Anslyn pp. 51 – 100

Now that I’m into Anslyn && Doughterty (2nd printing), a few words about the book.  It’s extremely well written and illustrated, reading more like a novel than a text.  There’s lots on each page, so the going will be slow.  The margins are wide and allow for notes.  I do have a Rip Van Winkle feeling as I read it, seeing the resolution of questions exercising organic chemists in the early 60s explored, and for the most part solved.  It would be nice if specific page numbers were given for forward and backward references in the text.

p. 52 — The explanation of what we’re now calling carbocations (e.g. carbonium ions (which is what we called them all back in the 60’s) and carbenium ions — makes sense at last.  Carbonium ions include R5C+ and what we used to call non-classical carbonium ions with a three center 2 electron bonds — chasing them around the bicyclo[2;2;1] heptane nucleus occupied Schleyer and lots of other chemists back then.  Carbenium ions are derived from carbenes (which were largely a theoretical construct in 1960) and correspond to what we were callling carbonium ions back then.  The discussion of the extra stability of the 2-norbornyl cation compared to the 2-methyl, 2 norbornyl cation on p. 90 was quite good, and an excellent argument for the actual existence of nonclassical carbocations. 

p. 53 — Nice to see some experimental evidence for MO calculations — e.g. shortening of the sp3-sp2 distance in CH3CH2+ and lengthening of the C-H bonds of the methyl group — hopefully the calculations were done first before the actually structure of the t-Butyl cation was known, so they really were a priori — It seems likely (to me) that there are a lot of parameters which can be ‘tweaked’ in MO calculations.

p. 54 – 55 — Carbocation potential energy surfaces — hopefully the book will show how these are actually calculated  rather than just assumed to exist.  Nonclassical ‘carbonium ions’ (what they were called in the 60’s ) were certainly a subject of contentious debate back then (certainly the norbornyl cation was always being discussed).

p. 55 — CH5+ going deeper — incredible discussion — I’m already loving this book.   It seems likely (to me) that some sort of quantum mechanical tunneling must be going on as well.  Granted that the proton is 2000 times heavier than the electron, but electrons tunnel some 20 Angstroms between two di-Copper centers in cytochrome oxidase. [ Proc. Natl. Acad. Sci. vol. 107 pp. 21470 – 21475 ’10 ]  With distances between C and H of 1.23 and H and H of .87  Angstroms and the ‘flat’ potential energy surface, some proton tunneling should be going on.  Has anyone looked at the obvious experiment (CD5+)?

p. 57 — In the connection box, I assume that the reason the s orbitals in the third row are smaller than the p orbitals goes something like this.  Even though the 2s orbitals contain one node, it isn’t at the nucleus, so they are exposed to a greater positive charge than the 2p orbitals, which have a node right at the nucleus, escaping the greater positive charge.  

pp. 59 – 61 — Pictures of d orbitals.  Hosanna ! “One theme of this textbook is to consistently tie organic chemistry to organometallic chemistry”  Hosanna again ! ! Clayden was valiant in their attempt to give a glimpse of the field, but their d orbital views and the corresponding bonding patterns was sketchy at best.  Certainly looking forward to enlightenment on this score.

p. 59 line -3  “When CITING down the x axis”

p. 61 “Hopefully this chapter has refreshed your memory”  — Not for QMOT which was rather new to me.  I thought the discussion was reasonably clear.

p. 62 — Answer to problem #7 — The hybridization formula somehow says that the hybrid orbitals between the C-C bonds in cyclopropane are misaligned with the straight line between the carbons by 21.4 degrees.  All very nice, but what does Xray crystallography of cyclopropane say?  Structural chemistry of proteins always gives electron density maps, so where are the electrons in cyclopropane? 

p. 62 — Answer to problem #14 — terrible problem — “Note that none of these examples has a charge distribution shaped exactly like a d(xy) orbital” — no wonder I couldn’t get it

p. 62 — Answer to problem #16 — Very nice extended discussion.  If this continues, the answer book will be required reading as it’s almost another text. 

p. 70 — Organic chemists have a simple and intuitive way of looking at entropy on a molecular basis.  Compare this to all the heavy lifting in the original definition of entropy on the macroscopic level (also compare the intuitiveness of entropy of a reaction to that of enthalpy — you get at enthalpy by looking at the internal energy of a molecule — something rather hard to see).  For details see https://luysii.wordpress.com/2011/05/26/second-law-of-thermodynamics-entropy-free-energy.

p. 72 — the mere existence of the term Normal Mode implies that Non-Normal modes (Abnormal modes??) must exist.  What are they? 

p. 73 — A nice explanation of why the hydroxyl radical is so toxic to cells.  I don’t recall seeing this in any biochemistry books or discussions of molecular biology — except to say that it is quite toxic, leaving it at that.  

pp. 73 – 78 — Marvellous discussion of bond motions and the spectra they give rise to.  On p. 76 it’s obvious that knowing the force constant, one can calculate the frequency, and the difference between energy levels given the difference in frequency, and how likely higher energy levels are to be populated at 298 Kelvin.  But how do you get the force constant of a covalent bond in the first place (without looking at the frequency first?).  On p. 77 how do they know that the various motions (symmetric stretch, asymmetric stretch, scissor, rock and wag ) correspond to these frequencies. 

p. 79 — The discussion of heat of formation and heat of combustion and internal energy would be vastly improved by a simple energy diagram showing the elements at 0 kilocalories/mole and CO2 at -94 kiloCalories/mole and H20 at -58 kiloCalories/mole and the compounds of interest between.  It would then be obvious that the heat of formation of a hydrocarbon + the heat of combustion of that hydrocarbon is constant for hydrocarbons of the same atomic composition, allowing inferences about internal energy, strain energy etc. etc.  It’s very klunky expressed in words, but quite clear with a diagram. 

p. 84 — How was the rotation barrier of the allyl radical determined? p. 94 possibly by microwave spectroscopy (see Going Deeper) — hopefully this will be explained later in greater detail. 

p. 84 — “BDE is really only the energy it takes to break a bond”   What about the activation energy?  Shouldn’t this be the net energy needed to break a bond? 

p. 91 — Hopefully chapter 5 will explain how you can make a statement like the pKa of ethane than is 50 — no one can possibly have found one proton and one ethylcarbanion in 10^27 moles of ethane — which is what pKa 50 implies. 

p. 93 — “Alternatively, the A-B-C-D dihedral angle is defined as the angle between the A-B-C plane and the B-C-D plane.”  This should have a pointer to the diagram in figure 2.7 on p. 95, where the sentence becomes obvious. 

p. 94 — “on average 3 kcal per Avogadro’s number of molecules”  — what on earth does this mean? 

p. 97  — A picture of Cp-Co-(CO)3 would be nice.

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