Rearrangements that change the connectivity of a carbon skeleton are often useful in synthesis, but it can be difficult to follow their mechanisms. Scanning probe microscopy can be used to manipulate a skeletal rearrangement at the single-molecule level, while monitoring the geometry of reactants, intermediates and final products with atomic resolution. We studied the reductive rearrangement of 1,1-dibromo alkenes to polyynes on a NaCl surface at 5 K, a reaction that resembles the Fritsch-Buttenberg-Wiechell rearrangement. Voltage pulses were used to cleave one C-Br bond, forming a radical, then to cleave the remaining C-Br bond, triggering the rearrangement. These experiments provide structural insight into the bromo-vinyl radical intermediates, showing that the C=C-Br unit is nonlinear. Long polyynes, up to the octayne Ph-(C≡C)-Ph, have been prepared in this way. The control of skeletal rearrangements opens a new window on carbon-rich materials and extends the toolbox for molecular synthesis by atom manipulation.

Extended triisopropylsilyl end-capped polyynes have been prepared from the corresponding tetracobalt complexes by removing the complexed dicobalt tetracarbonyldiphenylphosphinomethane (Co(CO)dppm) moieties. Unmasking of this "masked alkyne equivalent" was achieved under mild conditions with elemental iodine at room temperature, making it possible to obtain fragile polyynes with up to 20 contiguous sp-hybridized carbon atoms. The Co(CO)dppm moiety has a strong geometric and steric effect on the polyyne but does not have a marked electronic effect on the terminal alkyne, as indicated by NMR and IR spectroscopy, density functional theory calculations, and X-ray crystallography. An unusual "alkyne hopping" migration of the dicobalt group was noticed as a minor side reaction during copper-catalyzed Eglinton coupling.

Porphyrin–polyyne [3]- and [5]rotaxanes have been synthesized by condensing aldehyde–rotaxanes with pyrrole or dipyrromethane. The crystal structure of a [3]rotaxane shows that the macrocycles adopt compact conformations, holding the hexaynes near the porphyrin core, and that the phenanthroline units form intermolecular π-stacked dimers in the solid. Fluorescence spectra reveal singlet excited-state energy transfer from the threaded hexayne to the porphyrin, from the phenanthroline to the porphyrin, and from the phenanthroline to the hexayne.

Strapped or “basket-handle” porphyrins have been investigated previously as hemoglobin mimics and catalysts. The facial selectivity of their interactions with axial ligands is a sensitive test for noncovalent bonding. Here the binding of pyridyl ligands to zinc porphyrins with thioester-linked alkyl straps is investigated in solution by NMR spectroscopy and UV–vis titration, and in the solid state by X-ray crystallography. We expected that coordination of the axial ligand would occur on the less hindered face of the porphyrin, away from the strap. Surprisingly, attractive interactions between the strap and the ligand direct axial coordination to the strapped face of the porphyrin, except when the strap is short and tight. The strapped porphyrins were incorporated into π-conjugated cyclic porphyrin hexamers using template-directed synthesis. The strap and the sulfur substituents are located either inside or outside the porphyrin nanoring, depending on the length of the strap. Six-porphyrin nanorings with outwardly pointing sulfur anchors were prepared for exploring quantum interference effects in single-molecule charge transport.