The end (of my reading of) Anslyn pp. 1000 –> End

No question, Anslyn & Dougherty “Modern Physical Organic Chemistry” is a great book and a labor of love.  Now that I’ve read the whole thing (not as well as I might have since I stopped doing the problems midway through in order to finish it in 2011) here are a few general comments to start off. 

l. It is extremely well written.

2. There should be an errata list.  They just incorporate known errors in the next printing.  For my thoughts on this see —

3. It would be nice, when referring to figures, equations, sections more than 100 pages back, to put in the actual page where they are found.  It would save a lot of time for those of us with less than an eidetic memory.

4. As mentioned early on, Tom Lowry told me a few years ago, that he thought Physical Organic Chemistry had died in the USA.  The book makes a strong argument that it is alive and well, because its ideas and techniques are  being applied to new areas undreamed of 50 years ago – photochemistry, solid state, conducting polymers, etc. etc.

5. All the beautiful electron pushing and orbital diagrams seem to come to a screeching halt when applied to organometallic chemistry, which has revolutionized synthetic organic chemistry, and which, to my view, along with NMR (and possibly computational organic chemistry) are the most significant new developments in organic chemistry in the last 50 years.

6 It must have been a labor of love.  Thanks for writing it.  My (sometimes snarky) comments are written in the hopes of making of making future editions even better.

A whiff of physics and mathematical idealization is seen right off — an infinitely long, perfectly linear, defect free — polyene.  Reminds me of the ‘consider a spherical cow’ of the old joke.  Chemists just don’t think this way.  

p. 1010 — “Organic students generally come away from introductory courses viewing benzene as the prototype conjugated pi system with all C-C bond lengths equal.”  I sure did.   Most neutral closed shell pi systems show alternating bond lengths. 

p. 1014 — What is 1 electronVolt in terms of the wave length of electromagnetic radiation?  I had to look it up — a wavelength of 4000 Angstroms has an energy of 3.1 electronVolts.  

p. 1017 — I love the retro Diels Alder approach to polyAcetylene — it’s so clever.  

p. 1022 — Thanks for clearing up the terminology concerning magnetism (ferro-, ferri-, antiferro- etc. etc.) and letting us know that there are 14 different kinds of it.

p. 1024 — Unfortunately, I found  the discussion of negative spin densities incomprehensible.

p. 1027 — There is no section 14.7.5

p. 1030 — Superconductivity is Newton’s first law of motion in action.   These’s guys are chemists not physicists. Hopefully they’ve talked to the physicists at Cal Tech and Austin (where numerous Nobelists reside) to make sure their explanation of superconducitivity is correct.  It’s the best I’ve seen.  I just hope it’s correct.  What starts the electrons all moving in the same direction in the first place? 

p. 1035 — Second harmonic generation has found great use in neuroscience.  Good to see organic chemists have helped.  Here is an example —       [ Proc. Natl. Acad. sci. vol. 103 pp. 786 – 790 ’06 ] Second harmonic generation (SHG) is used to measure membrane potential in dendritic spines.  (Dendritic spines are so tiny (on the order of a micron — that it is impossible to stick an electrode across its membrane without wrecking it).   SHG linearly depends on the electric field, which makes it suited to image membrane potential.   (ibid p. 3124 – 3129) — it can measure membrane potential in living cells with a spatial resolution of 1 micron and a time resolution of 1 milliSecond.  

      An important advantage of SHG for membrane potential recording is that the signal emanates from only properly oriented dye molecules in the plasma membrane.  Randomly oriented dye molecules bound to nearby intracellular or extracellular components don’t contribute.  Thus the signal response isn’t degraded by background as it is for fluorescence.  The signal response to changes in membrane potential is linear (as it is with fluorescence).    The problem is that there is damage produced by the light used (they either have to use a lot of light or a lot of dye to get a usable signal).
Post a comment or leave a trackback: Trackback URL.


  • MJ  On December 31, 2011 at 1:07 pm

    Re: “spherical cow” thinking – I would suggest that being able to do that kind of thinking is important, if only to orient one’s thinking about a new problem. It’s something which should be in everyone’s cognitive toolbox. Then again, as I am a physical chemist, I might be expected to say that.

    Re: p. 1030 – Unfortunately, the free Google Book preview only showed me pgs. 1030 & 1031 before cutting me off. It looked OK based on what I saw, but some comments on the topic –

    – The BCS theory (named after John Bardeen, Leon Cooper, & Bob Schrieffer. The three shared the 1972 Nobel Prize in Physics for this work – ) managed to explain superconductivity without a significant challenge up until the mid-1980s, when the cuprate oxides (“high temperature” superconductors) were discovered. The discovery of the iron pnictide superconductors a few years ago also seem to not obey what is expected from BCS theory. We’re still finding superconductors that are “BCS-compliant” – magnesium diboride is one that was found to be superconducting about 10 years ago now.

    – The graphic on p. 1031 seems to be trying to convey which jargony physicists would term “phonon-mediated electron-electron interaction.” The electrons are interacting via their interactions with the lattice, which is oscillating coherently and not just scattering everything about at random.

    – The original BCS papers are actually free to download from the APS site, if anyone is interested in reading them for themselves.

    Re: pg. 1035 – SHG has always interested me for its interface selectivity. The list of important questions that involve interfaces isn’t getting any shorter, it seems.

  • luysii  On December 31, 2011 at 5:12 pm

    Thanks MG. Happy New Year!

    Bardeen won 2 Nobels, and a biography of him is quite interesting. Unlike the Europeans who landed in Princeton in the 30’s and complained about its lack of sophistication, Bardeen as a grad student there loved it, because he could go bowling and play golf whenever he wanted to.

  • Curious Wavefunction  On January 5, 2012 at 12:19 pm

    About Princeton, it’s interesting to read Freeman Dyson’s thoughts about it and the way he contrasts it with Cornell:

    “Cornell had always been my vision of America, whereas Princeton is not. Princeton is definitely an alien growth in America. Ithaca is the real thing.”

    For Dyson Princeton was simply a European imitation whereas Cornell was American and wholesome.

  • dieta  On January 18, 2012 at 7:02 pm

    The concept of the Donnan potential is analogous to that of the equilibrium electrode potential . Consider two table salt (sodium chloride) solutions of different concentrations separated by a cation -exchange membrane. The concentration difference will set up a diffusional force driving the sodium chloride from the higher concentration solution into the lower concentration solution through the membrane. However, the ion-exchange membrane will permit only the passage of the positively charged sodium cations . Consequently, excess positive electrical charges will accumulate on the low concentration solution side of the membrane, while excess negative electrical charges will accumulate on the high concentration side because of the negatively charged chloride anions that are left behind. This charge separation will induce an electrical potential difference that will drive the electromigration of the sodium ions in the direction opposite to that of the diffusion. The overall result will be that the net movement of the sodium ions into the lower concentration solution will slow and eventually stop when the two opposing forces are equal end the two opposing fluxes are equal. In this so called “Donnan equilibrium”, the diffusional flux of the sodium ions in one direction will be equal to the electromigrational flux in the opposite direction, resulting in net zero mass transport and zero charge transport . The electrical potential difference across the membrane under these equilibrium conditions is the “Donnan potential”.

Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Google photo

You are commenting using your Google account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s

%d bloggers like this: