Tag Archives: stereochemistry

The New Clayden pp. 1003 – 1028

p. 1004 — The nitrosoureas are known carcinogens.  They form DNA adducts (not sure exactly what they are) and are used experimentally to produce random mutations.  Could they be forming carbenes in vivo?

Also, how do you make N-Methyl N-nitroso urea?  N-methyl, N-nitroso toluene sulfonic acid?  

p. 1007 — I assume you make tosyl azide from tosyl chloride plus sodium azide

p. 1007 Rh2(OAc)4 — presumably the structure will be given in the next chapter. 

p. 1014 “Spin flipping, which can occur only through collision with another molecule (solvent usually) is relatively slow on the time scale of molecular rotations . . . “  Well how slow?  These numbers are known.  Why not give them.  Also why does a collision have to be involved for spin flipping to occur?  I think this question has been answered before.  Sorry about asking it again. How about another link to it. 

p. 1016 Interesting bunch of natural products containing cyclopropanes.  How does Nature actually manage their synthesis? 

p. 1018 — How do you make N2-CO2Et?  Possibly using the tosyl hydrazone?

p. 1023 — Metathesis at last.  When I type it, I have to stop myself from typing an awful word I’ve had to type (and utter) for years — Metastasis. 

p. 1024 — In the mechanism shown — why doesn’t the ‘carbene’ attached to Rh leave the Ru and form a cyclopropane with the other olefin? 

Also, all stereochemistry has vanished ! ! !

The catalyst goes from having 5 bonds to various things, to 6 with the bonds shown coming off the ruthenium atom like quills from a porcupine.  Surely the disposition of the bonds in space must be known?  Doesn’t it matter?   Ditto for the metathesis catalysts on 1025.  This is the way things were drawn (if they were drawn at all), in my orgo book of 54 years ago — English and Cassidy.

Hopefully the chapter on organometallics will be more enlightening about what is going on in metathesis reactions.  The discussion in this chapter takes me back to med school — this is what happens — remember it — never mind why.  At least in med school it was because no one knew why.  Here, perhaps they do but they aren’t telling.

The New Clayden pp. 269 – 327

If you  want to know what’s really  going on inside your NMR machine, read “Spin Dynamics”  (2nd Edition) by M. H. Levitt.  It weighs in at 700 pages, contains a 15 page symbol table (with at least 20 symbols/page).  It will probably tell you more than you want to know.  I don’t claim to have read whole thing, just the first 100 pages or so which describes the machine, the essential NMR experiment, and the physics.  Be prepared for detail — including how the Fourier transform of the data produces the spectra we see.  If I could inhabit another universe where time expands, I’d read the whole thing. 

 The following mnemonic may help you keep things straight
low field <==> downfield <==> bigger chemical shift <==> deshielded

mnemonic loadd of bs

It’s far from perfect, so if you can think of something better, please post a comment.

 The illustrations in the book that I comment on can be reached on the web by substituting the page number I give for xx in the following

p. 270 — “This 10 ppm scale is not the same as any part of the 13C NMR spectrum. It is at a different frequency altogether.”  This is because even though they use the same reference compound (Me4Si), the split between the two energy levels (with and against the field) of 13C and 1H are quite a bit different — so the frequency of the transition (energy is proportional to frequency by Planck’s constant) will be quite different.

It’s worth while thinking (again) why Me4Si should be used. Essentially it’s because the electronegativity of Si is 1.9 and that of carbon 2.5 meaning that carbon in C – Si bonds has far more electrons close to the nucleus than carbon in C – C bonds, making it highly shielded.  This means that the C – H bond has more electrons shielding the hydrogen. 

p. 274 — “Rotation about single bonds is generally very fast”  — well just how fast is it?

p. 278 — The pictures of a cyclophane and an annulene are not to be missed. 

p. 278 — If amino nitrogen feeds electrons into the pi system making it electron rich, this should result in an enhanced ring current deshielding the aryl hydrogens further resulting in an increased chemical shift.  This isn’t what happens ! The increase in electrons in the pi cloud somehow acts as a shield rather than a ring current shielding the aryl hydrogens.  I don’t understand why.  p. 279 — Similarly the withdrawal of electrons by conjugation with a nitro group removes electrons from the pi electron cloud, which somehow results in further deshielding of the ring hydrogens.  That’s the way it is, but it doesn’t make sense (to me at least).   Any ideas why this is so from the folks reading this.

p. 292 — The color labeling HA in the chemical structure is incorrect, it should be that labelling HX.  The colors are correct for the spectra.

p. 293 — dd should be in the table of abbreviations as well as in the text.

p. 293 — The example shows why coupling is NOT through space (or the coupling constant for cis hydrogens on a double bond would be larger than trans as they are physically closer).  However, I don’t see why coupling of bonds aligned parallel should be higher.

p. 293 — Double triplet is all very nice, but only 5 peaks are shown in the spectrum not 6 (although the middle peak of the quintet looks a bit funny).  Some note should be made of this.

p. 296 — W-coupling.  Something is fishy as in the pictures shown the angle between the two coupled H bonds is the same as it is in cis vicinal hydrogens (e.g. 120 degrees), yet the bonds are said to “line up in a zig-zag fashion to maximize interaction”.  

p. 303 — Rotating structures in space using Jmol is almost as good as having a model to play with.  The structure itself is rigid, perhaps later we will be able to play with conformations of a given molecule  (rather than rotating the molecule as a whole).

p. 306 — They do show rotation of a C – C bond beween two sp3 hybridized carbons.  But you can’t change the conformation of the other two sp3 hybridized carbons, although you can rotate the whole molecule in space to see how the rotation looks from various angles — pretty neat !

p. 308 — The periodic table is found in the back of the book, not the front.

p. 317 — Very slick to be able to rotate a molecule of meso tartartic acid into an identical configuration as its mirror image. 

p. 320 —  Watching a wire model of BINAP rotate in space is particularly impressive.  Notice how, at times, during the rotation the drawing appears to be rather flat (it’s a drawing after all), while at other times the molecule appears to jump off the page into three dimensional space.  This isn’t your brain playing tricks on you, but it’s your brain doing what your brain does best, inferring 3 dimensionality from the 2 dimensional projection of an image on your retina.  It’s worthwhile stopping the rotation, and seeing how two dimensional the images actually are.  Your brain is inferring 3 dimensionality by comparing images received over time.  Impressive, isn’t it?

p. 323 — I don’t think “Why nature uses only one enantiomer of most important biochemicals is an easier question to answer”  — I don’t think this was answered well.  They should have said what the ‘enormous number of diastereomers’ would mean.  What do you think? (answer below)

It’s the enormous number of DIFFERENT physical properties the different diastereomers would have.