A new type of bispericyclic reaction: Cyclopropanone + butadiene.

September 30th, 2022

The term bispericyclic reaction was famously coined by Caramella et al in 2002[1] to describe the unusual features of the apparently innocuous dimerisation of cyclopentadiene. It shows features of two paths for different pericyclic reactions, comprising a 2+4 cycloaddition in the early stages, but evolving into a (degenerate) pair of [3,3] sigmatropic reactions in the latter stages. Houk (who also uses the term ambimodal) has in recent years extended the number of examples of such pericyclic sequences to trispericyclic[2] (see here) and even an ambimodel tetrapericyclic reaction, as reported at the recent WATOC event. Here I show an example of a new type of bispericyclic reaction, comprising a 2+4 cycloaddition combined with a electrocyclic ring opening.

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References

  1. P. Caramella, P. Quadrelli, and L. Toma, "An Unexpected Bispericyclic Transition Structure Leading to 4+2 and 2+4 Cycloadducts in the Endo Dimerization of Cyclopentadiene", Journal of the American Chemical Society, vol. 124, pp. 1130-1131, 2002. http://dx.doi.org/10.1021/ja016622h
  2. X. Xue, C.S. Jamieson, M. Garcia-Borràs, X. Dong, Z. Yang, and K.N. Houk, "Ambimodal Trispericyclic Transition State and Dynamic Control of Periselectivity", Journal of the American Chemical Society, vol. 141, pp. 1217-1221, 2019. http://dx.doi.org/10.1021/jacs.8b12674

Examples of inverted or hemispherical carbon?

September 15th, 2022

In previously asking what the largest angle subtended at four-coordinate carbon might be, I noted that as the angle increases beyond 180°, the carbon becomes inverted, or hemispherical (all four ligands in one hemisphere). So what does a search for this situation reveal in the CSD? The query can be formulated as below, in which the distance from the centroid of the four ligands to the central carbon is specified to be in e.g. the range 0.8 to 1.1Å. For tetrahedral carbon surrounded by four carbon ligands, the value would be close to zero, so any value larger than say 0.8Å is worth inspecting.

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What is the largest angle possible at 4-coordinate carbon – 180°?

September 11th, 2022

Four-coordinate carbon normally adopts a tetrahedral shape, where the four angles at the carbon are all 109.47°. But how large can that angle get, and can it even get to be 180°?

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Why does octafluorocubane have such a high sublimation point?

September 8th, 2022

The recently reported synthesis[1] of octafluorocubane established a sublimation point as 168.1–177.1°C (a melting point was not observed). In contrast, the heavier perfluoro-octane has an m.p. of -25°C. Why the difference? Firstly, the crystal structure is shown below, albeit as a dimer rather than a periodic lattice (click on image to obtain 3D coordinates).

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References

  1. M. Sugiyama, M. Akiyama, Y. Yonezawa, K. Komaguchi, M. Higashi, K. Nozaki, and T. Okazoe, "Electron in a cube: Synthesis and characterization of perfluorocubane as an electron acceptor", Science, vol. 377, pp. 756-759, 2022. http://dx.doi.org/10.1126/science.abq0516

Octafluorocubane radical anion – where does the extra electron sit?

August 29th, 2022

Derek Lowe reports the story[1] that the recently synthesized octafluorocubane can absorb one electron to form a radical anion – an electron in a cube. So I thought it would be fun to compute exactly where that electron sits!

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References

  1. M. Sugiyama, M. Akiyama, Y. Yonezawa, K. Komaguchi, M. Higashi, K. Nozaki, and T. Okazoe, "Electron in a cube: Synthesis and characterization of perfluorocubane as an electron acceptor", Science, vol. 377, pp. 756-759, 2022. http://dx.doi.org/10.1126/science.abq0516

Four stages in the evolution of interactive ESI as part of articles in chemistry journals.

August 25th, 2022

A previous post was triggered by Peter alerting me that interactive electronic supporting information (IESI) we had submitted to a journal in 2005[1] appeared to be strangely missing from the article landing page. This set me off recollecting our journey, which had started around 1998, and to explore what the current state of these ancient IESIs were in 2022. I have now reached 2014 in this journey, which is being recorded as it happens in the comments page of the post. I discovered there were four distinct stages in that evolution of IESI which I thought it would be of interest to record here.

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References

  1. H.S. Rzepa, and M.E. Cass, "A Computational Study of the Nondissociative Mechanisms that Interchange Apical and Equatorial Atoms in Square Pyramidal Molecules", Inorganic Chemistry, vol. 45, pp. 3958-3963, 2006. http://dx.doi.org/10.1021/ic0519988

Unexpected Isomerization of Oxetane-Carboxylic Acids – an alternative autocatalytic mechanism evaluated.

August 17th, 2022

Previously, I looked at autocatalytic mechanisms where the carboxyl group of an oxetane-carboxylic acid could catalyse its transformation to a lactone, finding that a chain of two such groups were required to achieve the result. Here I look at an alternative mode where the oxetane-carboxylate itself acts as the transfer chain, via a H-bonded dimer shown below.

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Unexpected Isomerization of Oxetane-Carboxylic Acids – substrate design.

August 14th, 2022

Having established a viable model for the unexpected isomerism of oxetane carboxylic acids to lactones[1], and taken a look at a variation in the proton transfer catalyst needed to accomplish the transformation, I now investigate the substrate itself.

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References

  1. B. Chalyk, A. Grynyova, K. Filimonova, T.V. Rudenko, D. Dibchak, and P.K. Mykhailiuk, "Unexpected Isomerization of Oxetane-Carboxylic Acids", Organic Letters, vol. 24, pp. 4722-4728, 2022. http://dx.doi.org/10.1021/acs.orglett.2c01402

Unexpected Isomerization of Oxetane-Carboxylic Acids – catalyst design.

August 13th, 2022

Previously, a mechanism with a reasonable predicted energy was modelled for the isomerisation of an oxetane carboxylic acid to a lactone by using two further molecules of acid to transfer the proton and in the process encouraging an Sn2 reaction with inversion to open the oxetane ring.

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Web page decay and Journals: How an interactive “ESI” from 2006 was rescued.

August 12th, 2022

In 2006[1] we published an article illustrating various types of pseudorotations in small molecules. It’s been cited 20 times since then, so reasonable interest! We described rotations known as Lever and Turnstile as well as the better known Berry mode. Because the differences between these rotations are quite subtle, we included an interactive electronic supporting information to illustrate them. That ESI was written in HTML and used Jmol to animate the rotations. Now, 16 years is a long time in the Web ecosystem (some early wag suggested, like dogs, that one year in normal time approximates to about 7 years in Web time) and inevitably, like e.g. both Rasmol[2] and Chime before it, Jmol no longer works when invoked from a Web browser; Java applets are very much dead and we are now on the fourth generation of molecule viewer, JSmol. Two days ago I was contacted by someone (thanks Peter!) who had noticed that the journal landing page did not seem to point to any ESI. Here I tell the story of what happened next.

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References

  1. H.S. Rzepa, and M.E. Cass, "A Computational Study of the Nondissociative Mechanisms that Interchange Apical and Equatorial Atoms in Square Pyramidal Molecules", Inorganic Chemistry, vol. 45, pp. 3958-3963, 2006. http://dx.doi.org/10.1021/ic0519988
  2. O. Casher, G.K. Chandramohan, M.J. Hargreaves, C. Leach, P. Murray-Rust, H.S. Rzepa, R. Sayle, and B.J. Whitaker, "Hyperactive molecules and the World-Wide-Web information system", Journal of the Chemical Society, Perkin Transactions 2, pp. 7, 1995. http://dx.doi.org/10.1039/P29950000007