I thought I was done with exploring anomeric effects in small sulfur rings. However, I then realised that all the systems that I had described had an odd number of atoms and that I had not looked at any even numbered rings. Thus hexasulfur is a smaller (known) ring version of S8, the latter by far the best known allotrope of this element of course.
Archive for the ‘Interesting chemistry’ Category
Cyclo-S6 (Hexathiane) – anomeric effects again!
Sunday, June 1st, 2025S7I1+: The largest anomeric effect exhibited by sulfur.
Wednesday, May 21st, 2025In this series of posts about the electronic effects in small sulfur rings[1] I have explored increasingly large induced geometric effects. Here is the largest so far, for the compound S7I1+[2]
References
- H. Rzepa, "5-Imino-5λ<sup>4</sup>-heptathiepane 3-oxide. More exuberent anomeric effects.", 2025. https://doi.org/10.59350/rzepa.28615
- J. Passmore, G. Sutherland, P. Taylor, T.K. Whidden, and P.S. White, "Preparations and x-ray crystal structures of iodo-cyclo-heptasulfur hexafluoroantimonate(V) and hexafluoroarsenate(V), S7ISbF6 and S7IAsF6", Inorganic Chemistry, vol. 20, pp. 3839-3845, 1981. https://doi.org/10.1021/ic50225a048
5-Imino-5λ4-heptathiepane 3-oxide. More exuberent anomeric effects.
Tuesday, May 20th, 2025The two previous posts[1],[2] on the topic of anomeric effects in 7-membered sulfur rings illustrated how orbital interactions between the lone pairs in the molecules and S-S bonds produced widely varying S-S bond lengths in the molecules, some are shorter than normal (which is ~2.05Å for e.g. the S8 ring) by ~ 0.1Å and some are longer by ~0.24Å. Here we extend this to the unknown molecule shown below.
References
- H. Rzepa, "Cycloheptasulfur sulfoxide, S<sub>7</sub>O – Anomeric effects galore!", 2025. https://doi.org/10.59350/rzepa.28515
- H. Rzepa, "Cyclo-Heptasulfur, S<sub>7</sub> – a classic anomeric effect discovered during a pub lunch!", 2025. https://doi.org/10.59350/rzepa.28407
Cycloheptasulfur sulfoxide, S7O – Anomeric effects galore!
Monday, May 19th, 2025The monosulfoxide of cyclo-heptasulfur was reported along with cycloheptasulfur itself in 1977,[1] along with the remarks that “The δ modification of S7 contains bonds of widely differing length: this has never been observed before in an unsubstituted molecule. and “the same effect having also been observed in other sulfur rings (S8O, S7I1+ and S7O).” Here I take a look at the last of these other molecules, the monosulfoxide of S7, as a follow up to the commentary on S7 itself.[2]
References
- R. Steudel, R. Reinhardt, and T. Sandow, "Bond Interaction in Sulfur Rings: Crystal and Molecular Structure of <i>cyclo</i>‐Heptasulfur Oxide, S<sub>7</sub>O", Angewandte Chemie International Edition in English, vol. 16, pp. 716-716, 1977. https://doi.org/10.1002/anie.197707161
- H. Rzepa, "Cyclo-Heptasulfur, S<sub>7</sub> – a classic anomeric effect discovered during a pub lunch!", 2025. https://doi.org/10.59350/rzepa.28407
Cyclo-Heptasulfur, S7 – a classic anomeric effect discovered during a pub lunch!
Friday, May 16th, 2025Way back in 1977, the crystal structure of the sulfur ring S7 was reported.[1] The authors noted that “The δ modification of S7 contains bonds of widely differing length: this has never been observed before in an unsubstituted molecule.” No explanation was offered, although they note that similar effects have been observed in S8O, S7I+ and S7O. The S7 molecule was yesterday brought to my attention (thanks Derek!) over a pub lunch and in the time honoured manner of scientists, sketched out on a napkin – with a pen obtained from the waitress!. As an “organic chemist”, I immediately thought “anomeric effects”. And so indeed it has proven. A calculation using the MN15L/Def2-TZVPP DFT method and analysis using the Weinhold NBO7 procedure[2] reveals the following structure (with Cs symmetry) and indeed the four unique S-S distances are all different (experimental values in parentheses). So how does this arise?
References
- R. Steudel, R. Reinhardt, and F. Schuster, "Crystal and Molecular Structure of <i>cyclo</i>‐Heptasulfur (δ‐S<sub>7</sub>)", Angewandte Chemie International Edition in English, vol. 16, pp. 715-715, 1977. https://doi.org/10.1002/anie.197707151
- H. Rzepa, "Cyclo-Heptasulfur, S7 – a classic anomeric effect discovered during a pub lunch!", 2025. https://doi.org/10.14469/hpc/15228
Au-pseudocarbyne – a unusual example of a twelve coordination by carbon.
Saturday, February 1st, 2025Derek 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]
References
- 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
Molecules of the Year 2024: Molecular shuttle in a box.
Saturday, January 25th, 2025This is another in the C&E News list of candidates for the Molecule of the Year, Molecular shuttle in a box [1] (more…)
References
- 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
Molecules of the Year 2024: A crystal structure perspective on anti-Bredt olefins.
Wednesday, January 8th, 2025Data Discovery: A pick-n-mix library of useful FAIR Data searches – and a call for new search suggestions.
Monday, November 25th, 2024With 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]
References
- 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
- 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
Mechanism of the Masamune-Bergman reaction. Part 4. Why was the DFT energy barrier too high for the Calicheamicin reaction?
Tuesday, October 29th, 2024Michael 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.
References
- 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