Henry Rzepa's Blog Chemistry with a twist

April 20, 2014

Ribulose-1,5-bisphosphate + carbon dioxide → carbon fixation!

Ribulose-1,5-bisphosphate reacts with carbon dioxide to produce 3-keto-2-carboxyarabinitol 1,5-bisphosphate as the first step in the biochemical process of carbon fixation. It needs an enzyme to do this (Ribulose-1,5-bisphosphate carboxylase/oxygenase, or RuBisCO) and lots of ATP (adenosine triphosphate, produced by photosynthesis). Here I ask what the nature of the uncatalysed transition state is, and hence the task that might be facing the catalyst in reducing the activation barrier to that of a facile thermal reaction. I present my process in the order it was done.

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October 20, 2013

Six vs ten aromatic electrons?

Filed under: Interesting chemistry — Tags: , — Henry Rzepa @ 3:57 pm

Homoaromaticity is a special case of aromaticity in which π-conjugation is interrupted by a single sp3 hybridized carbon atom (it is sometimes referred to as a suspended π-bond with no underlying σ-foundation). But consider the carbene shown below. This example comes from a recently published article[1] which was highlighted on Steve Bachrach’s blog. Here aromaticity has resulted from a slightly different phenomenon, whereby a 4π-electron planar (and hence nominally anti-aromatic) molecule is elevated to aromatic peerage by promoting the two carbene σ-electrons to have π-status. 

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References

  1. B. Chen, A.Y. Rogachev, D.A. Hrovat, R. Hoffmann, and W.T. Borden, "How to Make the σ0π2 Singlet the Ground State of Carbenes", Journal of the American Chemical Society, vol. 135, pp. 13954-13964, 2013. http://dx.doi.org/10.1021/ja407116e

May 29, 2013

Mechanism of the Van Leusen reaction.

Filed under: Uncategorised — Tags: , , , — Henry Rzepa @ 2:23 pm

This is a follow-up to comment posted by Ryan, who asked about isocyanide’s role (in the form of the anion of tosyl isocyanide, or TosMIC): “In Van Leusen, it (the isocyanide) acts as an electrophile”. The Wikipedia article (recently updated by myself) shows nucleophilic attack by an oxy-anion on the carbon of the C≡N group, with the isocyanide group acting as the acceptor of these electrons (in other words, the electrophile). In the form shown below, one negatively charged atom appears to be attacking another also carrying a negative charge. Surely this breaks the rules that like charges repel? So we shall investigate to see if this really happens.

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July 6, 2011

Scalemic molecules: a cheminformatics challenge!

A scalemic molecule is the term used by Eliel to describe any non-racemic chiral compound. Synthetic chemists imply it when they describe a synthetic product with an observable enantiomeric excess or ee (which can range from close to 0% to almost 100%). There are two cheminformatics questions of interest to me: (more…)

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