Henry Rzepa's Blog

Derek Lowe tells the story of “carbyne”, a potential further allotrope of carbon, comprising linear chains of carbon atoms, C-C≡C-C≡C-C. Whether such a molecule can exist on its own has long been the the topic of speculation. Now a report has appeared of a “pseudocarbyne”, stabilised by gold atoms.[1]

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References

1. J. Wu, P. Tarakeshwar, S.G. Sayres, M. Meneghetti, H. Kim, J. Barreto, and P.R. Buseck, "Crystal structure of Au-pseudocarbyne(C6)", Scientific Reports, vol. 15, 2025. https://doi.org/10.1038/s41598-024-80359-5

This is another in the C&E News list of candidates for the Molecule of the Year, Molecular shuttle in a box [1] (more…)

References

1. S. Ibáñez, P. Salvà, L.N. Dawe, and E. Peris, "Guest‐Shuttling in a Nanosized Metallobox", Angewandte Chemie International Edition, vol. 63, 2024. https://doi.org/10.1002/anie.202318829

Each year C&E News publishes a list of candidates for the Molecule of the Year. For 2024 the list is (in order of votes cast for each) (more…)

With AI and Machine learning needing data in abundance, interest in data discovery is intense. However, this type of discovery is somewhat different from more traditional data base searches, in that it is particularly suited for machine discovery as well as by humans. The discovery searches are conducted using an aggregated and federated metadata store, such as that curated by DataCite. How to construct a suitable search is however still not entirely human-friendly. The start point for understanding how to search is this resource: XML to JSON mappings and the XML referred to can be found here. [1] Since the learning curve to construct such data searches can be quite steep, I thought I would share as a library some recent searches I constructed for a talk I am giving. This post is essentially an extension and update of an earlier challenge I was set along these lines and which appeared here.[2]

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References

1. DataCite Metadata Working Group., "DataCite Metadata Schema Documentation for the Publication and Citation of Research Data and Other Research Outputs v4.5", DataCite, 2024. https://doi.org/10.14454/g8e5-6293
2. H. Rzepa, and T. Davies, "Open publishing FAIR spectra for and by students", Spectroscopy Europe, pp. 22, 2022. https://doi.org/10.1255/sew.2022.a10

Michael in a comment here on the mechanism of the Masamune-Bergman reaction notes that when it occurs as part of the Calicheamicin (an antibody-drug conjugate or ADC) version of this mechanism, a pre-step is first necessary. As discussed in this review article,[1] the trisulfide linkage is reduced and the resulting thiolate undergoes a facile 1,4-addition to the adjacent enone.

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References

1. V. Kostova, P. Désos, J. Starck, and A. Kotschy, "The Chemistry Behind ADCs", Pharmaceuticals, vol. 14, pp. 442, 2021. https://doi.org/10.3390/ph14050442

In exploring one-electron carbon-carbon bonds, I had noted previously[1] that both hexafluoroethane and ethane itself could each lose an electron to produce such species. A discussion developed in which a molecule isoelectronic with ethane, namely the methyl-λ1-borane radical (H₃B-CH₃) was proposed by Jacob. The optimised structure at the ωB97XD/6-31G(d) level exhibited a B-C bond length of 1.57Å, with two of the B-H hydrogens forming a a 3c-3e bond with boron and so a one-electron B-C bond was discounted. Here I take a closer look at this system.

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References

1. https://doi.org/

In the previous post, I looked[1] at the recently reported[2] hexa-arylethane containing a carbon-carbon one-electron bond, its structure having been determined by x-ray diffraction (XRD). The measured C-C bond length was ~2.9aÅ and my conclusion was that the C…C region represented more of a weak “interaction” than of a bond as such. How about a much simpler system, hexafluoroethane? Here, the two-electron C-F bonds are much lower in energy than the C-C bond, so when the molecule is ionised, it escapes from the C-C bond rather than any of the C-F bonds. The below is the structure computed at the ωB97XD/Def2-TZVPP level, revealing a much shorter C-C bond of 2.149Å. The computed C-C stretching vibrational frequency is 179 cm^-1 (FAIR data DOI: [3])

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References

1. H. Rzepa, "A carbon-carbon one-electron bond! Or a weak carbon-carbon interaction?", 2024. https://doi.org/10.59350/xp5a3-zsa24
2. G.N. Lewis, "THE ATOM AND THE MOLECULE.", Journal of the American Chemical Society, vol. 38, pp. 762-785, 1916. https://doi.org/10.1021/ja02261a002
3. H. Rzepa, "A carbon-carbon one-electron bond! Or a weak carbon-carbon interaction?", 2024. https://doi.org/10.14469/hpc/14642

More than 100 years ago, before the quantum mechanical treatment of molecules had been formulated, G. N. Lewis proposed[1] a simple model for chemical bonding that is still taught today. This is the idea of the three categories of bond we know as single, double and triple, comprising respectively two, four and six shared electrons each, at least for the very common carbon-carbon bond. A little more than a decade ago, this was extended upwards to the eight-electron quadruple bond.[2]. Now, at the other extreme of downwards, a molecule has been characterised in the solid state with a one-electron C-C bond.[3] In this sub-two-electron region, bonds such as hydrogen bonds have long been recognised and they form part of a class of “weak” bonding known instead as exhibiting “non-covalent-interactions” or NCI. But specifically a one-electron carbon-carbon bond stands apart from these weaker types and so it is certainly news when one such is reported and characterised in the crystalline state by x-ray diffraction.

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References

1. G.N. Lewis, "THE ATOM AND THE MOLECULE.", Journal of the American Chemical Society, vol. 38, pp. 762-785, 1916. https://doi.org/10.1021/ja02261a002
2. S. Shaik, D. Danovich, W. Wu, P. Su, H.S. Rzepa, and P.C. Hiberty, "Quadruple bonding in C2 and analogous eight-valence electron species", Nature Chemistry, vol. 4, pp. 195-200, 2012. https://doi.org/10.1038/nchem.1263
3. T. Shimajiri, S. Kawaguchi, T. Suzuki, and Y. Ishigaki, "Direct evidence for a carbon–carbon one-electron σ-bond", Nature, vol. 634, pp. 347-351, 2024. https://doi.org/10.1038/s41586-024-07965-1