Tag Archives: Mathematical notation and why it’s confusing

The New Clayden pp. 877 – 908

p. 878 — “The transition state has 6 delocalized pi electrons and thus is aromatic in character”.  Numerically yes, but the transition state isn’t planar, and there is all sorts of work showing how important planarity is to aromaticity. 

p. 881 — It seems to me that the arrow is wrong in the equation at the bottom. Entropy should increase when a Diels Alder product is broken apart, and since deltaG = deltaH  – T * deltaS heating the product should break it apart not cause it to form.  I guess the heat shown is required to increase molecular velocity so that collisions result in reaction.   Enough kinetic energy will blow anything apart (see Higgs particle).

p. 890 — “It is not cheating to use the regioselectivity of chemical reactions to tell us about the coefficients of the orbitals involved.”    I do think that this sort of thing is  cheating when you use the regioselectivity of chemical reactions as an explanation.  They are adding nothing new.  A real explanation predicts new phenomena, the way the anomeric effect does, for example.  You should contemplate the point at which a description of something becomes an explanation (e.g. epistemology).   It’s not the case here, but it was the case for Newton’s laws of gravitation.  Famously he said Hypotheses non dingo (“I frame no hypotheses”).  It appears in the following

I have not as yet been able to discover the reason for these properties of gravity from phenomena, and I do not feign hypotheses.

Yet his laws of gravity were used to predict all sorts of events never before seen, so they are explanatory in some sense.  

This sort of thing is just what a neurologist experiences learning functional neuroanatomy (e.g.  which part of the nervous system has which function).  Initially almost all of it was developed by studying neurologic deficits due to various localized lesions of the brain and spinal cord.  There’s a huge caveat involved — pulling the plug on a radio will stop the sound, but that isn’t how the sound is produced.  People with lesions of the occipital lobe lose the ability to see in certain directions (parts of their visual fields).  Understanding HOW the occipital lobe processes sensory input from the eyes has taken 50 years and is far from over.  

p. 892 — Unfortunately the rationale behind  the Woodward Hoffmann rules isn’t covered, so it appears incredibly convoluted and arbitrary.  Read the book — “The Control of Orbital Symmetry” which they wrote.  Also, unfortunately, the description of the rules uses the term ‘component’ in two ways.  At step two butadiene and the dienophile are each considered a component, as they are in steps 3, 4, and 5, then the two are mushed together into a single component in step 6. 

p. 894 — I haven’t been looking at the animations for a while, but those of the Diels Alder type reactions are incredible, and almost sexual.  You can rotate the two molecules in space and watch them come together and react.

p. 894 –“Remember, the numbers in brackets, [ 4 + 2 ] etc., refer to the numbers of atoms.  The numbers (4q +2)s and (4r)s in The Woodward Hoffman (should be Hoffmann) refer to the numbers of electrons.”  This is so very like math, where nearly identical characters are used to refer to quite different things.  Bold capital X might mean one thing, italic x another, script X still another.  They all sound the same when you mentally read them to yourself.  It makes life confusing. 

p. 894 — The Alder ene reactions — quite unusual.  The worst thing is that I remember nothing about them from years ago.  They must have been around as they were discovered by Alder himself (who died in 1958).  They produce some rather remarkable transformations, the synthesis of menthol from citronellal being one.  I wonder if they are presently used much in synthetic organic chemistry. 

p. 900 — How do you make OCN – SO2Cl, and why is it available commercially?

p. 904 — The synthesis of the sulfur containing 5 membered ring of biotin is a thing of beauty.  It’s extremely non-obvious beginning with a 7 membered ring with no sulfur at all. 
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