July 3rd, 2013
C2 (dicarbon) is certainly interesting from a theoretical point of view. Whether or not it can be described as having a quadruple bond has induced much passionate discussion[1],[2],[3],[4]. Its occurrence in space and in flames is also well-known. But does it have what might be called a conventional chemistry? Other highly reactive species (cyclobutadiene is a well-known example) can often be tamed by trapping as a ligand coordinated to a metal and so one might speculate upon how C2 responds to the proximity of a metal. As is noted here[2], dicarbon as a ligand has been known a long time as part of what is referred to as carbide chemistry. In this regard it is thought of as the di-anion, C22- (and isoelectronic therefore with dinitrogen). Thus calcium carbide, but in fact the degree to which the dicarbon can absorb electrons is thought to be wide (as judged by the resulting C-C bond length, see[2]). Here I take a look at just one metal carbide[5] that caught my eye (there are hundreds of others, many no doubt equally interesting!).
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References
- 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
- S. Shaik, H.S. Rzepa, and R. Hoffmann, "One Molecule, Two Atoms, Three Views, Four Bonds?", Angewandte Chemie International Edition, vol. 52, pp. 3020-3033, 2013. https://doi.org/10.1002/anie.201208206
- G. Frenking, and M. Hermann, "Critical Comments on “One Molecule, Two Atoms, Three Views, Four Bonds?”", Angewandte Chemie International Edition, vol. 52, pp. 5922-5925, 2013. https://doi.org/10.1002/anie.201301485
- D. Danovich, S. Shaik, H.S. Rzepa, and R. Hoffmann, "A Response to the Critical Comments on “One Molecule, Two Atoms, Three Views, Four Bonds?”", Angewandte Chemie International Edition, vol. 52, pp. 5926-5928, 2013. https://doi.org/10.1002/anie.201302350
- E. Dashjav, Y. Prots, G. Kreiner, W. Schnelle, F.R. Wagner, and R. Kniep, "Chemical bonding analysis and properties of La7Os4C9—A new structure type containing C- and C2-units as Os-coordinating ligands", Journal of Solid State Chemistry, vol. 181, pp. 3121-3130, 2008. https://doi.org/10.1016/j.jssc.2008.08.005
Tags: metal, metal coordinating, Os-C
Posted in Interesting chemistry | 6 Comments »
June 26th, 2013
A reader asked me about the mechanism of the reaction of 2-picoline N-oxide with acetic anhydride to give 2-acetoxymethylpyridine (the Boekelheide Rearrangement[1]). He wrote ” I don’t understand why the system should prefer to go via fragmentation-recombination (… the evidence being that oxygen labelling shows scrambling) when there is an easy concerted pathway available (… a [3,3]sigmatropic shift). Furthermore, is it possible for two pathways to co-exist?” Here is how computation might enlighten us.
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References
- A. Massaro, A. Mordini, A. Mingardi, J. Klein, and D. Andreotti, "A New Sequential Intramolecular Cyclization Based on the Boekelheide Rearrangement", European Journal of Organic Chemistry, vol. 2011, pp. 271-279, 2010. https://doi.org/10.1002/ejoc.201000936
Tags: ATM, CF 3 CO, CH 3 CO, extraneous product, free energy, free energy barrier, recombination
Posted in Interesting chemistry, pericyclic, reaction mechanism | 3 Comments »
June 24th, 2013
The blog post by Rich Apodaca entitled “The Horrifying Future of Scientific Communication” is very thought provoking and well worth reading. He takes us through disruptive innovation, and how it might impact upon how scientists communicate their knowledge. One solution floated for us to ponder is that “supporting Information, combined with data mining tools, could eliminate most of the need for manuscripts in the first place“. I am going to juxtapose that suggestion on something else I recently discovered.
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Tags: data mining, data mining tools, Google, opendata, researcher
Posted in Chemical IT | 2 Comments »
June 12th, 2013
A little while ago, I set out some interpretations of how to push curly arrows. I also appreciate that some theoretically oriented colleagues regard the technique as neither useful nor in the least rigorous, whereas towards the other extreme many synthetically minded chemists view the ability to push a reasonable set of arrows for a proposed mechanism as of itself constituting evidence in its favour.[1] Like any language for expressing ideas, the tool needs a grammar (rules) and a vocabulary, and perhaps also an ability to carry ambiguity. These thoughts surfaced again via a question asked of me by a student: “is the mechanism for the hydrogens in protonated benzene whizzing around the ring a [1,2] or a [1,6] pericyclic sigmatropic shift?”.
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References
- M.J. Gomes, L.F. Pinto, P.M. Glória, H.S. Rzepa, S. Prabhakar, and A.M. Lobo, "N-heteroatom substitution effect in 3-aza-cope rearrangements", Chemistry Central Journal, vol. 7, 2013. https://doi.org/10.1186/1752-153x-7-94
Tags: first arrow-head, Reaction Mechanism, Tutorial material
Posted in Curly arrows | 8 Comments »
June 6th, 2013
Many moons ago, when I was a young(ish) lecturer, and much closer in time to my laboratory roots of organic synthesis, I made some chemistry videos. One of these has resurfaced, somewhat (to me at least) unexpectedly. Nowadays of course, such demonstrations are all carried out using virtual simulations (Flash animations etc) as the equipment itself becomes less common.
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Tags: Flash, lecturer, Tutorial material
Posted in Uncategorised | 1 Comment »
June 5th, 2013
In a time of change, we often do not notice that Δ = ∫δ. Here I am thinking of network bandwidth, and my personal experience of it over a 46 year period.
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Tags: acoustic coupler, Addison-Wesley, Austin Texas, BT, building I, California, Cambridge, computing, electronics, ethernet, Global Intelligence, Google, Historical, Imperial College, Leeds, London, New York, operating system, quantum chemical calculations, Samuel Butler, United Kingdom, University College London
Posted in Uncategorised | 4 Comments »
June 2nd, 2013
A few years ago, we published an article which drew a formal analogy between chemistry and iTunes (sic)[1]. iTunes was the first really large commercial digital music library, and a feature under-the-skin was the use of meta-data to aid discoverability of any of the 10 million (26M in 2013) or so individual items in the store.‡ The analogy to digital chemistry and discoverability of the 70 or so million known molecules is, we argued, a good one.
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References
- O. Casher, and H.S. Rzepa, "SemanticEye: A Semantic Web Application to Rationalize and Enhance Chemical Electronic Publishing", Journal of Chemical Information and Modeling, vol. 46, pp. 2396-2411, 2006. https://doi.org/10.1021/ci060139e
Tags: Apple, BBC, digital photography, engineer, Google, Historical, HTML, metadata, opendata, RDF, search term, Steve Bachrach, United Kingdom
Posted in Chemical IT | No Comments »
May 29th, 2013
This is a follow-up to comment posted by Ryan, who asked about isocyanide’s role (in the form of the anion of tosyl isocyanide, or TosMIC): “In Van Leusen, it (the isocyanide) acts as an electrophile”. The Wikipedia article (recently updated by myself) shows nucleophilic attack by an oxy-anion on the carbon of the C≡N group, with the isocyanide group acting as the acceptor of these electrons (in other words, the electrophile). In the form shown below, one negatively charged atom appears to be attacking another also carrying a negative charge. Surely this breaks the rules that like charges repel? So we shall investigate to see if this really happens.
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Tags: low energy, low free-energy barrier, Reaction Mechanism, Tutorial material
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May 24th, 2013
The title of this post comes from a comment posted by Ryan, who asks about isocyanide’s role (in the form of the anion of tosyl isocyanide, or TosMIC) in two named reactions, Van Leusen and Ugi FCR. “In Van Leusen, it (the isocyanide) acts as an electrophile: however, in Ugi, it acts as a nucleophile”. Here are some valence bond forms for this species;
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Tags: Ugi, Van Leusen
Posted in Interesting chemistry | 2 Comments »
May 22nd, 2013
Here is another example gleaned from that Woodward essay of 1967 (Chem. Soc. Special Publications (Aromaticity), 1967, 21, 217-249), where all might not be what it seems.
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Tags: free energy barrier, Historical, Reaction Mechanism, Tutorial material
Posted in Uncategorised | No Comments »