PIDapalooza 2018: the open festival for persistent identifiers.

November 14th, 2017

PIDapalooza is a new forum concerned with discussing all things persistent, hence PID. You might wonder what possible interest a chemist might have in such an apparently arcane subject, but think of it in terms of how to find the proverbial needle in a haystack in a time when needles might look all very similar. Even needles need descriptions, they are not all alike and PIDs are a way of providing high quality information (metadata) about a digital object.  

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VSEPR Theory: Octet-busting or not with trimethyl chlorine, ClMe3.

November 12th, 2017

A few years back, I took a look at the valence-shell electron pair repulsion approach to the geometry of chlorine trifluoride, ClF3 using so-called ELF basins to locate centroids for both the covalent F-Cl bond electrons and the chlorine lone-pair electrons. Whereas the original VSEPR theory talks about five “electron pairs” totalling an octet-busting ten electrons surrounding chlorine, the electron density-based ELF approach located only ~6.8e surrounding the central chlorine and no “octet-busting”. The remaining electrons occupied fluorine lone pairs rather than the shared Cl-F regions. Here I take a look at ClMe3, as induced by the analysis of SeMe6.

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Hypervalence revisited. The odd case of hexamethyl selenium.

November 7th, 2017

One thread that runs through this blog is that of hypervalency. It was therefore nice to come across a recent review of the concept[1] which revisits the topic, and where a helpful summary is given of the evolving meanings over time of the term hypervalent. The key phrase “it soon became clear that the two principles of the 2-centre-2-electron bond and the octet rule were sometimes in conflict” succinctly summarises the issue. Two molecules that are discussed in this review caught my eye, CLi6 and SeMe6. The former is stated as “anomalous in terms of the Lewis model“, but as I have shown in an earlier post, the carbon is in fact not anomalous in a Lewis sense because of a large degree of Li-Li bonding. When this is taken into account, the Lewis model of the carbon becomes more “normal”. Here I take a look at the other cited molecule, SeMe6.

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References

  1. M.C. Durrant, "A quantitative definition of hypervalency", Chemical Science, vol. 6, pp. 6614-6623, 2015. http://dx.doi.org/10.1039/c5sc02076j

Elongating an N-B single bond is much easier than stretching a C-C single bond.

October 24th, 2017

An N-B single bond is iso-electronic to a C-C single bond, as per below. So here is a simple question: what form does the distribution of the lengths of these two bonds take, as obtained from crystal structures? 

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Two stories about Open Peer Review (OPR), the next stage in Open Access (OA).

October 5th, 2017

We have heard a lot about OA or Open Access (of journal articles) in the last five years, often in association with the APC (Article Processing Charge) model of funding such OA availability. Rather less discussed is how the model of the peer review of these articles might also evolve into an Open environment. Here I muse about two experiences I had recently.

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Dyotropic Ring Expansion: more mechanistic reality checks.

October 1st, 2017

I noted in my WATOC conference report a presentation describing the use of calculated reaction barriers (and derived rate constants) as mechanistic reality checks. Computations, it was claimed, have now reached a level of accuracy whereby a barrier calculated as being 6 kcal/mol too high can start ringing mechanistic alarm bells. So when I came across this article[1] in which calculated barriers for a dyotropic ring expansion observed under mild conditions in dichloromethane as solvent were used to make mechanistic inferences, I decided to explore the mechanism a bit further.

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References

  1. H. Santalla, O.N. Faza, G. Gómez, Y. Fall, and C. Silva López, "From Hydrindane to Decalin: A Mild Transformation through a Dyotropic Ring Expansion", Organic Letters, vol. 19, pp. 3648-3651, 2017. http://dx.doi.org/10.1021/acs.orglett.7b01621

Hydrogen capture by boron: a crazy reaction path!

September 21st, 2017

A recent article reports, amongst other topics, a computationally modelled reaction involving the capture of molecular hydrogen using a substituted borane (X=N, Y=C).[1] The mechanism involves an initial equilibrium between React and Int1, followed by capture of the hydrogen by Int1 to form a 5-coordinate borane intermediate (Int2 below, as per Figure 11). This was followed by assistance from a proximate basic nitrogen to complete the hydrogen capture via a TS involving H-H cleavage. The forward free energy barrier to capture was ~11 kcal/mol and ~4 kcal/mol in the reverse direction (relative to the species labelled Int1), both suitably low for reversible hydrogen capture. Here I explore a simple variation to this fascinating reaction.

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References

  1. L. Li, M. Lei, Y. Xie, H.F. Schaefer, B. Chen, and R. Hoffmann, "Stabilizing a different cyclooctatetraene stereoisomer", Proceedings of the National Academy of Sciences, vol. 114, pp. 9803-9808, 2017. http://dx.doi.org/10.1073/pnas.1709586114

The di-anion of dilithium (not the Star Trek variety): Another “Hyper-bond”?

September 16th, 2017

Early in 2011, I wrote about how the diatomic molecule Be2 might be persuaded to improve upon its normal unbound state (bond order ~zero) by a double electronic excitation to a strongly bound species. I yesterday updated this post with further suggestions and one of these inspired this follow-up.

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Two new types in the chemical bonding zoo: exo-bonds and hyper-bonds?

September 6th, 2017

The chemical bond zoo is relatively small (the bond being a somewhat fuzzy concept, I am not sure there is an actual count of occupants). So when two new candidates come along, it is worth taking notice. I have previously noted the Chemical Bonds at the 21st Century-2017: CB2017 Aachen conference, where both were discussed.

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One more WATOC 2017 Report.

August 31st, 2017

Conferences can be intense, and this one is no exception. After five days, saturation is in danger of setting in. But before it does, I include two more (very) brief things I have learnt.

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