The New Clayden pp. 909 – 930

p. 915 — A bit more could be made of the the prenyl group, rather than just showing its structure.  A huge class of natural products (camphor, vitamin A, cholesterol precursors and in fact those of all steroids) can be considered as various ways of linking the 5 carbons of the prenyl group to form the their carbon skeleton.  Note that the aldehyde precursor of citral also has the prenyl backbone. 

p. 918 — So S, and Se have oxidation states of S– (easy) to understand, S -4 and S -6 (why not S – 5 and S – 7?).  This is unfortunately typical of the generally unsatisfying way organic chemistry treats elements below the second row in the periodic table.  Perhaps things will improve when metallo-organic chemistry of the higher rows is discussed.  Contrast this to the excellent and detailed explanation of pericyclic reaction stereochemistry given by the Woodward  Hoffmann rules in examples later in the chapter.

23 Sep ’12 — Irrelevant to the discussion — but Nature for 13 Sep ’12 (vol. 489 pp. 278 – 281) has a new and cute prostaglandin synthesis involving a double aldol reaction which shortens it to 7 steps.  900 pages of the new Clayden are enough to understand almost all of it (which is why I’m going to get through it before reading anything else)   The paper uses the retrosynthetic disconnection analysis described in Clayden, so that isn’t an academic exercise (something I was wondering about).   In the crucial reaction (the double aldol) two catalysts were used (one was S-proline to get more of one diastereomer — they show why in figure 3), and the order of the addition of the two catalysts and the time between the additions was crucial in increasing yield.  Some poor grad student must have run the reaction a zillion times varying the conditions.

p. 919 — Even the elegantly written Clayden has trouble explaining the [1,5] sigmatropic shift.  Here’s what they say — “The figure ‘1’ in the square brackets shows that the same atom is at one end of the new sigma bond as was at one end of the old sigma bond.”  One picture is worth a thousand words. 

p. 920 — The fused ring systems from intramolecular Diels Alder reactions shown here resemble several natural products — is this their biosynthetic route?  It seems to be given the endiandric acid A synthesis given on p. 926.

p. 925 — It might be a good idea when first discussing the Woodward Hoffmann rules initially (p. 933) to point out that they predict obscure stereochemistry, unpredictable by other methods.  Otherwise it seems like a lot of terminology without much point. You do note this on p. 893 — but saying something like the above rather than just  ‘very helpful’ would be better. 

p. 929 — Who would have predicted the formation of a cyclobutene ring by a rearaangement of a fairly unstressed cyclobutane/cyclohexane fused molecule?  Perhaps the exomethylene group on the cyclobutane drove it, as this would make the cyclobutane ring more strained. 
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  • MJ  On September 26, 2012 at 9:17 am

    “This is unfortunately typical of the generally unsatisfying way organic chemistry treats elements above the second row in the periodic table.”

    Remember, chemistry is the same community that teaches the octet rule although we all very well know that it only really applies to elements in the second row.

    “Some poor grad student must have run the reaction a zillion times varying the conditions.”

    I’ve always wondered if synthetic chemists ever have the urge to just throw their hands up in the air and say, “we should just figure out how to utilize enzymes to do this chemistry in the test tube – they can do it under generally modest pressure/temperature conditions in aqueous solution, after all.” Heh.

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