R-X≡X-R: G. N. Lewis’ 100 year old idea.

May 22nd, 2015
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As I have noted elsewhere, Gilbert N. Lewis wrote a famous paper entitled “the atom and the molecule“, the centenary of which is coming up.[1] In a short and rarely commented upon remark, he speculates about the shared electron pair structure of acetylene,  R-X≡X-R (R=H, X=C). It could, he suggests, take up three forms. H-C:::C-H and two more which I show as he drew them. The first of these would now be called a bis-carbene and the second a biradical.

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References

  1. G.N. Lewis, "THE ATOM AND THE MOLECULE.", J. Am. Chem. Soc., vol. 38, pp. 762-785, 1916. http://dx.doi.org/10.1021/ja02261a002

Impact factors, journals and blogs: a modern distortion.

May 21st, 2015
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A lunchtime conversation with a colleague had us both bemoaning the distorting influence on chemistry of bibliometrics, h-indices and journal impact factors, all very much a modern phenomenon of scientific publishing. Young academics on a promotion fast-track for example are apparently advised not to publish in a well-known journal devoted to organic chemistry because of its apparently “low” impact factor. Chris suggested that the real reason the impact factor was “low” is that this particular journal concentrates on full articles, which for a subject area such as organic chemistry can take years to assemble and hence years for others to assimilate and report their own results, and only then creating a citation for the first article. So this slow but steady evolution of citations in a long time frame apparently shows such a journal up as having less (short-term) impact than the fast-publishing notes-type variety where the impact is immediate but possibly less long-lived. That would be no reason of itself not to publish there of course!

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The Bürgi–Dunitz angle revisited: a mystery?

May 12th, 2015
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The Bürgi–Dunitz angle is one of those memes that most students of organic chemistry remember. It hypothesizes the geometry of attack of a nucleophile on a trigonal unsaturated (sp2) carbon in a molecule such as ketone, aldehyde, ester, and amide carbonyl. Its value obviously depends on the exact system, but is generally taken to be in the range 105-107°. A very good test of this approach is to search the crystal structure database (this was how it was originally established[1]).

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References

  1. H. B:urgi, J. Dunitz, J. Lehn, and G. Wipff, "Stereochemistry of reaction paths at carbonyl centres", Tetrahedron, vol. 30, pp. 1563-1572, 1974. http://dx.doi.org/10.1016/S0040-4020(01)90678-7

The status of blogging as scientific communication.

May 10th, 2015
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Blogging in chemistry remains something of a niche activity, albeit with a variety of different styles. The most common is commentary or opinion on the scientific literature or conferencing, serving to highlight what their author considers interesting or important developments. There are even metajournals that aggregate such commentaries. The question therefore occasionally arises; should blogs aspire to any form of permanence, or are they simply creatures of their time.

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Allotropic halogens.

April 26th, 2015
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Allotropes are differing structural forms of the elements. The best known example is that of carbon, which comes as diamond and graphite, along with the relatively recently discovered fullerenes and now graphenes. Here I ponder whether any of the halogens can have allotropes.

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ORCID identifiers galore!

April 21st, 2015
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Egon has reminded us that adoption of ORCID (Open researcher and collaborator ID) is gaining apace. It is a mechanism to disambiguate (a Wikipedia term!) contributions in the researcher community and to also remove much of the anonymity (where that is undesirable) that often lurks in social media sites.

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A new way of exploring the directing influence of (electron donating) substituents on benzene.

April 17th, 2015
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The knowledge that substituents on a benzene ring direct an electrophile engaged in a ring substitution reaction according to whether they withdraw or donate electrons is very old.[1] Introductory organic chemistry tells us that electron donating substituents promote the ortho and para positions over the meta. Here I try to recover some of this information by searching crystal structures.

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References

  1. H.E. Armstrong, "XXVIII.?An explanation of the laws which govern substitution in the case of benzenoid compounds", Journal of the Chemical Society, Transactions, vol. 51, pp. 258, 1887. http://dx.doi.org/10.1039/CT8875100258

The mechanism of borohydride reductions. Part 1: ethanal.

April 12th, 2015
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Sodium borohydride is the tamer cousin of lithium aluminium hydride (LAH). It is used in aqueous solution to e.g. reduce aldehydes and ketones, but it leaves acids, amides and esters alone. Here I start an exploration of why it is such a different reducing agent.
BH4

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A better model for the mechanism of Lithal (LAH) reduction of cinnamaldehyde?

April 10th, 2015
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Previously on this blog: modelling the reduction of cinnamaldehyde using one molecule of lithal shows easy reduction of the carbonyl but a high barrier at the next stage, the reduction of the double bond. Here is a quantum energetic exploration of what might happen when a second LAH is added to the brew (the usual ωB97XD/6-311+G(d,p)/SCRF=diethyl ether).

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Goldilocks Data.

April 8th, 2015
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Last August, I wrote about data galore, the archival of data for 133,885 (134 kilo) molecules into a repository, together with an associated data descriptor[1] published in the new journal Scientific Data. Since six months is a long time in the rapidly evolving field of RDM, or research data management, I offer an update in the form of some new observations.

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References

  1. R. Ramakrishnan, P.O. Dral, M. Rupp, and O.A. von Lilienfeld, "Quantum chemistry structures and properties of 134 kilo molecules", Scientific Data, vol. 1, 2014. http://dx.doi.org/10.1038/sdata.2014.22