Posts Tagged ‘Physical organic chemistry’

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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A periodic table for anomeric centres.

Saturday, August 6th, 2016
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In the last few posts, I have explored the anomeric effect as it occurs at an atom centre X. Here I try to summarise the atoms for which the effect is manifest in crystal structures.

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Anomeric effects at boron, silicon and phosphorus.

Friday, July 1st, 2016
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The anomeric effect occurs at 4-coordinate (sp3) carbon centres carrying two oxygen substituents and involves an alignment of a lone electron pair on one oxygen with the adjacent C-O σ*-bond of the other oxygen. Here I explore whether other centres can exhibit the phenomenon. I start with 4-coordinate boron, using the crystal structure search definition below (along with R < 0.1, no disorder, no errors).[1]anomeric-bo-sq

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References

  1. Henry Rzepa., "Anomeric effects at boron, silicon and phosphorus.", 2016. http://dx.doi.org/10.14469/hpc/696

How does an OH or NH group approach an aromatic ring to hydrogen bond with its π-face?

Wednesday, June 22nd, 2016
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I previously used data mining of crystal structures to explore the directing influence of substituents on aromatic and heteroaromatic rings. Here I explore, quite literally, a different angle to the hydrogen bonding interactions between a benzene ring and OH or NH groups.

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The geometries of 5-coordinate compounds of group 14 elements.

Monday, May 30th, 2016
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This is a follow-up to one aspect of the previous two posts dealing with nucleophilic substitution reactions at silicon. Here I look at the geometries of 5-coordinate compounds containing as a central atom 4A = Si, Ge, Sn, Pb and of the specific formula C34AO2 with a trigonal bipyramidal geometry. This search arose because of a casual comment I made in the earlier post regarding possible cooperative effects between the two axial ligands (the ones with an angle of ~180 degrees subtended at silicon). Perhaps the geometries might expand upon this comment?

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What is the approach trajectory of enhanced (super?) nucleophiles towards a carbonyl group?

Wednesday, May 11th, 2016
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I have previously commented on the Bürgi–Dunitz angle, this being the preferred approach trajectory of a nucleophile towards the electrophilic carbon of a carbonyl group. Some special types of nucleophile such as hydrazines (R2N-NR2) are supposed to have enhanced reactivity[1] due to what might be described as buttressing of adjacent lone pairs. Here I focus in on how this might manifest by performing searches of the Cambridge structural database for intermolecular (non-bonded) interactions between X-Y nucleophiles (X,Y= N,O,S) and carbonyl compounds OC(NM)2.

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References

  1. G. Klopman, K. Tsuda, J. Louis, and R. Davis, "Supernucleophiles—I", Tetrahedron, vol. 26, pp. 4549-4554, 1970. http://dx.doi.org/10.1016/S0040-4020(01)93101-1