Posts Tagged ‘microwave’

Interactions responsible for the lowest energy structure of the trimer of fluoroethanol.

Friday, October 23rd, 2015

Steve Bachrach on his own blog has commented on a recent article[1] discussing the structure of the trimer of fluoroethanol. Rather than the expected triangular form with three OH—O hydrogen bonds, the lowest energy form only had two such bonds, but it matched the microwave data much better. Here I explore this a bit more.

The stability of the lowest energy form, as is evident from the title of the article, was attributed to unusual H-Bond topology and bifurcated H-bonds as teased out from bond critical points in the QTAIM analysis of the topology of the electron density. Here I add to this analysis by displaying the computed NCI (non-covalent-interaction)[2] surfaces, as you might see in the comment I posted on Steve’s blog. In essence, the QTAIM had revealed bond paths connecting an oxygen to a H-C and also a bifurcation from an F to two H-C atoms, shown with orange lines in the diagram there. What might an NCI analysis reveal? The analysis[3] is shown below, where I have added orange arrows to indicate the location of these bond paths. The arrows point to an NCI feature which corresponds to a weak dispersion-like stabilisation.

Click for 3D

Click for 3D

However, as you can spot from the diagram above (and inspect in a 3D sense if you click on the diagram above to load a 3D Jmol model), there are many more regions where NCI features appear. The most obvious are the blue-coded ones, which in fact represent the conventional O…HO hydrogen bonds, but there are plenty of others as well, including a cyan one which is not part of the published attributions. I will recapitulate my comment on Steve’s blog; the point I make here is that apart from the two regions which have been picked out in the article as responsible for stabilisation of the low energy structure, there are around 4-5 OTHER regions that also may be stabilising but for which there is no corresponding critical point in the density. So whilst the above origins are not incorrect, they may well be very incomplete!.

There is a tendency to only highlight features which can be named, and perhaps to ignore or pay less attention to those which have no name. The latter may in fact be more common than we imagine, and cumulatively they can often have a big impact.


Postscript: A structure has recently been reported[4],[5] illustrating an exceptionally strong OH…F interaction of 1.52Å. This is noteworthy because such hydrogen bonds are rarely strong and indeed even their very existence is controversial. The cyan NCI region mentioned above is just such an interaction (of length ~2.0Å).


References

  1. J. Thomas, X. Liu, W. Jäger, and Y. Xu, "Unusual H‐Bond Topology and Bifurcated H‐bonds in the 2‐Fluoroethanol Trimer", Angewandte Chemie International Edition, vol. 54, pp. 11711-11715, 2015. https://doi.org/10.1002/anie.201505934
  2. J. Contreras-García, W. Yang, and E.R. Johnson, "Analysis of Hydrogen-Bond Interaction Potentials from the Electron Density: Integration of Noncovalent Interaction Regions", The Journal of Physical Chemistry A, vol. 115, pp. 12983-12990, 2011. https://doi.org/10.1021/jp204278k
  3. H.S. Rzepa, and H.S. Rzepa, "C 6 H 15 F 3 O 3", 2015. https://doi.org/10.14469/ch/191558
  4. M.D. Struble, C. Kelly, M.A. Siegler, and T. Lectka, "Search for a Strong, Virtually “No‐Shift” Hydrogen Bond: A Cage Molecule with an Exceptional OH⋅⋅⋅F Interaction", Angewandte Chemie International Edition, vol. 53, pp. 8924-8928, 2014. https://doi.org/10.1002/anie.201403599
  5. Struble, Mark D.., Kelly, Courtney., Siegler, Maxime A.., and Lectka, Thomas., "CCDC 991440: Experimental Crystal Structure Determination", 2014. https://doi.org/10.5517/cc128nyy

The dawn of organic reaction mechanism: the prequel.

Sunday, November 13th, 2011

Following on from Armstrong’s almost electronic theory of chemistry in 1887-1890, and Beckmann’s radical idea around the same time that molecules undergoing transformations might do so via a reaction mechanism involving unseen intermediates (in his case, a transient enol of a ketone) I here describe how these concepts underwent further evolution in the early 1920s. My focus is on Edith Hilda Usherwood, who was then a PhD student at Imperial College working under the supervision of Martha Whitely.1

The doctoral degree itself had only been introduced into British universities in 1919,1 and so Usherwood was very much a forerunner of the modern system of training.The academic staff and students at Imperial totalled 30, making it one of the largest research schools in UK chemistry at the time. Usherwood’s project was on tautomers, or isomers of molecules which differ only in the position of a labile hydrogen atom. The then quite novel electron-pair symbolism introduced by G. N. Lewis’ in 1916 was adopted to represent two tautomeric equilibria (the supposed mobile or tautomeric hydrogens being enclosed in […])2

  1. [H]C:::N ⇔ C::N[H]
  2. [H]C:::CH ⇔ C::CH[H]

or in our more modern representation (in which lines replace colons, and charges are used to ensure the octet rule is adhered to when possible):

  1. H-C≡N ⇔ C≡N+-H
  2. HC≡CH ⇔ :C=CH2

Modern structural techniques such as electron diffraction or microwave spectroscopies not yet existing, the problem was tackled using specific heat measurements as a function of temperature. This method suggested to Usherwood that for e.g. equilibrium 2, the concentration of iso-acetylene (we now call this vinylidene) was insignificant at ordinary temperatures, but it became appreciable between 200-300°C. Further evidence was claimed for the formation of the “unseen” vinylidene by observing ketene as a by-product of the oxidation of acetylene. This article very much set the trend of (an almost mandatory) speculation on the outcome of (nowadays much more complex) reactions by the need to formulate a reaction mechanism in which various (otherwise undetected but) plausible intermediates are involved.

Moving on some 90 years, and how might one approach such a problem nowadays? Well, I have oft argued on this blog that a good place to obtain an immediate reality check on a proposed mechanism is a calculation. It will come as no surprise that a very accurate calculation can be done on the systems shown above. For example, CCSD(T)/cc-pVTZ will yield a free energy for the equilibria with a pretty small error (< 1 kcal/mol). We use ΔG = -RT Ln K to inter-convert free energies and equilibrium constants. If we are generous and state that in order to observe an appreciable concentration of a minor species, the equilibrium constant can be no smaller than 10-3, its energy cannot be greater than 4 kcal/mol above the more abundant isomer. Our reality check will be to see if the free energy of vinylidene is indeed no more than 4 kcal/mol greater than acetylene. Well, CCSD(T)/cc-pVTZ predicts vinylidene is 41.3 kcal/mol higher @298K, reduced to 33.8 @2000K (and before you ask, these results took a total of perhaps 30 minutes to obtain).

In 1924, the concept of calculating the relative energies of two species using first principles was not even a glimmer on the horizon. The nature of mechanisms was slowly and often painfully established by recourse to experiments alone. And many of the unseen intermediates often remained just such, their existence only inferred indirectly from the models one constructed (of specify heats in Usherwood’s case). It is perhaps no great surprise that these models do not always stand the test of time. In this case, within a year of Usherwood’s publication, Partington was suggesting that the model for the specific heats of acetylene should have included allowance for polymer formation.3 The modern take, armed with the calculation I note above, might in fact side with Partington after all. As for the formation of ketene by oxidation, it is indeed known that (peracid) oxidation of an alkyne will produce ketene, but the modern mechanism (an interesting exercise in arrow pushing for a student) does not involve vinylidene intermediates.

I will add at this point that Hilda Usherwood was married to Christopher Ingold, and the pair of them subsequently published many of the seminal articles in what became known as physical organic chemistry. That legacy continues to this day with (as I noted above) the almost mandatory speculation about the mechanism of any new reaction. But it is only in the last five years or so that these speculations have started to be increasingly tested against reliably accurate computation. A new era is underway.


1 My post was inspired by reading W. H. Brock, “The case of the Poisonous Socks”, chapter 28, RSC Publishing, 2011, 978-1-84973-324-3.

2 These representations are taken from ref 1, p 225 (and including a correction of replacing C:C as drawn there by C::C). The original article apparently appeared in the proceedings of the British Association of 1924, which is not yet available online.

3 Brock, in ref 1, p226, suggests that Usherwood stood her ground on this one, and won her case by showing that Partington’s evidence for polymerization was valid for only a small part of the temperature range she had investigated. I have not managed to track down the original sources for this exchange.