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Updated: Jun 25, 2026

Stable DNA Motifs, 1D and 2D Nanostructures Constructed from Small Circular DNA Molecules
Published on: April 12, 2019
Two-dimensional oligo(phenylene-ethynylene-butadiynylene)s: all-covalent nanoscale spoked wheels
Shengbin Lei1, An Ver Heyen, Steven De Feyter
1Department of Chemistry, Laboratory of Photochemistry and Spectroscopy, and Institute for Nanoscale Physics and Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200-F, 3001 Leuven, Belgium.
Abstract:
Round and round: Covalently bound spokes induce an efficient template-directed cyclization towards a rigid molecular wheel (see figure) and afford dramatically increased shape-persistence properties compared with non-strutted macrocycles.The synthesis and characterization of a shape-persistent two-dimensional (2D) organic compound is described in detail. In a rational modular synthesis of a dodecaacetylene precursor and its subsequent template-aided cyclization, we obtained a molecularly defined, stable, C(6)-symmetric, rigid, spoked wheel. Peripheral tert-butyl groups and alkyl chains attached to the plane of the molecule provide sufficient solubility, so that the 2D oligomer can be fully characterized by MALDI-MS, GPC, and (1)H NMR, UV/Vis absorption, and fluorescence spectroscopy. Molecular mechanics and dynamics simulations indicate that the most stable conformer of the molecule in vacuum is a shallow boat conformation with a small dihedral angle. Comparisons with the precursor as well as a ring-only structure clearly reveal the high rigidity of the title compound. Small-angle neutron scattering (SANS) experiments in [D(8)]THF and CDCl(3) affirm the rigid backbone structure in solution, that is, a radius of about 2.7 nm and a thickness of about 0.22 nm. STM investigations illustrate that the wheel molecules adsorb with their molecular plane parallel to the surface and can form hexagonal crystalline domains (unit cell parameters are a=b=6.0+/-0.2 nm and theta=60+/-2 degrees ), with the tert-butyl groups on the apexes staggered. Such staggering induces chirality in the organized domains. AFM investigations demonstrate that the wheel molecules inside overlayers organize in the same way as in the layer directly in contact with the surface. This indicates an epitaxial growth characteristic of the film.
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