The New Clayden pp. 1029 – 1068

p. 1034 — “Small amounts of radicals are formed in many reactions in which the products are actually formed by simple ionic processes.”  Interesting — how ‘small’ is small?  

p. 1036 — A very improbable mechanism (but true) given in the last reaction involving breaking benzene aromaticity and forming a cyclopropene ring to boot.  

p. 1043 — Americans should note that gradient (as in Hammett’s rho constant) means slope (or derivative if the plot of substituents vs. sigma for a particular reaction isn’t a straight line).  However we are talking log vs. log plots, and you can fit an elephant onto a log log plot.  It’s worth remembering why logarithms are necessary iin the first place.  Much of interest to chemists (equilibrium constants, reaction rates) are exponential in free energy (of products vs. reactants in the first case, of transition state vs. reactions in the second).

p. 1044 — Optimally I shouldn’t have to remember that a positve rho (for reaction value) means electrons flow toward the aromatic ring in the rate determining step), but should gut it out from the electron withdrawing or pushing effects on the transition state, and how this affects sigma, by remembering what equilibrium constant is over what for sigma, and rho), but this implies a very high working memory capacity (which I don’t have unfortunately).  I think mathematicians do, which is why I’m so slow at it.  They have to keep all sorts of definitions in working memory at once to come up with proofs (and I do to follow them).  

If you don’t know what working memory is, here’s a link — http://en.wikipedia.org/wiki/Working_memory.  

Here are a few literature references 

        [ Proc. Natl. Acad. Sci. vol. 106 pp. 21017 – 21018 ’09 ] This one is particularly interesting to me as it states that differences among people in working memory capacity are thought to reflect a core cognitive ability, because they strongly predict performance in fluid inteliigenece, reading, attentional control etc. etc.  This may explain why you have to have a certain sort of smarts to be a mathematician (the sort that helps you on IQ tests).  

       [ Science vol. 323 pp. 800 – 802 ’09 ] Intensive training on working memory tasks can improve working memory capacity, and reduce cognitively related clinical symptoms.  The improvements have been associated with an increase in brain activity in parietal and frontal regions. 

I think there are some websites which will train working memory (and claim to improve it).  I may give them a shot. 

Unrelated to this chapter, but Science vol. 337 pp. 1648 – 1651 ’12, but worth bringing to the attention of the cognoscenti reading this –as there is some fascinating looking organometallic chemistry in it.  This is a totally new development since the early 60’s and I look forward to reading the next chapter on Organometallic chemistry.   Hopefully orbitals and stereochemistry will be involved there, as they are in this paper.  Fig 1 C has A uranium atom bound to 3 oxygens and 3 nitrogens, and also by dotted bonds to H and C.

p. 1050 — The unspoken assumption about the kinetic isotope effect is that the C-D and C-H bonds have the same strength (since the curve of potential energy vs. atomic separation is the same for both — this is probably true — but why?    Also, there is no explanation of why the maximum kinetic isotope effect is 7.1.  So I thought I’d look and see what the current Bible of physical organic chemistry had to say about it. 

Anslyn and Dougherty (p. 422 –> ) leave the calculation of the maximum isotope effect (at 298 Kelvin) as an exercise.  They also assume that the force constant is the same.  Exercise 1 (p. 482) says one equation used to calculate kinetic isotope effects is given below — you are asked to derive it 

kH/kD = exp [ hc (vbarH – vbarD)/2KT }, and then in problem #2 plug in a stretching frequency for C-H of 3000 cm^-1 to calculate the isotope effect at 298 Kelvin coming up with 6.5

Far from satisfying.  I doubt that the average organic chemist reading Anslyn and Dougherty could solve it.  Perhaps I could have  done it back in ’61 when I had the incredible experience of auditing E. B. Wilson’s course on Statistical Mechanics while waiting to go to med school (yes he’s the Wilson of Pauling and Wilson).   More about him when I start reading Molecular Driving Forces. 

On another level, it’s rather surprising that mass should have such an effect on reaction rates.  Bonds are about the distribution of charge, and the force between charged particles is 10^36 times stronger than that between particles of the same mass. 

p. 1052 — Entropy is a subtle concept (particularly in bulk thermodynamics), but easy enough to measure there.    Organic chemists have a very intuitive concept of it as shown here.

p. 1054 — Very slick explanation of the inverse isotope effect.  

Again out of context — but more chemistry seems to be appearing in Nature and Science these days.   A carbon coordinated to 6 iron atoms ( yes six ! ! ! ) exists in an enzyme essential for life itself — the plant enzyme nitrogenase which reduces N2 to usable ammonia equivalents for formation of amino acids, nucleotides.   No mention seems to be made about just how unusual this is.  See Science vol. 337 pp. 1672 – 1675 ’12. 

p. 1061 — The trapping of the benzyne intermediate by a Diels Alder is clever and exactly what I was trying to do years ago in a failed PhD project — see https://luysii.wordpress.com/2012/10/04/carbenes-and-a-defense-of-pre-meds-and-docs/

p. 1064 — In the mechanism of attack on epichlorohydrin, the reason for the preference of attack on the epoxide isn’t given — it’s probably both steric and kinetic, steric because attack on the ring is less hindered — the H’s are splayed out, and kinetic, because anything opening up a strained ring should have a lower energy transition state. 
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Comments

  • Curious Wavefunction  On October 14, 2012 at 4:27 pm

    The original elephant quote is ascribed to von Neumann: With three parameters you can fit an elephant to a curve, with four you can make him dance.

  • MJ  On October 14, 2012 at 11:15 pm

    Re: C-D vs. C-H bonds – I’d say you answered your own question regarding the shape of the potential energy function. As you noted, the distribution of charges remains the same in both cases Otherwise, the most noticeable kinetic isotope effects tend to be seen with heavy isotopes of hydrogen. As personal experience has taught me, it is fairly trivial to culture bacteria in a broth enriched in 15N and 13C compounds – it is far more troublesome doing so using 2H-rich broth.

    Re: nitrogenase – the FeMo cluster is pretty unusual in and of itself, that it “traps” a carbide in there is almost like icing on the cake. It was originally proposed to be a nitrogen atom back in the day, as memory serves.

  • luysii  On October 15, 2012 at 4:29 pm

    MJ and Ashutosh — thanks for commenting Starting the Organometallic chapter of Clayden. Hopefully all will be revealed about FeMo — but what about hexacoordinated carbon there. The paper treated it in a very matter of fact fashion

    Science vol. 337 pp. 1672 – 1675 ’12.

  • MJ  On October 16, 2012 at 9:48 pm

    I took another look at the 2011 structure ( http://www.rcsb.org/pdb/explore/explore.do?structureId=3U7Q ) where they claimed an interstitial carbon in nitrogenase, as I wanted to confirm – it really is *coordinated* as the six metal-carbon distances are all right around 2 Angstroms (literally – the deviation is plus/minus 0.02 Angstroms). I don’t think they’re claiming a hypervalent carbon. It actually reminds me of something like one of the iron carbides, as if it was plucked from something a solid-state chemist would look at and dumped into an enzyme. (And people say biochemistry doesn’t involve any chemistry! Heh.) But you’ll see these sorts of formal coordinations in extended solids that can throw off those accustomed to proper molecular species. It’s important to remember that it’s not necessarily forming something you’d consider to be a proper chemical bond, though.

  • luysii  On October 16, 2012 at 10:41 pm

    MJ — interesting way of looking at it (which had totally escaped me). I no longer have my copy of that issue of Science. Na+ and Cl- are hexacoordinated in ordinary salt (but not at the edges of the crystal). It’s hard for me to think of a solid state comprised of so few atoms though.

  • dianas.  On March 8, 2013 at 3:53 pm

    Hi! I’m searching for the chapter 35 of the book. Can somebody help me with it? In my book is a jump from page 903 to 970. Thank you!

  • luysii  On March 8, 2013 at 10:08 pm

    I assume you are talking about the 2nd edition. Very Strange ! My book has this material. You appear to be missing two chapters Pericyclic reactions: 2 (Ch.35) and Participation, Rearrangement and Fragmentation (Ch. 36).

    Where did you get your book?

    • dianas.  On March 9, 2013 at 12:29 pm

      In fact is an e-book (i couldn’t find it in any printed edition here in Romania). I‘m searching for a reaction, the osonolisys of the pirene and that chapter was my last chance. Could you check for me, please, if it contains this reaction? Thank you very much!

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