Henry Rzepa's Blog

Sometimes, the properties of a molecule are predicted long before it is synthesised. One such is diberyllocene. I first encountered a related molecule, beryllocene itself, many moons ago.[1] This was unusual because unlike the original metallocenes, the metal atom was not symmetrically disposed between the two cyclopentadienyl faces. Now diberyllocene is finally reported in which replacing one Be by Be-Be induces (according to calculation, D₂) symmetry[2]. I will not repeat the excellent analysis of the wavefunction reported in this article, but confine myself to showing two molecular orbitals which examplify its bonding.

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References

1. M.J.S. Dewar, and H.S. Rzepa, "Ground states of molecules. 45. MNDO results for molecules containing beryllium", Journal of the American Chemical Society, vol. 100, pp. 777-784, 1978. http://dx.doi.org/10.1021/ja00471a020
2. J.T. Boronski, A.E. Crumpton, L.L. Wales, and S. Aldridge, "Diberyllocene, a stable compound of Be(I) with a Be–Be bond", Science, vol. 380, pp. 1147-1149, 2023. http://dx.doi.org/10.1126/science.adh4419

This is a venerable organic reaction, which curiously I have not previously covered here. First described in 1859, its nature was only properly elucidated in 1873. It is a member of a class of reaction I have previously named “solvolytically assisted pericyclic”, or “perisolvolytic“. Here I explore some of the subtle stereoelectronic effects observed for this apparently simple reaction.

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This editorial from Nature[1] is a timely reminder of the importance of data. But also, not just any data, but “accurate and accessible training data“. Accessible of course is one of the attributes of FAIR (Findable, Accessible, Interoperable and Re-usable). The editorial also states “data need to be recorded in agreed and consistent formats, which they are not at present“. That is covered by the I and R of FAIR, often applied in conjunction with metadata recording the Media type that the data is held in (See DOI https://doi.org/jvk9 for examples of the use of Media types in chemical computation and chemical NMR). Again, “The best possible training sets would also include data on negative outcomes“. This relates to the separation of the two publication processes, namely the article itself (or the story behind the data) and the data itself as a first class scientific object. Thus when we publish FAIR data in association with articles, the data archive will often contain data that is not used in the article itself (perhaps because it led to a negative outcome), but is nevertheless part of the FAIR data collection for that topic. Even if the data does not lead to journal publication, publishing it in a data repository means it will not be lost. Somebody (or AI software) may still find it useful.

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References

1. "For chemists, the AI revolution has yet to happen", Nature, vol. 617, pp. 438-438, 2023. http://dx.doi.org/10.1038/d41586-023-01612-x

I have previously looked at the pigments used to colour the Book of Kells, which dates from around 800 AD and which contained arsenic sulfide as the yellow colourant. The Bayeaux tapestry is a later embroidery dating probably from around 1077 and here the colours are based entirely on mordanted natural dyes. These are generally acknowledged to be blue woad (principle component indigo), red madder (principle component alizarin) and the less well-known yellow weld, which comes from the plant Reseda Luteola and the principle component of which is luteolin.[1]

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References

1. C. Chavanne, A. Verney, C. Paquier-Berthelot, M. Bostal, P. Buléon, and P. Walter, "Bayeux Tapestry: First use of early synthetic dyes for the restoration of a masterpiece", Dyes and Pigments, vol. 208, pp. 110798, 2023. http://dx.doi.org/10.1016/j.dyepig.2022.110798

In the previous post, I discussed how data associated with two of the candidates for molecules of the year – 2022 could be retrieved and then used to inspect their three dimensional structures. Here I focus on the ultra large cavitands recently reported[1]. As I noted, these have an associated data coordinate archive published on Zenodo (DOI: 10.5281/zenodo.6953961) although this is not cited in the article itself.

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References

1. J. Pfeuffer‐Rooschüz, S. Heim, A. Prescimone, and K. Tiefenbacher, "Megalo‐Cavitands: Synthesis of Acridane[4]arenes and Formation of Large, Deep Cavitands for Selective C70 Uptake", Angewandte Chemie International Edition, vol. 61, 2022. http://dx.doi.org/10.1002/anie.202209885

The list of molecules of the year is out now at C&E News (but you have to have an account to view the list, unlike previous years).^♣ These three caught my eye:

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