Posts Tagged ‘Tutorial material’

Mechanistic arrow pushing. A proposed addition to its rules.

Wednesday, June 12th, 2013

A little while ago, I set out some interpretations of how to push curly arrows. I also appreciate that some theoretically oriented colleagues regard the technique as neither useful nor in the least rigorous, whereas towards the other extreme many synthetically minded chemists view the ability to push a reasonable set of arrows for a proposed mechanism as of itself constituting evidence in its favour.[1] Like any language for expressing ideas, the tool needs a grammar (rules) and a vocabulary, and perhaps also an ability to carry ambiguity. These thoughts surfaced again via a question asked of me by a student: “is the mechanism for the hydrogens in protonated benzene whizzing around the ring a [1,2] or a [1,6] pericyclic sigmatropic shift?”. 



  1. M.J. Gomes, L.F. Pinto, P.M. Glória, H.S. Rzepa, S. Prabhakar, and A.M. Lobo, "N-heteroatom substitution effect in 3-aza-cope rearrangements", Chemistry Central Journal, vol. 7, pp. 94, 2013.

Secrets of a university lecturer: 1981-1983.

Thursday, June 6th, 2013

Many moons ago, when I was a young(ish) lecturer, and much closer in time to my laboratory roots of organic synthesis, I made some chemistry videos. One of these has resurfaced, somewhat  (to me at least) unexpectedly. Nowadays of course, such demonstrations are all carried out using virtual simulations (Flash animations etc) as the equipment itself becomes less common.


Mechanism of the Van Leusen reaction.

Wednesday, May 29th, 2013

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.


Another Woodward pericyclic example dissected: all is not what it seems.

Wednesday, May 22nd, 2013

Here is another example gleaned from that Woodward essay of 1967 (Chem. Soc. Special Publications (Aromaticity), 1967, 21, 217-249), where all might not be what it seems.


Transition states for the (base) catalysed ring opening of propene epoxide.

Wednesday, May 8th, 2013

The previous post described how the acid catalysed ring opening of propene epoxide by an alcohol (methanol) is preceded by pre-protonation of the epoxide oxygen to form a “hidden intermediate” on the concerted intrinsic reaction pathway to ring opening. Here I take a look at the mechanism where a strong base is present, modelled by tetramethyl ammonium methoxide (R4N+.OMe), for the two isomers R=Me; R’=Me, R”=H and R’=H, R”=Me.


How to predict the regioselectivity of epoxide ring opening.

Sunday, April 28th, 2013

I recently got an email from a student asking about the best way of rationalising epoxide ring opening using some form of molecule orbitals. This reminded me of the famous experiment involving propene epoxide.[1]



  1. H.C. Chitwood, and B.T. Freure, "The Reaction of Propylene Oxide with Alcohols", Journal of the American Chemical Society, vol. 68, pp. 680-683, 1946.

Feist’s acid. Stereochemistry galore.

Thursday, April 4th, 2013

Back in the days (1893) when few compounds were known, new ones could end up being named after the discoverer. Thus Feist is known for the compound bearing his name; the 2,3 carboxylic acid of methylenecyclopropane (1, with Me replaced by CO2H). Compound 1 itself nowadays is used to calibrate chiroptical calculations[1], which is what brought it to my attention. But about four decades ago, and now largely forgotten, both 1 and the dicarboxylic acid were famous for the following rearrangement that gives a mixture of 2 and 3[2]. I thought I might here unpick some of the wonderfully subtle stereochemical analysis that this little molecule became subjected to.



  1. E.D. Hedegård, F. Jensen, and J. Kongsted, "Basis Set Recommendations for DFT Calculations of Gas-Phase Optical Rotation at Different Wavelengths", Journal of Chemical Theory and Computation, vol. 8, pp. 4425-4433, 2012.
  2. J.J. Gajewski, "Hydrocarbon thermal degenerate rearrangements. IV. Stereochemistry of the methylenecyclopropane self-interconversion. Chiral and achiral intermediates", Journal of the American Chemical Society, vol. 93, pp. 4450-4458, 1971.

The mechanism of ester hydrolysis via alkyl oxygen cleavage under a quantum microscope

Tuesday, April 2nd, 2013

My previous dissection of the mechanism for ester hydrolysis dealt with the acyl-oxygen cleavage route (red bond). There is a much rarer[1] alternative: alkyl-oxygen cleavage (green bond) which I now place under the microscope.



  1. C.A. Bunton, and J.L. Wood, "Tracer studies on ester hydrolysis. Part II. The acid hydrolysis of tert.-butyl acetate", Journal of the Chemical Society (Resumed), pp. 1522, 1955.

A sideways look at the mechanism of ester hydrolysis.

Friday, March 29th, 2013

The mechanism of ester hydrolysis is a staple of examination questions in organic chemistry. To get a good grade, one might have to reproduce something like the below. Here, I subject that answer to a reality check.


The mysterious (aromatic) structure of n-Butyl lithium.

Sunday, March 17th, 2013

n-Butyl lithium is hexameric in the solid state and in cyclohexane solutions. Why? Here I try to find out some of its secrets.