Posts Tagged ‘Nature’

π-Facial hydrogen bonds to alkenes (revisited): how close can an acidic hydrogen approach?

Saturday, April 15th, 2017
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Back in the early 1990s, we first discovered the delights of searching crystal structures for unusual bonding features.[1] One of the first cases was a search for hydrogen bonds formed to the π-faces of alkenes and alkynes. In those days the CSD database of crystal structures was a lot smaller (<80,000 structures; it’s now ten times larger) and the search software less powerful. So here is an update. 

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References

  1. H.S. Rzepa, M.H. Smith, and M.L. Webb, "A crystallographic AM1 and PM3 SCF-MO investigation of strong OH ⋯π-alkene and alkyne hydrogen bonding interactions", J. Chem. Soc., Perkin Trans. 2, pp. 703-707, 1994. http://dx.doi.org/10.1039/P29940000703

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

Thursday, April 13th, 2017
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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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Supporting information: chemical graveyard or invaluable resource for chemical structures.

Friday, March 31st, 2017
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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, pp. 160018, 2016. http://dx.doi.org/10.1038/sdata.2016.18

George Olah and the norbornyl cation.

Friday, March 10th, 2017
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George Olah passed away on March 8th. He was part of the generation of scientists in the post-war 1950s who had access to chemical instrumentation that truly revolutionised chemistry. In particular he showed how the then newly available NMR spectroscopy illuminated structures of cations in solvents such “Magic acid“. The obituaries will probably mention his famous “feud” with H. C. Brown over the structure of the norbornyl cation (X=CH2+), implicated in the mechanism of many a solvolysis reaction that characterised the golden period of physical organic chemistry just before and after WWII. 

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Stable “unstable” molecules: a crystallographic survey of cyclobutadienes and cyclo-octatetraenes.

Sunday, March 5th, 2017
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Cyclobutadiene is one of those small iconic molecules, the transience and instability of which was explained theoretically long before it was actually detected in 1965.[1] Given that instability, I was intrigued as to how many crystal structures might have been reported for this ring system, along with the rather more stable congener cyclo-octatetraene. Here is what I found.

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References

  1. L. Watts, J.D. Fitzpatrick, and R. Pettit, "Cyclobutadiene", Journal of the American Chemical Society, vol. 87, pp. 3253-3254, 1965. http://dx.doi.org/10.1021/ja01092a049

More tetrahedral fun. Spherical aromaticity (and other oddities) in N4 and C4 systems?

Thursday, March 2nd, 2017
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The thread thus far. The post about Na2He introduced the electride anionic counter-ion to Na+ as corresponding topologically to a rare feature known as a non-nuclear attractor. This prompted speculation about other systems with such a feature, and the focus shifted to a tetrahedral arrangement of four hydrogen atoms as a dication, sharing a total of two valence electrons. The story now continues here.

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The H4 (2+) dication and its bonding.

Wednesday, February 15th, 2017
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This post arose from a comment attached to the post on Na2He and relating to peculiar and rare topological features of the electron density in molecules called non-nuclear attractors. This set me thinking about other molecules that might exhibit this and one of these is shown below.

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Braiding a molecular knot with eight crossings.

Friday, January 20th, 2017
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This is one of those posts of a molecule whose very structure is interesting enough to merit a picture and a 3D model. The study[1] reports a molecular knot with the remarkable number of eight crossings.

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References

  1. J.J. Danon, A. Krüger, D.A. Leigh, J. Lemonnier, A.J. Stephens, I.J. Vitorica-Yrezabal, and S.L. Woltering, "Braiding a molecular knot with eight crossings", Science, vol. 355, pp. 159-162, 2017. http://dx.doi.org/10.1126/science.aal1619

The “hydrogen bond”; its early history.

Saturday, December 31st, 2016
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My holiday reading has been Derek Lowe’s excellent Chemistry Book setting out 250 milestones in chemistry, organised by year. An entry for 1920 entitled hydrogen bonding seemed worth exploring in more detail here.

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The dipole moments of highly polar molecules: glycine zwitterion.

Saturday, December 24th, 2016
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The previous posts produced discussion about the dipole moments of highly polar molecules. Here to produce some reference points for further discussion I look at the dipole moment of glycine, the classic zwitterion (an internal ion-pair).

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