Archive for the ‘crystal_structure_mining’ Category

More examples of crystal structures containing embedded linear chains of iodines.

Sunday, October 17th, 2021

The previous post described the fascinating 170-year history of a crystalline compound known as Herapathite and its connection to the mechanism of the Finkelstein reaction via the complex of Na+I2 (or Na22+I42-). Both compounds exhibit (approximately) linear chains of iodine atoms in their crystal structures, a connection which was discovered serendipitously. Here I pursue a rather more systematic way of tracking down similar compounds.

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Herapathite: an example of (double?) serendipity.

Thursday, October 14th, 2021

On October 13, 2021, the historical group of the Royal Society of Chemistry organised a symposium celebrating ~150 years of the history of (molecular) chirality. We met for the first time in person for more than 18 months and were treated to a splendid and diverse program about the subject. The first speaker was Professor John Steeds from Bristol, talking about the early history of light and the discovery of its polarisation. When a slide was shown about herapathite[1] my “antennae” started vibrating. This is a crystalline substance made by combining elemental iodine with quinine in acidic conditions and was first discovered by William Herapath as long ago as 1852[2] in unusual circumstances. Now to the serendipity!

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References

  1. B. Kahr, J. Freudenthal, S. Phillips, and W. Kaminsky, "Herapathite", Science, vol. 324, pp. 1407-1407, 2009. http://dx.doi.org/10.1126/science.1173605
  2. W.B. Herapath, "XXVI. On the optical properties of a newly-discovered salt of quinine, which crystalline substance possesses the power of polarizing a ray of light, like tourmaline, and at certain angles of rotation of depolarizing it, like selenite", The London, Edinburgh, and Dublin Philosophical Magazine and Journal of Science, vol. 3, pp. 161-173, 1852. http://dx.doi.org/10.1080/14786445208646983

More record breakers for the anomeric effect involving C-N bonds.

Saturday, September 4th, 2021

An earlier post investigated large anomeric effects involving two oxygen atoms attached to a common carbon atom.

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Sterically stabilized cyclopropenylidenes. An example of Octopus publishing?

Sunday, August 15th, 2021

Whilst I was discussing the future of scientific publication in the last post, a debate was happening behind the scenes regarding the small molecule cyclopropenylidene. This is the smallest known molecule displaying π-aromaticity, but its high reactivity means that it is unlikely to be isolated in the condensed phase. A question in the discussion asked if substituting it with a large sterically hindering group such as R=Et3C might help prevent its dimerisation and hence allow for isolation of the monomer so that its properties can be studied.

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Another very large anomeric effect – with a twist.

Thursday, July 22nd, 2021

In the earlier post on the topic of anomeric effects, I identified a number of outliers associated with large differences in the lengths of two carbon-oxygen bonds sharing a common carbon atom.

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Two record breakers for the anomeric effect; one real, the other not.

Thursday, July 1st, 2021

The classic anomeric effect operates across a carbon atom attached to oxygens. One (of the two) lone pairs on the oxygen can donate into the σ* orbital of the C-O of the other oxygen (e.g. the red arrows) tending to weaken that bond whilst strengthening the donor oxygen C-O bond. Vice versa means e.g. the blue arrows weakening the other C-O bond. This effect tends to increase charge separation and the question then arises: how large can this effect get? To try to find out, we are going to do some crystal structure mining in this post!

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A reality-based suggestion for a molecule with a metal M⩸N quadruple bond.

Thursday, May 13th, 2021

I noted in an earlier post the hypothesized example of (CO)3Fe⩸C[1] as exhibiting a carbon to iron quadruple bond and which might have precedent in known five-coordinate metal complexes where one of the ligands is a “carbide” or C ligand. I had previously mooted that the Fe⩸C combination might be replaceable by an isoelectronic Mn⩸N pair which could contain a quadruple bond to the nitrogen. An isoelectronic alternative to FeC could also be FeN+. Here I explore the possibility of realistic candidates for such bonded nitrogen.

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References

  1. A.J. Kalita, S.S. Rohman, C. Kashyap, S.S. Ullah, and A.K. Guha, "Transition metal carbon quadruple bond: viability through single electron transmutation", Physical Chemistry Chemical Physics, vol. 22, pp. 24178-24180, 2020. http://dx.doi.org/10.1039/d0cp03436c

Two new reality-based suggestions for molecules with a metal M⩸C quadruple bond.

Saturday, May 8th, 2021

Following from much discussion over the last decade about the nature of C2, a diatomic molecule which some have suggested sustains a quadruple bond between the two carbon atoms, new ideas are now appearing for molecules in which such a bond may also exist between carbon and a transition metal atom. A suggested, albeit hypothetical example was C⩸Fe(CO)3[1]. Iron has a [Ar].3d6.4s2 electronic configuration and if we ionise to balance a C4- ligand, the iron becomes formally FeVI or [Ar].3d4. By adding 14 electrons deriving from the seven “bonds” to the 3d4, including a quadruple count from carbon, the Fe formally completes its 18-electron valence shell, as also found in e.g. Ferrocene.

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References

  1. A.J. Kalita, S.S. Rohman, C. Kashyap, S.S. Ullah, and A.K. Guha, "Transition metal carbon quadruple bond: viability through single electron transmutation", Physical Chemistry Chemical Physics, vol. 22, pp. 24178-24180, 2020. http://dx.doi.org/10.1039/d0cp03436c

The thermal reactions … took precisely the opposite stereochemical course to that which we had predicted

Wednesday, January 20th, 2021

The quote of the post title comes from R. B. Woodward explaining the genesis of the discovery of what are now known as the Woodward-Hoffmann rules for pericyclic reactions.[1] I first wrote about this in 2012, noting that “for (that) blog, I do not want to investigate the transition states”. Here I take a closer look at this aspect.

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References

  1. R.B. Woodward, and R. Hoffmann, "Stereochemistry of Electrocyclic Reactions", Journal of the American Chemical Society, vol. 87, pp. 395-397, 1965. http://dx.doi.org/10.1021/ja01080a054

Fascinating stereoelectronic control in Metaldehyde and Chloral.

Tuesday, June 9th, 2020

Metaldehyde is an insecticide used to control slugs. When we unsuccessfully tried to get some recently, I discovered it is now deprecated in the UK. So my immediate reaction was to look up its structure to see if that cast any light (below, R=CH3, shown as one stereoisomer).

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