Away for a bit + The New Clayden pp. 427 – 470

We’ll be away for a bit, leaving before I could post anything on 3 or 4 very interesting molecular biology papers from a chemical and medical perspective.  Relax and enjoy the summer.

p. 427 — The ‘reason’ that Br2 has a low energy empty (antibonding) orbital, is because the Br-Br bond is exceptionally weak, and bonding and antibonding orbitals are usually fairly symmetrically disposed about the energy of two isolated atoms (with the antibonding orbital being a bit higher than the bonding orbital is lower).  The actual values are Br-Br 46, C-H 96, C-C 81 kiloCalories/mole (multiply by 4.184 for kiloJoules/mole).

p. 429 — “with Bromine being lower in the periodic table and having more diffuse lone pairs”  — another way of saying that the atom is larger.  The C-Br bond is 1.93 Angstroms (vs. 1.54 for C-C), but bonds don’t emanate from the center of the atom, but from the periphery, likely making the bromonium ion considerably less strained.  The ionium ion should be even more stable as the C-I bond is 2.16 Angstroms. 

p. 431 — There is an apparent conflict between the fact that aliphatic substitutions on a double bond RAISE the energy of the bonding pi orbital (pi) — e.g. the Highest Occipied Molecular Orbital (HOMO) while they lower the total energy of the molecule.  The explanation given on p. 394 is that it allows the sigma electrons of a CH or a CC bond to interact with the nonbonding pi* orbital, spreading them out in space with a concomitant lowering of the energy.  The more you localize an electron the more energy it has (it’s the uncertainty principle in drag).

p. 432 — What is KHSO5? — they don’t even name it. 

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

www.chemtube3d.com/clayden/xx

p. 442 — It’s worthwhile looking at the animation of dihydroxylation of ethane by OsO4.  While you can rotate the two molecules in space allowing you to really understand the reaction, what you can’t  do is alter the perfact orientation of the two molecules relative to each other allowing the reaction to occur.   Obviously this sort of thing doesn’t happen all the time or even most of it.  How ‘off’ can the orientations be and still allow the reaction to occur.  Perhaps the solvent cage enclosing the two molecules keeps them together until the proper approach is found.  Does anyone out there know if the lifetime of such a solvent cage can be measured? 

p. 444 — Important to know that transition metal cations are soft electrophiles.  Clearly a cation is an electrophile, but it’s probably the large size of the Hg++ ion (diameter 3.48 Angstroms) which makes it soft (e.g. polarizable, as the orbital electrons are so far from the nucleus). 

p. 445 — The large size of Hg++ is probably why it is able to form a cyclopropene derivative (in addition to the Huckel aromaticity of such a molecule). 

” C = 0 bonds are stronger than C = C bonds”  — why not give the numbers?  They are 172 kiloCalories/mole and 143 respectively.

p. 453 — Its definitely worth a look back to p. 150 looking at the HOMO of the allyl anion — there are no orbitals on the middle carbon.  The node was put on the central carbon to maintain orbital symmetry.  

The enolate anion is a great example of a hard nucleophile (the oxygen) and a soft nucleophile (the alpha carbon) in the same (italics) molecule. 

p. 456 — “only about one part in 10^4 – 10^6 is enol for most compounds”.  It’s worth reminding ourselves of the the numbers we casually throw about as chemists, one part in 10^6 still leaves 6 * 10^17 enols floating around in a 1 molar solution of acetone ! ! !

p. 457 — The fact that you see only one NMR peak from dimedone implies that the tautomerism is occurring faster than every milliSecond (see p. 374 — it’s good that the new edition gives page numbers when pointing to previous discussions, rather than just chapters the way the first edition did). 

p. 459 — Why not give the pKa of vitamin C rather than say it is an acid?

GABA (gamma amino butyric acid) is the major inhibitory neurotransmitter in our brains. 

p. 466 — In the reaction of LDA with acetone, turn on the more controls button and in what appears the space fill button.  It’s almost impossible to see what’s going on (as opposed to the ball and stick models where everything is clear).  How do the little molecules know what to do?
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Comments

  • silver price  On July 4, 2012 at 2:39 am

    hybridization, involves d orbitals of lower principal quantum number. This is possible because of the rather small energy differences between the d orbitals in one “shell” with the s and p orbitals of the next higher one— hence the term “inner orbital” complex which is sometims used to describe ions such as hexamminecobalt(III), shown below.. Both arrangements produce octahedral coordination geometries.

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