p. xxii — “Some would argue that the last century also saw the near death of the field” . My friend, Tom Lowry (Mechanism and Theory in Organic Chemistry) told me (this century) that he thought the field had died.
Similarly, the huge and unsolved protein folding problem doesn’t involve covalent bond making or breaking. This is certainly physical chemistry. Whether or not it is physical organic chemistry is unclear. Hopefully the book will have something to say about these matters. Certainly proteins are organic molecules, and physical organic chemistry should be able to say something about the way their parts interact.
p. 4 “Most of this material should be familiar to you” — not to this boy. Molecular orbitals were just coming in in 60 – 62. Lionel Salem was a post-doc (or something) when I was a grad student.
p. 5 ”the ability of an electron to feel the trajectory of another electron”. Certainly informal, but do electrons really have feelings? There’s also a strong argument that they don’t even have trajectories — if they did, how would they get past a node (zero probability of finding them there) in a 2 p orbital.
p. 18 — How are dipole moments for molecules determined? Since the dipole moment is the product of a distance and a charge separation. Increasing the amount of charge separated and decreasing the distance between them will yield the same Dipole moment. Is there any way to measure the two separately? Anslyn makes the point with CH3Br and CH3F — which have the same dipole moment.
p. 21 — In the Going Deeper box “The potential energy cannot be infinite . .. ” is wrong — it should be “The kinetic energy cannot be infinite .. ” Now I have the 2nd printing and they don’t have an errata page (which I think is awful) correcting errors as they are found with each new printing, so this may have been corrected already.
Now I doubt that the average chemist, organic or otherwise, knows the following. The potential difference across the cell membrane isn’t that large (70 milliVolts), but the field is enormous, because the 70 milliVolts is across a distance of 70 Angstroms (7 nanoMeters). So that’s an electric field of
p. 27 — “Modern calculational methods now provide accurate representations of the molecular orbitals not only of stable molecules, but of reactive intermediates and even transition states.” — How do you know they are accurate? Do they predict reaction rates?
p.28 (added 13 June ’11) — It wasn’t until I arrived at “Orbital effects” on p. 128 that the utility of the molecular orbital approach made it seem worth learning. My eyes glazed over in the section on Qualitative Molecular Orbital Theory (pp. 28 –> ) the first time I read it. So I went back and reread it.
Another point (see figure 1.12 p. 37) — This is the mixing diagram of two CH3 groups to form ethane — there is no significance to which side of the energy levels of the mixed orbitals the orbital diagrams are placed. This is true of all mixing diagrams in the book.
p. 31 — “We will constantly be checking our qualitative reasoning against quantitative calculations to be sure we are getting things right.” Well, you’re really checking consistency, but how accurate are the calculations?
p. 34 — I found the handwaving about the CH2 group rather difficult to believe until the mention of the different ionization energies of the electrons in water’s lone pairs — proving the two ‘lone pair’ orbitals aren’t equivalent. Can they actually show the different ionization energies leaving H20 as just lacking one electron (e.g. H3O+) and not stripping out a second electron from H3O+ ??
p. 35 — Even more interesting — the approach of another molecule to water (or any other for that matter) lowers the symmetry of the system allowing orbital mixing, giving two sp3-like orbitals. QMOT might be proven correct by studying isolated molecules in the gas phase, but most chemistry happens when one molecule approaches another — so how useful is the theory described up to now?
p. 36 — the fact that orbital mixing of filled identical orbitals from two identical atoms produces two molecular orbitals (bonding and antibonding), which when filled is destabilizing isn’t stressed in most introductory organic books. But why is this so? I don’t recall seeing an explanation in the QM course I audited. “Closed shell repulsion” sounds almost like an explanation but it could use some elaboration. Hopefully Ch. 14 on perturbation theory some 800 pages later will make this clear.
p. 37. (added 13 June ’11 ) — very important to note that the highest occupied molecular orbital in ethane has an antibonding interaction between the p orbitals of the two carbons, but it still is a bonding molecular orbital, because the overlap of the carbon p orbitals with the s orbitals of the 6 hydrogens results in a net bonding effect — so not every orbital interaction in a bonding molecular orbital must be bonding, some can be antibonding.
p. 42 — Most books I’ve read don’t talk about the tilting of the antibonding pi orbital away from the region between the two ‘antibonded’ atoms — nice ! p. 46 — Even better this partially explains the rearward attack on R-Cl in an Sn2 reaction — but simple stereochemistry and physics explains it better.
p. 50 — The 3 center 2 electron bond of the diboranes and death of Bill Lipscomb this month is an appropriate way to end this post. A girlfriend got her PhD with him, liked him a lot (as did everyone) and has a publication with him listed in his Wikipedia article.
Apparently, it was a very different time from the present — the 21 Apr ’11 Nature has a bunch of articles about “The future of the PhD” — something we had no worries about back then. I still wonder if the situation is as grim for the PhD’s coming out of the Harvard chemistry department — no chauvanism intended, just curiosity.