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A 2024 study showed that chemists can remove a nitrogen atom from the axle of a crown ether rotaxane and join the remaining axle fragments with a carbon–carbon bond, while keeping the ring mechanically interlocked. The reported products were isolated in 23–36% yields, and the reaction depended on the ring’s position and the axle fragments recombining before the ring could slip off.
What nitrogen deletion changes in a rotaxane
A rotaxane consists of a ring-shaped molecule threaded over a linear component called an axle. Bulky groups at the axle’s ends act as stoppers, preventing the ring from sliding off. The ring and axle are therefore mechanically interlocked, rather than joined by a conventional chemical bond. Chemistry World’s overview describes the 2024 result as a skeletal-editing technique that removes nitrogen atoms from rotaxanes.
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In the 2024 study, the nitrogen belonged to a dibenzylammonium site on the axle. That site had helped template the rotaxane’s assembly; the researchers then removed its nitrogen and connected the remaining axle fragments. The result was a changed axle skeleton inside an architecture that retained its mechanical bond.
How the 2024 reaction works
Gauthier and colleagues reported the study online on October 21, 2024, in the Journal of the American Chemical Society. Their method uses an anomeric amide to activate the secondary amine and replace its nitrogen with a carbon–carbon bond. The paper’s abstract summarizes the transformation as: “The reaction uses an anomeric amide that activates secondary amines to generate a carbon–carbon bond that replaces the amine nitrogen.”
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- Deprotonation: The ammonium/amine site is deprotonated, allowing the macrocycle to shift away from the reactive site.
- Amine activation: The anomeric amide activates the secondary amine. The proposed reaction sequence passes through an isodiazene intermediate.
- Nitrogen extrusion: Molecular nitrogen is expelled, leaving a pair of reactive radical fragments.
- Axle reconnection: The fragments recombine to form the new carbon–carbon bond. The ring must remain threaded while this happens.
The mechanistic account is proposed by the authors; it explains why the reaction’s success depends on both chemical reactivity and the interlocked molecule’s motion. If the ring blocks access to the amine, activation can be inhibited. If the radical fragments do not recombine before the ring dethreads or the fragments escape their solvent cage, the desired interlocked product will not form. The open-access full text discusses these constraints.
What the study established—and what it did not
The 2024 paper demonstrated nitrogen deletion across a series of crown ether–dibenzylammonium rotaxanes, with reported isolated product yields of 23–36%. These are results for the specific laboratory substrates and reactions studied, not a general success rate for rotaxane chemistry or evidence of commercial readiness. The authors characterized products using NMR spectroscopy, mass spectrometry and X-ray crystallography.
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In the solid-state structure of one product, the authors observed weak interactions between crown-ether oxygen atoms and benzylic methylene groups. In that crystal, these CH···O interactions replaced the ammonium-based binding motif found in the parent structure. This is an observation about one crystallographic structure, not proof that every product adopts the same arrangement in solution.
The central limitation is architectural as well as chemical: the macrocycle must be able to occupy a coconformation that leaves the amine accessible, and the axle fragments must reconnect quickly enough to preserve the interlock. The reported scope does not establish that every rotaxane, ring, or axle can undergo this transformation.
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How the 2025 follow-up differs
A separate study by Couto and colleagues, published online August 28, 2025, extended nitrogen deletion to multiple template sites in rotaxanes, catenanes and a molecular knot. It used O-diphenylphosphinylhydroxylamine (DPPH), not the anomeric-amide procedure reported in 2024. The authors reported improved rotaxane deletion yields of up to 51% and found that only one secondary-amine substituent needed to be radical-stabilizing. The examples below are specific experimental yields, not directly comparable head-to-head measurements: the studies used different reagents, substrates and reaction designs.
| 2025 example | Reported result |
|---|---|
| Two template-site deletions from a doubly threaded [3]rotaxane | 37% yield |
| Two template-site deletions from a [3]catenane | 45% yield |
| Four amine deletions from both rings of a [2]catenane | 33% yield |
| Six amine deletions from a molecular trefoil knot | 7% yield |
Repeated deletions raise additional structural risks: components may dethread, catenane rings may unlink, or strands in a knot may uncross. The 2025 results show that nitrogen extrusion can be extended to more elaborate interlocked structures, but the individual yields vary substantially with the example. See the 2025 JACS paper for that distinct set of experiments.
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Why the result matters
Skeletal editing changes the atoms in an existing molecular framework rather than building an entirely new framework from scratch. Here, the nitrogen site served first as part of a template used to assemble an interlocked molecule, then as the atom removed during editing. The work demonstrates a way to alter an axle’s connectivity while preserving the ring–axle mechanical bond—a difficult combination because the deletion creates reactive intermediates that could let the structure come apart.
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