Posts Tagged ‘Physical organic chemistry’

Organocatalytic cyclopropanation of an enal: (computational) assignment of absolute configurations.

Saturday, September 1st, 2018
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I am exploring the fascinating diverse facets of a recently published laboratory experiment for undergraduate students.[1] Previously I looked at a possible mechanistic route for the reaction between an enal (a conjugated aldehyde-alkene) and benzyl chloride catalysed by base and a chiral amine, followed by the use of NMR coupling constants to assign relative stereochemistries. Here I take a look at some chiroptical techniques which can be used to assign absolute stereochemistries (configurations).

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References

  1. M. Meazza, A. Kowalczuk, S. Watkins, S. Holland, T.A. Logothetis, and R. Rios, "Organocatalytic Cyclopropanation of (E)-Dec-2-enal: Synthesis, Spectral Analysis and Mechanistic Understanding", Journal of Chemical Education, 2018. http://dx.doi.org/10.1021/acs.jchemed.7b00566

Tetrahedral carbon and cyclohexane.

Wednesday, August 22nd, 2018
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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. W.H. Bragg, and W.L. Bragg, "The Structure of the Diamond", Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, 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

The conformation of enols: revealed and explained.

Thursday, April 6th, 2017
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Enols are simple compounds with an OH group as a substituent on a C=C double bond and with a very distinct conformational preference for the OH group. Here I take a look at this preference as revealed by crystal structures, with the theoretical explanation.

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What is the (calculated) structure of a norbornyl cation anion-pair in water?

Saturday, April 1st, 2017
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In a comment appended to an earlier post, I mused about the magnitude of the force constant relating to the interconversion between a classical and a non-classical structure for the norbornyl cation. Most calculations indicate the force constant for an “isolated” symmetrical cation is +ve, which means it is a true minimum and not a transition state for a [1,2] shift. The latter would have been required if the species equilibrated between two classical carbocations. I then pondered what might happen to both the magnitude and the sign of this force constant if various layers of solvation and eventually a counter-ion were to be applied to the molecule, so that a bridge of sorts between the different states of solid crystals, superacid and aqueous solutions might be built.

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Silyl cations?

Thursday, March 23rd, 2017
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It is not only the non-classical norbornyl cation that has proved controversial in the past. A colleague mentioned at lunch (thanks Paul!) that tri-coordinate group 14 cations such as R3Si+ have also had an interesting history.[1] Here I take a brief look at some of these systems.

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References

  1. J.B. Lambert, Y. Zhao, H. Wu, W.C. Tse, and B. Kuhlmann, "The Allyl Leaving Group Approach to Tricoordinate Silyl, Germyl, and Stannyl Cations", Journal of the American Chemical Society, vol. 121, pp. 5001-5008, 1999. http://dx.doi.org/10.1021/ja990389u

Expanding on the curious connection between the norbornyl cation and small-ring aromatics.

Sunday, March 12th, 2017
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This is another of those posts that has morphed from an earlier one noting the death of the great chemist George Olah. The discussion about the norbornyl cation concentrated on whether this species existed in a single minimum symmetric energy well (the non-classical Winstein/Olah proposal) or a double minimum well connected by a symmetric transition state (the classical Brown proposal). In a comment on the post, I added other examples in chemistry of single/double minima, mapped here to non-classical/classical structures. I now expand on the examples related to small aromatic or anti-aromatic rings.

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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

Long C=C bonds.

Thursday, December 1st, 2016
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Following on from a search for long C-C bonds, here is the same repeated for C=C double bonds.

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A periodic table for anomeric centres, this time with quantified interactions.

Monday, August 8th, 2016
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The previous post contained an exploration of the anomeric effect as it occurs at an atom centre X for which the effect is manifest in crystal structures. Here I quantify the effect, by selecting the test molecule MeO-X-OMe, where X is of two types:

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