I need some help: Clayden pp. 905 – 927

I’ve been trying to put all my comments, questions, and possible errors in Clayden’s in 100 page blocks.  I’m writing the  present post because I can’t  understand what’s on p. 927, particularly the orbital diagrams, which I think are incorrectly drawn.  One thing I was good at back then was understanding theoretical chemical concepts and applying them.  Photochemistry is extremely important (and always has been) and I don’t want to get the underpinnings of it  wrong (or ignore them and just memorize what happens — which is typical of med school where the theoretical underpinnings are far fewer than we’d like).    If any of the readers can help out please do so. 

p. 905 – 906 — “no intermediates at all”  — really?  The chapter spends a lot of time talking about transition states.  If you have to heat a reaction to get it to go, presumably the heat is providing activation energy to get things to a transition state (which you later do say is something rather different from an intermediate, which is presumably a valley in the plot of energy vs. reaction coordinate).

p. 906 — “The electrons do not realy rotate at all” — of course they don’t, but after 900 pages of thinking this way to explain chemistry, it begins to take on a reality of its own.  The electron distribution does change.  This is part of the hocus pocus you get into trying to describe quantum mechanical phenomena macroscopically.  Recall that the 2s orbital and all the 2p orbitals have nodes (e.g. places there the probability of finding an electron is zero).  That being the case, how can an electron cross the node.   The standard answer is that the notion of trajectory is meaningless in quantum mechanics.  

p. 906 — third block of text — “The black p orbitals are perfectly aligned to1”

p. 906 — while the transition state has 6 pi electrons in it (making it formally aromatic), it certainly isn’t planar for maximum overlap like most aromatic molecules.

p. 913 — In step 3 of the (very helpful) series of diagrams about stereochrmistry of the Diels Alder reaction, it isn’t obvious why the trans methyl groups are pushed down and cis hydrogens.  At first glance, the diagram is so symmetrical that both rotations to form the sigma bonds between the diene and the dienophile are possible.  On some further thought, the newly forming sigma bonds are directed inward toward the plane of symmetry of the diene.  Two rotations are possible, one pushing the Hs up and the Me’s down, and the other pushing the Me’s up and the H’s down.  The first rotation is by a smaller angle — my guess is this is why it is chosen.  Correct? 

p. 914 — It’s important to note that the term Frontier Orbital is nowhere explicitly defined in the book.  It’s pretty clear what is meant by the term given by the discussion here.  This should be attended to in the next edition. 

Also, back in ’60 – ’62 HOMOs and LUMOs were in the air, but not used much in the explanation of reaction mechanisms (arrow pushing was the main explanatory device).  I pretty much ignored the HOMO, LUMO discussions in this book until right here (the old familiar arrow pushing along with the electronegativities of the atoms involved was quite enough to get by).  This chapter (35) really impressed me with their explanatory power, so I’ll have to go back and look at the earlier stuff again (paying attention this time).  

However, we see MOs in the initial and final state, has anyone calculated what they look like in the transition state, or do you just morph the orbitals from the initial state into the final state, the way you can do it with pictures on the computer using Photoshop or a similar program. 

p. 915 — What does Ni(O) mean? 

p. 916 — I guess ‘aromatic’ is quoted because the transition state is NOT planar. 

p. 918 — I certainly don’t see the chair form of the linking chain mentioned in the second paragraph. 

p. 920 — sidebar — well it seems like cheating to me.  If the theoretical chemists calculated the HOMO energies before the reaction patterns were known (doubtful) it would be OK.  There is a lot of fiddling in orbital calculations, because solutions of the Schrodinger equation in closed mathematical form are impossible in these systems.

p. 922 — As an old Woodward grad student, I’d have liked more on the Woodward Hoffmann rule.

p. 923 – textline -2  ‘oribitals’

p. 927 — The discussion of promotion by a photon to the excited state, and the accompanying diagrams are confusing and probably there is an error in there somewhere.   Any help the readership can give would be appreciated.
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  • Yggdrasil  On July 26, 2010 at 2:15 pm

    I know a bit of photochemistry so perhaps I could help. Unfortunately, I don’t have the Clayden text, so could you describe the diagram that you are having trouble with? Is it a Jablonski diagram (for example, see http://www.olympusmicro.com/primer/java/jablonski/jabintro/index.html )?

  • luysii  On July 26, 2010 at 5:09 pm

    Yggdrasil: thanks for your help. However, I’ve got it figured out after a night of sleep. The diagram as written is correct. I’ve sort of been ignoring molecular orbital theory till this chapter (as noted we pushed arrows with abandon back then, but didn’t talk about molecular orbitals, probably because nothing other than H2+ could be calculated).

    My fellow grad students of 50 years ago (who cringed at my arrogance back then) would have a good laugh at the egg on my face, but most are retired and want little to do with chemistry (as I want little to do with neurology any more). Just another virtue of posting anonymously.

  • James  On August 30, 2010 at 8:05 am

    -Ni(0) is nickel in the zero-valent oxidation state. Not having Clayden by my side, not sure what the context is, but a good source of Ni(0) is the bright yellow nickel (bis cyclo-octadiene) Ni[COD]2 which is extremely “hot” (reactive) for cross couplings as well as being very air sensitive (glovebox storage mandatory). It binds nicely to dienes and other electron rich pi systems

    -The fact that molecules have “alternate” rotating modes is called “torquoselectivity” – surprisingly no wikipedia entry. Steric factors usually dominate but I recall seeing some interesting studies by a Japanese group on a boron-containing system where the opportunity for orbital overlap with the empty p orbital of the boron produced some contrasteric rotation by a t-butyl if I recall correctly.

    -MO theory is an extremely powerful lens for looking at organic chem – Evans’ 206 lectures at Harvard used to start with it. The bible in this respect for the practicing organic chemist is still Fleming, “Frontier Orbitals and Organic Chemical Reactions”. I read it thrice, extremely crisply written with good examples.

  • luysii  On August 30, 2010 at 10:11 pm

    James: Thanks for the book tip, two of the local colleges have it. I’ll check it out. Rereading the first 200 pages of Clayden now that I see how useful molecular orbital theory is.

    Question: can the lone pair on the oxygen in a carbonyl group be considered a molecular orbital (as opposed to a hybridized atomic one)?

    Any thoughts on:

    “However, we see MOs in the initial and final state, has anyone calculated what they look like in the transition state, or do you just morph the orbitals from the initial state into the final state, the way you can do it with pictures on the computer using Photoshop or a similar program. ”

    Thanks again

  • Wavefunction  On September 2, 2010 at 7:50 am

    -can the lone pair on the oxygen in a carbonyl group be considered a molecular orbital

    Yes, it is typically considered to be in a non-bonding MO. By the way I second the quip about the Fleming book, although I never got to the end.

  • luysii  On September 2, 2010 at 5:01 pm

    Thanks all: I decided to back and reread the first 1000 pages of Clayden before finishing, for the stuff I skipped (because I though I knew better) particularly the HOMO LUMO way of looking at things. Back in the day, we just pushed electrons without worrying about molecular orbitals (I don’t think they could be calculated with any degree of accuracy back then). Lionel Salem was in the department in some capacity or other and just starting up.

    There the answer to my question sits on p. 230 — “The HOMO in acrolein is not the highest filled pi orbital, but the long pairs on oxygen”. A an orbital localized to an ATOM in a molecule can be considered a MOLECULAR orbital. Language strikes again.

    Such antics are similar to the idea of vector spaces being OVER a field. In day to day existence, when you are over something, you control it (so you can change its behavior) However, the scalars in the field control the size of the vectors, and the vector never changes the scalar.

  • N.N  On December 21, 2010 at 7:49 am

    did anybody know why the values of ms on page 87, 88, 93 are +1 and -1 instead of +1/2 and -1/2.

  • luysii  On December 21, 2010 at 11:16 am

    This comment really doesn’t belong here but in an earlier post on the Clayden’s book (Clayden through p. 175). I looked at the above pages. I think that you misread those pages, because the values of ms are actually correct and given as +1/2 and -1/2 as they should be. The values of ml are +1 and -1 as they should also be.

  • N.N  On December 21, 2010 at 12:28 pm

    thanks for the answear. I dont think it was a misreading. On page 88 you kann find a table with the wrong values. Anyway its for me clear what are the right values but i wondered how such a good book can include such mistakes on several pages. That will be confused for the people who learn the quantum numbers for first time.

    • luysii  On December 21, 2010 at 2:23 pm

      Probably we’re both right. I looked at the table on p. 88 again, and it is correct. However, we probably have different editions. Mine (bought 21 April ’08) is an edition Reprinted with corrections in 2004. What edition is your book?

  • N.N  On December 22, 2010 at 8:57 am

    i think that. Mine is from 2000.

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