Anslyn pp. 101 – 143

The book keeps getting better and better.  Here are comments, questions, addenda, errors accumulated as I went through the rest of Chapter 2 and the 52 problems at the end.

p. 102 — Nice to see the C3 and C2 endo forms of ribose drawn out at last.  Papers I’ve read use the term, but never show the structures.  Cn endo means that the endo carbon is above the plane of the ring on the same side as the DNA or RNA base.

p. 105 — In the connections box it is stated that deltaG was determined by infrared spectroscopy — hopefully there will be some detail on exactly how IR spectroscopy can do this later in the book. 

p.106 — deltaE * deltaT = pi * sqrt(2) .  This looks like the Heisenberg Uncertainty principle, in a somewhat different garb, but the units are the same.  However the principle says deltaE * deltaT = hBar.  So what gives.  Nonetheless it is a nice explanation of the NMR timescale — if you accept it.

      Clearly the formula is wrong as later they say that 2.22 is pi * sqrt(2)

but 3.14 * 1.414 = 4.44, so 2.22 is pi/sqrt(2).

      Sad — because I’ve always wondered how NMR was used for kinetics, and I thought this would be an explanation.  I wrote Anslyn about it 10 Jun and I’ll put his reply here. 

      I wrote Anslyn who promptly got back, saying that Dougherty wrote this section.  Here is Dougherty’s reply of 16 June.  Pretty quick responses !   

There is indeed a typo on p 106 that has been corrected in later print runs. pi/sqrt(2) = 2.22.
Typically statements of the uncertainty principle have an h on the right side – see the Wikipedia page.  I think this version just is based on a certain set of units and plugging in values for the fundamental constants.  Right now I don’t really remember where it came from.
Glad that you are (mostly) enjoying the book.

Dennis Dougherty

So beware if you bought a used copy trying to save money and have an earlier printing than the current one which I think is #4 as of 6/11.  My edition  is the second printing)– there is no errata page (which there should be).

p. 108 — “A major role of cholesterol is to insert into and thereby stabilize cell membranes.”    Actually exactly the opposite is true — cholesterol fluidizes cellular membranes by preventing the hydrocarbon chains of phospholipids from packing to each other forming a semi-crystallized state as they do in the membrane of a soap bubble.

p. 111 — Amazing that someone has made bicyclo[1,1,1] pentane, pristane and cubane.  They were chemical hallucinations in the early 60s.  

p. 117 — the Trishomocyclopropenium ion looks like benzene missing an electron.  Is it?  Is it C6H6+ ??

p. 118 — What is photoacoustic calorimetry — sounds like laser accupressure.

p. 122 — It wasn’t until I arrived at “Orbital effects” 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.  

       Looking back, there are several things which threw me.  Chemists use lines between atoms to represent bonds — not so (italics, bold) in figures 1.7, 1.8 and the rest of the book — the lines just represent the positions of the atoms in space.  Only when the color of the orbital on atom #1 is the same as the color of the orbital on atom #2 is there bonding.  If the colors are different there is antibonding.  If there is no colored orbital on atom #2 the line between atoms #1 and #2 remains, but there is no bonding interaction, so the orbital on atom #1 is a nonbonding orbital. The lines between the atoms remain faking me out.  

     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.  Also true of all mixing diagrams in the book.

p. 122 — Some values for the equilibrium constants of the different conformations of CH2F NH2 and CH2F-CH2F would be nice. Also, it would be nice to know how were the relative amounts of the conformations are determined (perhaps this will appear later in the book)

p. 128 –> The discussion of the molecular mechanics method was great, particularly all the caveats.  This appears to be the origin of the force fields used in determining protein structures, and it’s good to see where it comes from.  Presumably molecular dynamics simulations come from the same sort of thing.  The last half of the year will (hopefully) be the year of PChem for me (assuming life doesn’t supervene). 

p. 131 — “They do not necessarily reflect any kind of experimental reality” but two sentences before that we have “Apparently, this particular combination (of parameters) gives the best fit to experimental data.”  Which is it?

p. 135  — also great to see the feet of clay of the force field as applied to biopolymers (my primary interest in knowing this stuff). 

p. 136 — Good to see that Dr. Schleyer got adamantane from a simple Diels Alder condensate (after it was hydrogenated !).   Did he calculate it first using molecular mechanics, predicting the synthesis ?  Amusing that I used Symmetrel (1 amino adamantane) as a therapeutic adjunct in Parkinson’s disease treatment (never enough by itself).

PP. 138 – 143 — Problem set.  In general they’re fun and challenging.  Sometimes the page that a table or a figure referred to in a problem is given.  This is helpful since the chapter contains 73 pages of text.  Usually the page isn’t given — it should be.   Also the answers are long and discursive and bring in material by way of explanation and elaboration that isn’t covered in the text.  It took a while to do all 52 problems and plow through their answers (many of which surprised me), but it was well worth it.  I recommend doing this. 

P. 138  Problem #5 — great problem, I doubt that anyone anticipated that the double bond in trans cyclo-octene is slightly shorter than a normal double bond.  Or did they?  This is likely a case of post hoc propter hoc.  Does anyone know?

Problem #7 — the answer is great and almost constitutes a course in various ways to figure out aromaticity.  If this keeps up, the answer book will be required reading, and essentially another textbook. 

Problem #9 — What about the anomeric effect using the pi bond of the olefin as the donor and the sigma* C  – C bond as the (weak acceptor)? 

Problem #13 — Another explanation (mine) is that with gauche conformations, the two rings lie (to some extent) over each other, while with the anti conformation of the hydrogens, they do not.

Problem #14 benezoid?   Probably should be benzene

Problem #16  — Answer.  Again a nice discussion.  If K = B/A  Then B = K/(K+1),  A = 1(k+1)

Problem #17 — Amazing that people have made the two isomers of benzene and calculated their heats of formation.  It’s sort of chemial bonsai.

Problem #24 — I’m not sure what they’re calling anti (the hydrogens?).  All conformations have phenyl groups on carbons 1 and 2 anti.   A diagram would be nice.

Problem #28 — Dipoles calculated from electronegativities of atoms — but electronegativities weren’t part of the discussion of molecular mechanics, unless it snuck in under coulombic forces.  Molecular mechanics presumably gives you geometry assuming you know how to minimize the various force fields.  No discussion of how this is actually done ! 

Problem #29 — The central geometry of the quaternary carbon must have typical sp3 angles of 109.  The bonds in the cyclopropanes are squished to 35 degrees, and molecular mechanics is poor for strained molecules — since molecules with similar distortions aren’t well represented in the parameterization set. 

Problem #34 — Not sure which isomer is s-trans and which is s-cis in this problem.

Problem #38 — Just the opposite of what I would have expected.  The rationale is interesting and makes sense.  I won’t spoil the fun — look at the problem and see which is harder to bend — sp3 or sp2 or sp1.  Now look at the answer.

Answer:  The more p character in the bond the more directional (and the more s character in a bond the less direction).

Problem #40 — The answer is a whole text on transition states of cyclohexane by itself.  

I did the remaining 12 problems, but this post is long enough
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  • hemp  On July 1, 2011 at 8:09 pm

    It is now easy enough to do computational ..chemistry that you do not have to know what you are doing to do a computation…As a result many people dont understand even the most basic description..of how the calculation is done and are therefore sucessufully doing..a lot of work which is frankly garbage….Many universities are now offering classes which are an overview..of various aspects of computational chemistry. Note that this is not intended to ..teach the fundamentals of chemistry quantum mechanics or mathematics only..most basic description of how chemical computations are done….The term theoretical chemistry may be defined as the mathematical..description of chemistry. The term computational usually used when a mathematical method is sufficiently well developed..that it can be automated for implementation on a computer.

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