The New Clayden pp. 43 – 106

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

My guess is that people who haven’t bought the book, will be tempted to do after looking at a few of them.

p. 50         The reason that exact masses of various isotopes of a given element aren’t integers lies in the slight mass difference between a proton 1.67262 * 10^-27 kiloGrams and a neutron 1.67493 * 10^-27,  Also electrons have a mass of 9.10956 * 10^-31 kiloGrams.   I didn’t realize that particle masses can now be measured to 6 significant figures.  Back in the day it was 4.  Impressive.

p. 52 — Nice to see a picture of an MRI scanner (not NMR scanner).  MRI stands for magnetic resonance imaging.  The chemist might be wondering why the name change.  Because it would be very difficult to get a fairly large subset of patient to put their head in anything with nuclear in the name.

It’s also amusing to note that in the early days of NMR, chemists worked very hard to keep out water, as the large number of hydrogens in water would totally swamp the signal of the compound you were trying to study.  But the brain (and all our tissues) is quite wet with lots of water.

p. 53 — (sidebar).  Even worse than a workman’s toolbox permanently attaching itself to an NMR magnet, is the following:  Aneurysms of brain arteries are like bubbles on an inner tube.  Most have a neck, and they are treated by placing a clip across the neck.  Aneurysm clips are no longer made with magnetic materials, and putting a patient with such a clip in an MRI is dangerous.     A patient with a ferromagnetic aneurysm clip suffered a fatal rupture of the aneurysm when she was placed in an MRI scanner [ Radiol. vol. 187 pp. 612 – 614, 855 – 856 ’93 ].

p. 53 —     NMR  shows the essential weirdness of phenomena at the quantum mechanical level, and just how counter intuitive it is.  Consider throwing a cannonball at a brick wall.  At low speeds (e.g. at low energies) it hits the wall and bounces back.  So at the end you see the cannonball on your side of the wall.  As speeds and energies get higher and higher the cannonball eventually goes through the wall, changing the properties of the wall in the process.  Radiowaves have very low energies relative to visible light (their wavelengths are much longer so their frequencies are much lower, and energy of light is proportional to frequency).  So what happens when you throw radiowaves at an organic compound with no magnetic field present — it goes right through it (e.g. it is found on the other side of the brick wall).  NMR uses a magnetic field  to separate the energy levels of a spinning charged nucleus enough that they can absorb light.  Otherwise the light just goes past the atom without disturbing it.  Imagine a brick wall that a cannonball goes through without disturbing and you have the macroscopic analogy.

p. 53 Very nice explanation of what the actual signal picked up by the NMR machine actually is — it is the energy put into flipping a spin up against the field, coming out again.  It’s the first text I’ve read on the subject that makes this clear at the start.

p. 54 — Note that the plot of absorption (really emission) of energy has higher frequencies to the left rather than the right (unlike every other of anything numeric I’ve ever seen).  This is the way it is.  Get used to it.

p. 55 — The stronger the magnetic field, the more nuclear energy levels are pulled apart, the greater the energy difference between them, and thus the higher frequency of electromagnetic radiation resulting from the jump between nuclear energy levels.

p. 56 — I was amazed to think that frequencies can be measured with accuracies better than 1 part per million, but an electrical engineer who married my cousin assures me that this is not a problem.

p. 57  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.

p. 64 — Error — Infrared wavelengths are “not between 10 and 100 mm”  They start just over the wavelength of visible light (8000 Angstroms == 800 nanoMeters == .8 microMeter) and go up to 1 milliMeter (1,000 microMeters)

p. 64 — Here’s what a wavenumber is, and how to calculate it.  The text says that the wavenumber in cm^-1 (reciprocal centimers) is the number of wavelengths in a centimeter.  So wavenumbers are proportional to frequency.

To figure out what this is the wavelength (usually given in Angstroms, nanoMeters, microMeters, milliMeters) should be expressed in meters.  So should centimeters (which are 10^=2 meters).  Then we have

#wavelengths/centiMeters * wavelength in meters = 10^-2 (centimeters in meters)

Thus visible light with a wavelength of 6000 Angstroms == 600 nanoMeters can pack

(# wavelength/cm) * 600 * 10^-9 = 10^-2

waves into a centimeter

so its wavenumber is l/6 * 10^5 reciprocal centimeters — e.g

  16,666 cm(-1).  The highest wavenumber of visible light is 12,500 cm(-1) — corresponding to 8000 Angstroms.

Infrared wavenumbers can be converted to frequencies by multiplying by the velocity of light (in centimeters) e.g. 3 * 10^10 cm/sec. So the highest frequency of visible light is 7.5 * 10^14 — nearly a petaHertz

IR wavenumbers range from 4000 (25,000 Angstroms) to 500 (200,000 Angstroms)

p. 65 — In the bottom figure — the line between bonds to hydrogen and triple bonds shold be at 2500 cm^-1 rather than 3000 to be consistent with the ext.

p. 71 — “By contrast, the carbonyl group is very polarized with oxygen attracting the electrons”  — the electronegativity values 2.5 and 3.5 of C and O could be mentioned here.

p. 81-1, 81-2 — The animations contingue to amaze.  The latest shows the charge distribution, dipole moments of each bond, electron density, stick model, space filling models of a variety of small molecules — you can rotate the molecule, shrink it or blow it up.

To get to any given model mentioned here type
with the page number replacing xx.  The 81-1 and 81-2 are to be substituted for xx as there are two interactive web pages for page 81.  Fabulous.

Look at enough of them and you’ll probably buy the book.

p. 82 — “Electrons have quantized energy levels”  Very misleading, but correct in a sense which a naive reader of this book wouldn’t be expected to know.   This should be changed to “Atoms (and/or Molecules) have quantized electronic energy levels.”   In the first paragraph of the section the pedagogical boat is righted.

p. 85 — The introspective will pause and wonder about the following statement — “In an atom, a node is a point where the electron can never (italics) be found — a void separating the two parts of the orbital”.  Well, how does a given electron get past a node from one part of an orbital to the other.  This is just more of the wierdness of what’s going on at the quantum mechanical level (which is dominant at atomic scales).  There is no way you can regard the electron in the 2 s orbital as having a trajectory (or an electron anywhere else according to QM).  The idea that that trajectories need to be abandoned in QM isn’t my idea but that of a physicist, Mark P. Silverman. His books are worth a look, if you’re into getting migraines from considering what quantum mechanics really means about the world. He’s written 4 according to Amazon.

p. 86 — Very worthwhile looking at the web page for the 3 dimensional shapes of atomic orbitals — particularly the d and f orbitals.  FYI  p orbitals have 1 nodal planes d have 2 and f have 3.   If you’re easily distractable, steel yourself, as this web page has links to other interesting web pages with all sorts of moleculara orbitals.  This one has links to ‘simple’ molecular orbitals for 11 more compounds ranging from hydrogen to benzene.

p. 87 — Nice to know where s, p, d, and f come from — the early days of spectroscopy — s = sharp, p = principal, d = diffuse, f = fundamental.

p. 87 — “There doesn’t have to be someone standing on a stair for it to exist”  great analogy for empty orbitals.

*Ap. 89 — The first diagram on the page is misleading and, in fact, quite incorrect.  The diagram shows that the bonding orbital is lower in energy than the atomic 1s orbitals by exactly the same amount as the antibonding orbitals are higher.  This is not the case.  In such a situation the antibonding orbital is higher in energy by a greater amount than the bonding orbital is lower.  The explanation is quite technical, involving overlap integrals and the secular equation (far too advanced to bring in here, but the fact should be noted nonetheless).  Anslyn and Dougherty has a nice discussion of this point pp. 828 – 831.

p. 91 — The diagram comes back to bite as “Since there is no overall bonding holding the two atoms together, they can drift apart as two separate atoms with their electrons in 1s AOs”.  Actually what happens is that they are pushed apart because the destabilization of the molecule by putting an electron in the antibonding  molecular orbital is greater than the stabilization of the remaining electron in the bonding molecular orbital (so the bonding orbital can’t hold the atoms together).   Ditto for the explanation of why diatomic Helium doesn’t exist.

p. 94 — The rotating models of the bonding and antibonding orbitals of N2 are worth a look, and far better than an projection onto two dimensional space (e.g. the printed page)  See the top of this post  for how to get them.

p. 95 — It’s important to note that nitric oxide is used by the brain in many different ways — control of blood flow, communication between neurons, neuroprotection after insults, etc. etc.  These are just a few of its effects, more are still being found.

p. 100 — I guess British undergraduates know what a pm is.  Do you?  It’s a picoMeter (10^-12 Meters) or 100 Angstroms.  Bond lengths of ethylene are given as C-H = 108 pm, C=C as 133 pm.  I find it easier to think of them as 1.08 Ansgroms and 1.33 Angstroms — but that’s how I was brung up.

p. 103 — It is mentioned that sp orbitals are lower in energy than sp2 orbitals which are lower in energy than sp3 orbitals.  The explanation given is that s orbitals are of lower energy than p orbitals — not sure if the reason for why this is so was given.  It’s because the s electrons get much closer to the nucleus (on average) than electrons in p orbitals (which have a node there).  Why should this lower energy?  Because the closer an electron gets to the positively charge nucleus, the less charge separation there is, and separating charges costs energy.

p. 105 — Mnemonic for Z (cis) and E (trans) just say cis in French — it sounds like Zis.
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  • Curious Wavefunction  On May 13, 2012 at 4:26 pm

    Strange that the official price of the book suddenly doubled, from 64$ to 126$.

  • Panama  On May 22, 2012 at 9:24 am

    orbitals on the other to form molecular orbitals that have a different shape, as shown in the figure below. These molecular orbitals are called pi () orbitals because they look like p orbitals when viewed along the bond. Whereas and * orbitals concentrate the electrons along the axis on which the nuclei of the atoms lie, and * orbitals concentrate the electrons either above or below this axis.

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