to draw parallels between these compounds
classes, we have developed a series of descriptors for intramolecular
dynamics of aromatic side chains to discern whether these dynamics,
in a preassembly condition,
can be related to experimentally observed nanoscale assemblies. To
do this, we have built on the atomistic peptoid force field reported
by Weiser and Santiso (CGenFF-WS) through the rigorous fitting of
partial charges and the collation of Charmm General Force Field (CGenFF)
parameters relevant to these systems. Our study finds that the intramolecular
dynamics of side chains, for a given sequence, is dependent on the
specific combination of backbone ω torsions and that homogeneity
of sampling across these states correlates well with the experimentally
observed ability to assemble into nanomorphologies with long-range
order. Sequence patterning is also shown to affect sampling, in a
manner consistent for both tripeptoids and tripeptides. Additionally,
sampling similarities between the nanofiber forming tripeptoid, Nf-Nke-Nf
in the
cc
state, and the nanotube forming dipeptide
FF, highlight a structural motif which may be relevant to the emergence
of extended linear assemblies. To assess these properties, a variety
of computational approaches have been employed.