October 26th, 2013
The 1H NMR spectrum of an aromatic molecule such as benzene is iconic; one learns that the unusual chemical shift of the protons (~δ 7-8 ppm) is due to their deshielding by a diatropic ring current resulting from the circulation of six aromatic π-electrons following the Hückel 4n+2 rule. But rather less well-known is the spectacular inversion of these effects as induced by the paratropic circulation of 4n electrons. A 4n+2 rule can be converted to a 4n one by the addition of two electrons, and chemically this can be done by reduction with lithium metal to form a dianion. Fortunately, this experiment has been done for a molecule known as methano[10]annulene. This is a 4n+2 aromatic molecule 1 with ten π-electrons (n=2) that can be reduced with lithium metal to form an ion-pair 2 comprising lithium cations and the twelve π-electron (4n, n=3) methano[10]annulene dianion.[1]
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References
- D. Schmalz, and H. Günther, "1,6‐Methano[10]annulene Dianion, a Paratropic 12π‐Electron Dianion with a C<sub>10</sub> Perimeter", Angewandte Chemie International Edition in English, vol. 27, pp. 1692-1693, 1988. https://doi.org/10.1002/anie.198816921
Tags: chemical shifts, lithium metal, unusual chemical shift
Posted in Interesting chemistry | No Comments »
October 20th, 2013
Homoaromaticity is a special case of aromaticity in which π-conjugation is interrupted by a single sp3 hybridized carbon atom (it is sometimes referred to as a suspended π-bond with no underlying σ-foundation). But consider the carbene shown below. This example comes from a recently published article[1] which was highlighted on Steve Bachrach’s blog. Here aromaticity has resulted from a slightly different phenomenon, whereby a 4π-electron planar (and hence nominally anti-aromatic) molecule is elevated to aromatic peerage by promoting the two carbene σ-electrons to have π-status.
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References
- B. Chen, A.Y. Rogachev, D.A. Hrovat, R. Hoffmann, and W.T. Borden, "How to Make the σ<sup>0</sup>π<sup>2</sup> Singlet the Ground State of Carbenes", Journal of the American Chemical Society, vol. 135, pp. 13954-13964, 2013. https://doi.org/10.1021/ja407116e
Tags: low energy, Steve Bachrach
Posted in Interesting chemistry | 1 Comment »
October 13th, 2013
I reminisced about the wonderfully naive but exciting Web-period of 1993-1994. This introduced the server-log analysis to us for the first time, and hits-on-a-web-page. One of our first attempts at crowd-sourcing and analysis was to run an electronic conference in heterocyclic chemistry and to look at how the attendees visited the individual posters and presentations by analysing the server logs.
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Tags: aspiring tenure-track young scientist, author, Google, head of department, Imperial College, research group leader, United Kingdom, Web-period
Posted in Chemical IT, General | No Comments »
October 11th, 2013
In 1993-1994, when the Web (synonymous in most minds now with the Internet) was still young, the pace of progress was so rapid that some wag worked out that one “web-year” was like a dog-year, worth about 7 years of normal human time. So in this respect, 1994 is now some 133 web-years ago. Long enough for an archaeological excavation.
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Tags: chemical, Peter Murray-Rust, Web-pages, web-years
Posted in Chemical IT | 1 Comment »
October 2nd, 2013
This is a continuation of the discussion started on Steve Bachrach’s blog about a molecule with a very short H…H interaction involving two Si-H groups with enforced proximity. It had been inferred from the X-ray structure[1] that the H…H distance was in the region of 1.50Å. It’s that cis-butene all over again! So is that H…H region a bond? Is it attractive or repulsive? Go read Steve’s blog first.
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References
- J. Zong, J.T. Mague, and R.A. Pascal, "Exceptional Steric Congestion in an <i>in</i>,<i>in</i>-Bis(hydrosilane)", Journal of the American Chemical Society, vol. 135, pp. 13235-13237, 2013. https://doi.org/10.1021/ja407398w
Tags: Postscript, Steve Bachrach, X-ray
Posted in Interesting chemistry | 17 Comments »
October 2nd, 2013
In the two-publisher model I proposed a post or so back, I showed an example of how data can be incorporated (transcluded) into the story narrative of a scientific article, with both that story and the data each having their own independently citable reference (using a doi for the citation). Here I take it a step further, by publishing a functional procedure in a digital repository[1] and assigned its own doi:10.6084/m9.figshare.811862.
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References
- H.S. Rzepa, "Script for creating an NCI surface as a JVXL compressed file from a (Gaussian) cube of total electron density", 2013. https://doi.org/10.6084/m9.figshare.811862
Tags: HTML, Java, separate web page
Posted in Chemical IT | 2 Comments »
September 21st, 2013
The best known example of the gauche effect is 1,2-difluoroethane, which exhibits a relatively small preference of ~0.5 kcal/mol for this conformer over the anti orientation, which is also a minimum. But FSSF, which I discussed in the previous post, beats this hands down! It also, by the way, must surely be the smallest molecule (only four atoms) which could be theoretically resolved into two enantiomers (possibly at say 273K?).‡
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Tags: ELF, Transition state
Posted in Interesting chemistry, reaction mechanism | 2 Comments »
September 19th, 2013
Paul Schleyer sent me an email about a pattern he had spotted, between my post on F3SSF and some work he and Michael Mauksch had done 13 years ago with the intriguing title “Demonstration of Chiral Enantiomerization in a Four-Atom Molecule“.[1] Let me explain the connection, but also to follow-up further on what I discovered in that post and how a new connection evolved.
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References
Tags: energy, energy profile, head, low energy barrier, lowest energy route, Michael Mauksch, Paul Schleyer, reactant/product
Posted in Interesting chemistry | 3 Comments »
September 15th, 2013
I do go on rather a lot about enabling or hyper-activating[1] data. So do others[2]. Why is sharing data important?
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References
- 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. https://doi.org/10.1039/p29950000007
- R. Van Noorden, "Data-sharing: Everything on display", Nature, vol. 500, pp. 243-245, 2013. https://doi.org/10.1038/nj7461-243a
Tags: chemical tagger, data mining, datument, David Scheschkewitz, e-notebook, Google, opendata, Peter Murray-Rust, pre-processor, researcher, scientific tool, supervisor, United Kingdom
Posted in Chemical IT, Interesting chemistry | 9 Comments »
September 12th, 2013
Andy Extance at the Chemistry World blog has picked up on a fascinating article[1] on the dimer of SF2. This molecule has three F atoms on one S, and only one on the other; FSSF3. But all four S-F bonds are of different length. Lindquist and Dunning claim that the minimum energy pathway to dissociation to two SF2 molecules does not involve breaking either the longest or the weakest SF bond. This was too much for me to resist investigating further!
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References
- B.A. Lindquist, and T.H. Dunning, "Bonding in FSSF<sub>3</sub>: Breakdown in Bond Length-Strength Correlations and Implications for SF<sub>2</sub> Dimerization", The Journal of Physical Chemistry Letters, vol. 4, pp. 3139-3143, 2013. https://doi.org/10.1021/jz401578h
Tags: Andy Extance, minimum energy pathway
Posted in Interesting chemistry, reaction mechanism | 6 Comments »