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Structural Characterization of Supramolecular Hollow Nanotubes with Atomistic Simulations and SAXS
Preprints are manuscripts made publicly available before they have been submitted for formal peer review and publication. They might contain new research findings or data. Preprints can be a draft or final version of an author's research but must not have been accepted for publication at the time of submission.
submitted on 27.08.2020 and posted on 27.08.2020by Ilias Patmanidis, Alex H. de Vries, Tsjerk A. Wassenaar, Wenjun Wang, Giuseppe Portale, Siewert-Jan Marrink
Self-assembled nanostructures arise when building blocks spontaneously organize into ordered aggregates that exhibit different properties compared to the disorganized monomers.
Here, we study an amphiphilic cyanine dye (C8S3) that is known to self-assemble into doublewalled, hollow, nanotubes with interesting optical properties. The molecular packing of the
dyes inside the nanotubes, however, remains elusive. To reveal the structural features of
the C8S3 nanotubes, we performed atomistic Molecular Dynamics simulations of preformed
bilayers and nanotubes. We find that different packing arrangements lead to stable structures, in which the tails of the C8S3 molecules are interdigitated. Our results are verified
by SAXS experiments. Together our data provide a detailed structural characterization of
the C8S3 nanotubes. Furthermore, our approach was able to resolve the ambiguity inherent from cryo-TEM measurements in calculating the wall thickness of similar systems. The
insights obtained are expected to be generally useful for understanding and designing other