Henry Rzepa's Blog Chemistry with a twist

August 22, 2018

Tetrahedral carbon and cyclohexane.

Following the general recognition of carbon as being tetrahedrally tetravalent in 1869 (Paterno) and 1874 (Van’t Hoff and Le Bell), an early seminal exploitation of this to the conformation of cyclohexane was by Hermann Sachse in 1890.[1] This was verified when the Braggs in 1913[2], followed by an oft-cited article by Mohr in 1918,[3] established the crystal structure of diamond as comprising repeating rings in the chair conformation. So by 1926, you might imagine that the shape (or conformation as we would now call it) of cyclohexane would be well-known. No quite so for everyone!

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References

  1. H. Sachse, "Ueber die geometrischen Isomerien der Hexamethylenderivate", Berichte der deutschen chemischen Gesellschaft, vol. 23, pp. 1363-1370, 1890. http://dx.doi.org/10.1002/cber.189002301216
  2. "The structure of the diamond", Proceedings of the Royal Society of London. Series A, Containing Papers of a Mathematical and Physical Character, vol. 89, pp. 277-291, 1913. http://dx.doi.org/10.1098/rspa.1913.0084
  3. E. Mohr, "Die Baeyersche Spannungstheorie und die Struktur des Diamanten", Journal f�r Praktische Chemie, vol. 98, pp. 315-353, 1918. http://dx.doi.org/10.1002/prac.19180980123

May 6, 2017

How does carbon dioxide coordinate to a metal?

Mention carbon dioxide (CO2) to most chemists and its properties as a metal ligand are not the first aspect that springs to mind. Here thought I might take a look at how it might act as such.

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April 13, 2017

The π-π stacking of aromatic rings: what is their closest parallel approach?

Layer stacking in structures such as graphite is well-studied. The separation between the π-π planes is ~3.35Å, which is close to twice the estimated van der Waals (vdW) radius of carbon (1.7Å). But how much closer could such layers get, given that many other types of relatively weak interaction such as hydrogen bonding can contract the vdW distance sum by up to ~0.8Å or even more? This question was prompted by the separation calculated for the ion-pair cyclopropenium cyclopentadienide (~2.6-2.8Å).

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March 31, 2017

Supporting information: chemical graveyard or invaluable resource for chemical structures.

Nowadays, data supporting most publications relating to the synthesis of organic compounds is more likely than not to be found in associated “supporting information” rather than the (often page limited) article itself. For example, this article[1] has an SI which is paginated at 907; almost a mini-database in its own right! Here I ponder whether such dissemination of data is FAIR (Findable, accessible, interoperable and re-usable).[2]

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References

  1. J.M. Lopchuk, K. Fjelbye, Y. Kawamata, L.R. Malins, C. Pan, R. Gianatassio, J. Wang, L. Prieto, J. Bradow, T.A. Brandt, M.R. Collins, J. Elleraas, J. Ewanicki, W. Farrell, O.O. Fadeyi, G.M. Gallego, J.J. Mousseau, R. Oliver, N.W. Sach, J.K. Smith, J.E. Spangler, H. Zhu, J. Zhu, and P.S. Baran, "Strain-Release Heteroatom Functionalization: Development, Scope, and Stereospecificity", Journal of the American Chemical Society, vol. 139, pp. 3209-3226, 2017. http://dx.doi.org/10.1021/jacs.6b13229
  2. M.D. Wilkinson, M. Dumontier, I.J. Aalbersberg, G. Appleton, M. Axton, A. Baak, N. Blomberg, J. Boiten, L.B. da Silva Santos, P.E. Bourne, J. Bouwman, A.J. Brookes, T. Clark, M. Crosas, I. Dillo, O. Dumon, S. Edmunds, C.T. Evelo, R. Finkers, A. Gonzalez-Beltran, A.J. Gray, P. Groth, C. Goble, J.S. Grethe, J. Heringa, P.A. ’t Hoen, R. Hooft, T. Kuhn, R. Kok, J. Kok, S.J. Lusher, M.E. Martone, A. Mons, A.L. Packer, B. Persson, P. Rocca-Serra, M. Roos, R. van Schaik, S. Sansone, E. Schultes, T. Sengstag, T. Slater, G. Strawn, M.A. Swertz, M. Thompson, J. van der Lei, E. van Mulligen, J. Velterop, A. Waagmeester, P. Wittenburg, K. Wolstencroft, J. Zhao, and B. Mons, "The FAIR Guiding Principles for scientific data management and stewardship", Scientific Data, vol. 3, 2016. http://dx.doi.org/10.1038/sdata.2016.18

July 25, 2015

Intermolecular atom-atom bonds in crystals? The O…O case.

I recently followed this bloggers trail; link1link2 to arrive at this delightful short commentary on atom-atom bonds in crystals[1] by Jack Dunitz. Here he discusses that age-old question (to chemists), what is a bond? Even almost 100 years after Gilbert Lewis’ famous analysis,[2] we continue to ponder this question. Indeed, quite a debate on this topic broke out in a recent post here. My eye was caught by one example in Jack's article: "The close stacking of planar anions, as occurs in salts of croconic acid …far from producing a lowering of the crystal energy, this stacking interaction in itself leads to an increase by several thousand kJ mol−1 arising from Coulombic repulsion between the doubly negatively charged anions" I thought I might explore this point a bit further in this post.

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References

  1. J.D. Dunitz, "Intermolecular atom–atom bonds in crystals?", IUCrJ, vol. 2, pp. 157-158, 2015. http://dx.doi.org/10.1107/S2052252515002006
  2. G.N. Lewis, "THE ATOM AND THE MOLECULE.", Journal of the American Chemical Society, vol. 38, pp. 762-785, 1916. http://dx.doi.org/10.1021/ja02261a002

April 26, 2015

Allotropic halogens.

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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