l. properties of the varnish

2. effects of the Little Ice Age on violin wood

3. Differences in the relative densities of early and late growth layers in wood

4. Chemical treamtnets of the wood

5. Plate tuning methods (whatever that is)

6. Spectral balance of the radiated sound

The paper gives references for all 6 should you like theorizing, but wait until you see what actually happened before you look.

So at the September 2010 International Violin Competition in Indianapolis — the home of one of the great  University music departments in the country, or anywhere, the authors decided to actually check out the superiority of Strads and Guarneris  They studied 21 violinists, 19 professional,  ranging in age from 20 – 65, playing for 15 – 61 years.  The prices of the violins they owned  ranged from  $1,800 to 10 million.  4 violinists were contestants, 2  the were jurors in the competition, and most of the rest were from the Indianapolis symphony.

The violinists were told that they were going to decide which instrument was the best, and that 1 of the 6 was a Strad (actually there were 2 Strads and a Guarneri among the 6, the rest being new instruments).   So how in the world did they blind the musicians?  The 3 new violins were at most a few years old.  It would be obvious which was new and which wasn’t just  from looking.  The authors put welder’s goggles on the violinists, and a dab of scent under the chin rest of the violins to make them all smell the same.

The violinists were given a pair of violins (one new, one old) and asked to choose which was best.   They used their own bows (the price of bows is another story).  There were 9 possible new/old pairs of violins. All 21 violinists were asked to chose the instrument they preferred from each pair (21 * 9 = 189)   They chose the new violin 112/189 times and the Strad or the Guarneri only 77/189 times.  The aggregate market value of the 3 new violins was 100,000 (so they were hardly cheap instruments, and had been selected by the authors for their high quality), but that of the old ones was 10,000,000.

There’s a lot more but you get the idea.  It’s going to be interesting to see the reactions of the 7 or so string players I play with on a fairly regular basis (I xeroxed the paper for them).

p. 51 — Note all the heavy lifting  required to produce an object with only (italics) C4 symmetry (figure 3.6)  First,  you need 4 objects in a plane (so they rotate into each other), separated by 90 degrees.  That’s far from enough objects as there are multiple planes of symmetry for 4 objects in a plane (I count 5 — how many do you get?)  So you need another 4 objects in a plane parallel to the first.  These objects must be a different distance from the symmetry axis, otherwise the object will have A C2 axis of symmetry, midway between the two planes. Lastly no object in the second plane can lie on a line parallel to the axis of symmetry which contains an object in the first plane — e.g. the two groups of 4 must be staggered relative to each other.    It’s even more complicated for S4 symmetry.  

p. 51 — The term classes of operation really hasn’t been defined (except by example).   Also this is the first example of (the heading of) a character table — which hasn’t been defined at this point.

p. 52 — Note H2O2 has C2 symmetry because it is not (italics) planar.   Ditto for 1,2 (S, S) dimethyl cyclopropane (more importantly this is true for disulfide bonds between cysteines forming cystines — a way of tying parts of proteins to each other. 

p. 55 — Pay attention to the nomenclature: Cnh means that an axis of degree n is present along with a horizontal plane of symmetry.  Cnv means that, instead, a vertical plane of symmetry is present (along with the Cn axis)

p. 57 — Make sure you understain why C4h doesn’t  have vertical planes of symmetry.

p. 59 — A bizarre pedagogical device — defining groups whose first letter is D by something they are not (italics) — which itself (cubic groups) is at present undefined.  

Willock then regroups by defining what Dn actually is.

It’s a good exercise to try to construct the D4 point group yourself. 

p. 61 — “It does form a subgroup” — If subgroup was ever defined, I missed it.  Subgroup is not in the index (neither is group !).  Point group is in the index, and point subgroup is as well appearing on p. 47 — but point subgroup isn’t defined there.  

p. 62 — Note the convention — the Z direction is perpendicular to the plane of a planar molecule.

p. 64 — Why are linear molecules called Cinfinity ? — because any rotation around the axis of symmetry (the molecule itself) leaves the molecule unchanged, and there are an infinity of such rotations.

p. 67 — Ah,  the tetrahedron embedded in a cube — exactly the way an organic chemist should think of the sp3 carbon bonds.  Here’s a mathematical problem for you.  Let the cube have sides of 1, the bonds as shown in figure 3.27, the carbon in the very center of the cube — now derive the classic tetrahedral bond angle — answer at the end of this post. 

p. 67 — 74 — The discussions of symmetries in various molecules is exactly why you should have the conventions for naming them down pat.  

p. 75 — in the second paragraph affect should be effect (at least in American English)

p. 76 — “Based on the atom positions alone we cannot tell the difference between the C2 rotation and the sigma(v) reflection, because either operation swaps the positions of the hydrogen atoms.”   Do we ever want to actually do this (for water that is)? Hopefully this will turn out to be chemically relevant. 

p. 77 — Note that the definition of character refers to the effect of a symmetry operation on one of an atom’s orbitals (not it’s position).  Does this only affect atoms whose position is not (italics) changed by the symmetry operation?  Very important to note that the character is -1 only on reversal of the orbital — later on, non-integer characters will be seen.  Note also that each symmetry operation produces a character (number) for each orbital, so there are (number of symmetry operations) * (number of orbital) characters in a character table

p. 77 – 78 — Note that the naming of the orbitals is consistent with what has gone on before.  p(z) is in the plane of the molecule because that’s where the axis of rotation is.

Labels are introduced for each of the possible standard sets of characters (but standard set really isn’t defined).  A standard set (of sets of characters??) is an irreducible representation for the group.  

Is one set of characters an irreducible representation by itself or is it a bunch of them? The index claims that this is the definition of irreducible represenation, but given the amiguity about what a standard set of characters actually is (italics) we don’t really know what an irreducible representation actually is.   This is definition by example, a pedagogical device foreign to math, but possibly a good pedagogical device — we’ll see.  But at this point, I’m not really clear what an irreducible represenation actually is.

p. 77 — In a future edition, it would be a good idea to lable the x, y and z axes (and even perhaps draw in the px, py and pz orbitals), and, if possible, put figure 4.2 on the same page as table 4.2.  Eventually things get figured out but it takes a lot of page flipping. 

p. 79 — Further tightening of the definition of a representation — it’s one row of a character table.

p. 79 — Nice explanation of orbital phases, but do electrons in atoms know or care about them?

p. 80 — Note that in the x-y axes are rotated 90 degrees in going from figure 4.4a to figure 4.4b  (why?).   Why talk about d orbitals? — they’re empty in H20 but possibly not in other molecules with C2v symmetry.  

p. 80 — Affect should be effect (at least in American English)

p. 81 — B1 x B2 = A2 doesn’t look like a sum to me.  If you actually summed them you’d get 2 for E, -2 for C2, and 0 for the other two.  It does look like the product though.

pp. 81 – 82 — Far from sure what is going on in section 4.3

p.82 — Table 4.4b does look like multiplication of the elements of B1 by itself. 

p. 82 — Not sure when basis vectors first made their appearance, possibly here.  I slid over this on first reading since basis vectors were quite familiar to me from linear algebra (see the category http://luysii.wordpress.com/category/linear-algebra-survival-guide-for-quantum-mechanics/ ).  But again, the term is used here without really being defined.  Probably not to confuse, the first basis vectors shown first are at 90 degrees to each other (x and y), but later on (p. 85 they don’t have to be — the basis 0vectors point along the 3 hydrogens of ammonia).

p. 83 — Very nice way to bring in matrices, but it’s worth nothing that each matrix stands for just one symmetry operation.  But each matrix lets you see what happens to all (italics) the basis vectors you’ve chosen. 

p. 84 — Get very clear in your mind that when you see an expression of the form

symmetry_operation1 symmetry_operation2 

juxtaposed to each other — that you do symmetry_operation2  FIRST.

p. 87  – Notice that the term character is acquiring a second meaning here — it no longer is the effect of a symmetry operation on one of an atom’s orbitals (not the atom’s position), it’s the effect of a symmetry operation on a whole set of basis elements.

p. 88 — Notice that in BF3, the basis vectors no longer align with the bonds (as they did in NH3), meaning that you can choose the basis vectors any way you want.  

p.89 — Figure 4.9 could be markedly improved.  One must distinguish between two types of lines (interrupted and continuous), and two types of arrowheads (solid and barbed), making for confuion in the diagrams where they all appear together (and often superimposed).  

p. 91 — A definition of irreducible representations as the ‘simplest’ symmetry behavior.  Simplest is not defined.  Also for the first time it is noted that symmetries can be of orbitals or vibrations.  We already know they can be of the locations of the atoms in a molecule.  

Section 4.8 is extremely confusing.

p. 92 — We now find out that what was going on with a character sum of 2 on p. 81 — The sums  were 2 and 0 because the representations were reducible.  

p. 100 — Great to have the logic behind the naming of the labels used for irreducible representations (even if they are far from intuitive)

p. 101 — There is no explanation of the difference between basis vector and basis function. 

All in all, a very difficult chapter to untangle.  I’m far from sure I understand from p. 92 – 100.  However, hope lies in future chapters and I’ll push on.  I think it would be very difficult to learn from this book (so far) if you were totally unfamiliar with symmetry.  

Flynn, rather self-servingly, thinks that the exposure to the populace to abstract scientific reasoning plays a large part in this, something I think is baloney.  Parables and stories play a huge role in the Bible, and reasoning about extremely abstract concepts such as right and wrong and ethics was far more prevalent 100 years ago.  Talmudic, in some circles,  became an epithet for extremely abstract hairsplitting reasoning divorced from reality.

This brings us to Proc. Natl. Acad. Sci. vol. 109 pp. 425 – 430 ’12 which looks at the Norwegian experience from 1955 – 1972 to see how important a role adolescent education plays in the Flynn effect.  They found that 2 extra years of education in adolescence had a ‘substantial effect’ on IQ scores at age 19 (increasing it).

That’s not what I found so fascinating about the paper.  The question before you is, how many years of education did all Norwegian children receive, before 1955?  Make a guess. Now scroll down

SEVEN ! ! !  Amazing ! !  The number of years of education received by all was increased to 9 years by 1972.   So very different from the USA in the entire 20th century.  My mother (born 1907) grew up in a rural town so small, that each room in her grade school housed 2 grades. I went to the same high school that she did, and she was appalled that I was only exposed to 2 years of Latin (she had 4).   It’s such a different philosophy over there.  The USA is definitely following Jefferson who thought that, for a functioning democracy, all should be educated.

Things may be different over there now.  My son has a few Norwegian friends living over there now, and apparently pre-school has become very big, but this may be a function of their education and social class.  I don’t know.

[ Cell vol. 147 pp. 789 - 802 '11 ] Is an incredible paper, showing that of 5000 protein coding genes in mouse embryonic stem cells, translation of the mRNA begins at 13,454 initiation sites, with 65% of the mRNAs having more than one site where translation begins (start sites), 16% had more than 4 start sites.   All the background a pure chemist needs to understand all this is in the Category “Molecular Biology Survival Guide for Chemists”.

The start sites could be within the coding section of the gene, giving amino truncated products, or upstream (5′ to) the coding section giving proteins with an amino terminal extensions.  A recent paper [ Proc. Natl. Acad. Sci. vol. 109 pp. 197 - 202 '12 ] gives an example of just how important an amino truncated protein can be.  Checkpoint kinase 1 (Chk1) is a crucial regulator of the cell cycle, preventing mitosis from occuring in cells with damaged DNA.  An amino terminally truncated variant (due to alternative splicing, not different initiation) of Chk1 binds Chk1 and represses its activity, letting the cell cycle proceed.  DNA damage results (by a complicated mechanism) in phosphorylation of Chk1, relieving the inhibition by the amino truncated variant, and allowing Chk1 to stop the cell cycle.

The authors also found a class of short RNAs coding for multiple small proteins (they call them sprcRNAs — short polycistronic ribosome associated coding RNAs.)  These short proteins (or peptides if you wish — when a peptide is long enough to be called a protein is a matter of taste) weren’t known.

So now we have a whole bunch of new proteins in the cell, most related to known ones.  Could the drugs we have be affecting the new ones rather than what we’ve thought was their actual target?

The way this was found is almost as interesting as what they found.  It involves a technique called ribosomal profiling.  For background on the ribosome see https://luysii.wordpress.com/2012/01/09/molecular-biology-survival-guide-for-chemists-v-the-ribosome/.

The ribosome is large — a roughly spherical blob 250 – 300 Angstroms in diameter, with the active site of protein synthesis nearly in the center of the molecule.  The messenger RNA within an active ribosome is protected from enzymes which can destroy it (nucleases). So chop up all the RNA in the cell, disassemble the ribosome, then use reverse transcriptase to make a DNA copy of the messenger RNA that’s left, and sequence all of it (using Illumina deep sequencing).

By using inhibitors of either translation initiation (harringtonine) or progression, it is possible to find translation start sites, along with their distribution.  You can also find out just how fast ribosomes are translating mRNA (about 6 amino acids/second in this system).

The article gives the structure of the Saccharomyces cerevisiae ribosome at 3 Angstroms resolution.  Quite a feat.  It comes in two parts, a large subunit which sediments at 60 Svedberg units, and a ‘small’ one at 40S.

The large subunit contains 3 RNA molecules and 46 proteins, the small one contains 1 RNA and 33 proteins.  Total molecular mass is around 2.5 megadaltons.  It’s maddening, but I can’t seem to find out just how many nucleotides our ribosomal RNAs (rRNAs) contain in toto.  It is well over 5,000 however.   So the number of atoms in the RNAs alone is over 200,000.  There must be many more atoms than that contained in the associated proteins, as the phosphates have a mass of 98, the ribose 115, the pyrmidines around 100.  So they don’t account for more than 40% of the total ribosomal mass.  If anyone can give me exact numbers, I’ll update this.

The actual catalysis is not accomplished by the 79 proteins, but by the RNAs themselves.  This is thought to be a living relic of an RNA world where life actually began.  The proteins are mostly found on the surface of the ribosome.

There are a gigantic number of things to say about the ribosome, but I’m just going to put in the facts needed so pure chemist types can read other posts. This post will be expanded as necessary when further background is needed.

Amino acids are linked together (the rate is only 2 – 6 per second) by the beast. This is OK as the average cell has over 10 million ribosomes (neurons probably have more).  The article above notes that most of the changes between the ribosome of bacteria and that of celled organisms (eukaryotes) make our ribosomes bigger.  The proteins are bigger, the rRNAs are longer.

The actual synthesis of proteins takes place deep in the center of the ribosome, where the two subunits come together.  How does the protein get out?  It is extruded (like sausage) through the exit tunnel, which is 100 Angstroms long in the E. Coli ribosome, where it’s diameter varies between 10 to 20 Angstroms.  Since the alpha helix is 11 Angstroms wide, this means that little if any other secondary structures (beta turns, beta sheets) and no tertiary structure at all can form within it.  It’s probably longer (and possibly wider) in our ribosomes.

p. 5 — Distinguish in carefully in your mind the difference between a symmetry element and a symmetry operation as you read the book. 

      A symmetry element  is a geometric structure (point, line, plane) about which a molecule is symmetric.  On p. 23 This definition is clarified — a symmetry element is the set of points which aren’t moved when a symmetry operation takes place.  Points of what? The points of the space in which the molecule is embedded.

      A symmetry operation is an action carried out using a symmetry element which leaves the shape of the molecule unchanged (although no atom of the molecule may wind up where it was after the operation).  Ammonia has a 3 fold axis of rotation (e.g. the symmetry element is a line), but 3 distinct symmetry operations about the symmetry element (rotation by 120, 240 and 360 == 0 degrees). 

p.  7 — Principal axis — the line of symmetry (axis) with the largest (highest) order of rotation.  Always aligned with the Z axis (vertical).  One of the many important conventions you’ll need to remember is that the highest (largest) symmetry axis defines  the vertical direction.  You’ll need to know what vertical is to appreciate the labelling of the symmetry planes of water on p. 10, and how to distinguish it from horizontal in the case of BF3 (p. 11).

p. 7. — Also very important to keep straight — after a symmetry operation the atoms of a molecule may move, but the axes do not move – why is this important?  – because it’s very easy to get confused about how to do the a second symmetry operation after you’ve done the first. Remembering this will save you later on (see figure 2.4 p. 30). 

p. 9 — Another convention — the Greek letter sigma is always used for a plane of symmetry.  If you’re reading this on your own — start yourself a symbol table with the page the symbol is first defined (not the same as when Willock first mentions the term, definitions sometimes come later — this takes some getting used to if you’re used to math books where everything is defined before being used).  Molecular Symmetry should have a symbol table  (newer math books do) but it doesn’t.

p. 21 “The absorption in an NMR experiment takes a short, but finite time”.  It is truly maddening to find out how long this time is using Google or any of my NMR books.   I’ve speculated about the time it takes for absorption of a wavelength of light in an earlier post.  Here it is again — if any physicist types are reading this, please correct me if I’m wrong, or enlighten me further. 

          Nonetheless, in a meatball sort of way, apply this to the (massless) photon.  Consider light from the classical point of view, as magnetic and electrical fields which fluctuate in time and space.  The fields of course exert force on charged particles, and one can imagine photons exerting forces on the electrons around a nucleus, changing their momentum, hence doing work on them.  Since energy is conserved (even in quantum mechanics), it’s easy to see how the electrons get a higher energy as a result.  The faster the fields fluctuate, the more energy they impart to the electrons.

        In one second, light moves 3 * 10^8 meters, regardless of how many many wavelengths it contains. If the wavelength were 1 meter it would move past a point in 1/(3 * 10^8) seconds But wavelength of the visible  light  I chose is 6 * 10 ^-7 meters, so the wavelength moves past in 6*10^-7/3 * 10^8 = 2 x 10^-15 seconds, which (I think) is how long it takes visible light to be absorbed.  Have I made a mistake?  Are there any cognoscenti out there to tell me different?

p. 26 — Note that sigma(v’) is in the plane of benzene and water here, while in the case of BF3 (p. 11) the mirror plane in the plane of BF3 is called sigma(h) — this is because the latter is perpendicular to the principal axis of rotation (p. 7), while the former two are parallel to it.   It’s best to have these things clear in your mind when reading further.

p. 26 — Note which of the two operations in C2sigma(v’) is done first — it is always the rightmost — this is standard in the mathematical literature, and probably comes from the way functions within functions are applied – sin(3x) means that you do 3x first and then apply sine to it.  Yet another convention to keep straight and crucial in what follows.

p. 26 — Point group — all the symmetry operations a molecule can undergo. None of the amino acids making up our proteins (except glycine) have more than 1 (the identity operation).

p. 27 — Note the convention for the X, Y and Z axes — Z points in the direction of the principal axis.  Y in the plane of the molecule (assuming there is one) and X perpendicular to Y and Z.  None of this tells you which is positive and negative on each axis — but (without saying so) the X,Y and Z axes are a right handed coordinate system (remember the old right hand rule — use the fingers of your right hand to coil the positive X into the positive Y, and your thumb will point in the positive Z direction.

p. 27 -  I think the bottom diagram of sigma(v’) is incorrect H1 and H2 aren’t changed by it.

p. 27 — The following is also very important to note (and not especially clear),  Distinguish the global coordinate axes (capital X, Y, Z) which aren’t changed by the symmetry operation and the vectors attached to atoms (small x, y, z) which   are (italics) changed by the symmetry operations.  So capital X, Y, Z means global coordinate axis, while small x, y, z means vector.  Easy to confuse the two.

p. 28 — Another important convention — when faced with a table for the multiplication of symmetry operations, do the operation in the row of operations at the top of the table first and the operation in the column of operations on the left side of the table second. 

Remember all this advice and you’ll do a lot less looking back. 

p. 31 — the Sn operation.  Note that in the example given (staggered ethane), that neither S6 nor C2 in the plane horizontal to it is an actual symmetry element of the molecule. 

p. 36 — The term basis is mentioned but not really defined.  It appears to be an arrow attached to an atom which follows the atom through various symmetry operations.  Apparently not the same as vectors attached to the oxygen of water (p. 27) which are labeled x, y and z. 

p. 37 — Perhaps the improper rotation on BF3 which requires applications (with a total of 720 degrees) to get things back to where they started, is relative to some rotations in particle space that I recall reading about, that took 720 degrees of rotation to get things back together.  

p. 38 — Requiring that an  inverse of a symmetry operation exist is a crucial property of groups, but here it is introduced by fiat without saying why.  For what a group is see the first post in the series. 

End of chapter 2 — The fact that the set of symmetry operations of a molecule must be closed, along with the fact that there are only finitely many of them, means that for any symmetry operation (S), applying it over and over eventually gets you back to the original operation.  This means there is some n in the non-negative integers such that for every symmetry operation S, S^n = S (S^n is a Mathematica convention meaning S to the nth power — multiplying S by itself n times — multiplication of symmetry operations just means applying one after the other — rightmost first .  A bit of thought then shows that S^(n-1) = E (the identity).  A bit more thought shows that the powers of S form a group by themselves (they contain 1, and have an inverse).  

      This means that they are a subgroup of group of all symmetry operations.  Subgroup isn’t in the index, as this is a chemistry book, not a math book.  It’s simple enough concept — a subset of a group of symmetry operations which is also a group (e.g. it contains E, the identity, every element has an inverse and a more obscure characteristic called associativity — which it inherits from the parent group).

       This is true for each symmetry operation.  What molecular geometry allows you to do, which isn’t obvious when group theory is studied abstractly, is to see how the powers of each element combine with each other. E.g. For water what is C2*sigma(v)?  The symmetries of water are an example of a very peculiar group called the viergruppe (German — four group).   Nice ! ! ! ! 

p. 45 — Introduces the character table, and notes that not all the symbols in it have been defined yet.  The term character also isn’t defined at this point.  It’s an interesting teaching technique, and very different from those used in math books. 

p. 46 — Pasteur was lucky to find tartaric acid which crystalizes in two form each containing a pure enantiomer.   How often does this happen? 

p. 48 — Watch out when reading about point groups. Lots of molecules contain a 2 fold rotation axis (e.g. C2), but the C2 point group contains only that symmetry operation and none other (except the identity) — this is why it must have at least 4 points (because 3 points define a plane, which is a different symmetry element). 

p. 48 — The drawing of the C(s) symmetry group is truly terrible and should be improved in a second edition.  Notice that the symmetry plane sigma is labelled sigma(h) even though it appears vertical. 

I got the following (edited) response back.

” Alas, the energy and time to accomplish a 3rd edition has eluded me up to this point. And, bit torrent pirate copies haven’t exactly increased my motivation.”

So how often do you think other authors of good scientific books have similar thoughts (and behavior)?   Statistics on this sort of thing will be impossible to get in the same way that negative results aren’t published.

On a more serious note, in addition to reading the new stuff as it comes out, I’m going to focus on two things in the coming year — computational chemistry (including protein folding, which is essentially computational) and relativity.  I think I’ve finally acquired the necessary background for the first (after Clayden et. al. and Anslyn and Dougherty), and plan to spend the year picking up what I need to know for the second.  Fortunately, an alum of recent vintage is a math prof at one of the local schools and has agreed to answer my questions as they arise in two excellent books I plan to go through — “Introduction to Topological Manifolds”, and “Smooth Manifolds”  both by John M. Lee.  I’ve looked at them and like their writing style, particularly the motivation and the  clarity.   Why Manifolds before studying relativity proper?  Because the spacetime of relativity is a manifold.

Why relativity?  It’s something I’ve always wanted to understand at a deeper level than the popularizations of it (reading the sacred texts in the original so to speak).  I may have enough background in math, to understand how to study it.  Topology is something I started looking at years ago as a chief neurology resident, to get my mind off the ghastly cases I was seeing.

I’d forgotten about it, but a fellow ancient alum, mentioned our college president’s speech to us on opening day some 55 years ago.  All the high school guys were nervously looking at our neighbors and wondering if we really belonged there.  The prez told us that if they accepted us that they were sure we could do the work, and that although there were a few geniuses in the entering class, there were many more people in the class who thought they were.

Which brings me to our class relativist.  I knew a lot of the physics majors as an undergrad, but not this guy.  The index of the new book on Hawking by Ferguson has multiple entries about his work with Hawking (which is ongoing).  Another physicist (now a semi-famous historian) felt validated when the guy asked him for help with a problem.  He never tooted his own horn, and seemed quite modest at the 50th reunion.  As far as I know, one physics self-proclaimed genius (and class valedictorian) has done little work of any significance.  Maybe at the end of the year I’ll be able to read the relativist’s textbook on the subject.  Who knows?  It’s certainly a personal reason for studying relativity.  Maybe at the end of the year I’ll be able to ask him a sensible question.

We’ll see if my brain holds out, something not a given at 73+.  I’ve seen all too many cognitively impaired people far, far younger.  Hopefully I chose my parents carefully, as my 100 year old father would say when asked for the secret of his longevity.

Happy New Year to all !

Wish me luck

l. It is extremely well written.

2. There should be an errata list.  They just incorporate known errors in the next printing.  For my thoughts on this see – http://luysii.wordpress.com/2011/02/09/chemistry-textbook-errotica/

3. It would be nice, when referring to figures, equations, sections more than 100 pages back, to put in the actual page where they are found.  It would save a lot of time for those of us with less than an eidetic memory.

4. As mentioned early on, Tom Lowry told me a few years ago, that he thought Physical Organic Chemistry had died in the USA.  The book makes a strong argument that it is alive and well, because its ideas and techniques are  being applied to new areas undreamed of 50 years ago – photochemistry, solid state, conducting polymers, etc. etc.

5. All the beautiful electron pushing and orbital diagrams seem to come to a screeching halt when applied to organometallic chemistry, which has revolutionized synthetic organic chemistry, and which, to my view, along with NMR (and possibly computational organic chemistry) are the most significant new developments in organic chemistry in the last 50 years.

6 It must have been a labor of love.  Thanks for writing it.  My (sometimes snarky) comments are written in the hopes of making of making future editions even better.

A whiff of physics and mathematical idealization is seen right off — an infinitely long, perfectly linear, defect free — polyene.  Reminds me of the ‘consider a spherical cow’ of the old joke.  Chemists just don’t think this way.  

p. 1010 — “Organic students generally come away from introductory courses viewing benzene as the prototype conjugated pi system with all C-C bond lengths equal.”  I sure did.   Most neutral closed shell pi systems show alternating bond lengths. 

p. 1014 — What is 1 electronVolt in terms of the wave length of electromagnetic radiation?  I had to look it up — a wavelength of 4000 Angstroms has an energy of 3.1 electronVolts.  

p. 1017 — I love the retro Diels Alder approach to polyAcetylene — it’s so clever.  

p. 1022 — Thanks for clearing up the terminology concerning magnetism (ferro-, ferri-, antiferro- etc. etc.) and letting us know that there are 14 different kinds of it.

p. 1024 — Unfortunately, I found  the discussion of negative spin densities incomprehensible.

p. 1027 — There is no section 14.7.5

p. 1030 — Superconductivity is Newton’s first law of motion in action.   These’s guys are chemists not physicists. Hopefully they’ve talked to the physicists at Cal Tech and Austin (where numerous Nobelists reside) to make sure their explanation of superconducitivity is correct.  It’s the best I’ve seen.  I just hope it’s correct.  What starts the electrons all moving in the same direction in the first place? 

p. 1035 — Second harmonic generation has found great use in neuroscience.  Good to see organic chemists have helped.  Here is an example –       [ Proc. Natl. Acad. sci. vol. 103 pp. 786 - 790 '06 ] Second harmonic generation (SHG) is used to measure membrane potential in dendritic spines.  (Dendritic spines are so tiny (on the order of a micron — that it is impossible to stick an electrode across its membrane without wrecking it).   SHG linearly depends on the electric field, which makes it suited to image membrane potential.   (ibid p. 3124 – 3129) — it can measure membrane potential in living cells with a spatial resolution of 1 micron and a time resolution of 1 milliSecond.  

Nonetheless, in a meatball sort of way, apply this to the (massless) photon.  Consider light from the classical point of view, as magnetic and electrical fields which fluctuate in time and space.  The fields of course exert force on charged particles, and one can imagine photons exerting forces on the electrons around a nucleus and  changing their momentum, hence doing work on them.  Since energy is conserved (even in quantum mechanics), it’s easy to see how the electrons get a higher energy as a result.  The faster the fields fluctuate, the more energy they impart to the electrons.

Now consider a photon going past an atom, and being absorbed by it.  It seems that a full cycle of field fluctuation must pass the atom.  So here’s a back of the envelope calculation, which seems to work out.  Figure an atomic diameter of 1 Angstrom (10^-10 meters).  The chapter is about photochemistry, which is absorption of light energetic enough to change electronic energy levels in an atom or a molecule.  All the colored things we see, are colored because their electronic energy levels are absorbing photons of visible light — the colors actually result from the photons NOT absorbed.  So choose light of 6000 Angstroms — which has a wavelength of 6 * 10^-7 meters.

In one second, light moves 3 * 10^8 meters, regardless of how many many wavelengths it contains. If the wavelength were 1 meter it would move past a point in 1/3 * 10^8 seconds But wavelength of the visible  light  I chose is 6 * 10 ^-7 meters, so the wavelength moves past in 6*10^-7/3 * 10^8 = 2 x 10^-15 seconds, which (I think) is how long it takes visible light to be absorbed.  Have I made a mistake?  Are there any cognoscenti out there to tell me different?

That was a classical way of looking at it.  Now for the bizarrity of quantum mechanics.  How does the wavelength of the photon get sucked up by something 1/6000th of itself, particularly when there are probably at least 10^9 atoms in a volume 6,000 on a side?  It gets worse with NMR, because the radioWave absorbed by a nucleus is 1 meter, and the nucleus is 10^-4 the size of an atom.  Essentially I’m asking about the collapse of the wavefunction of a photon (assuming they have one?).

p. 936 — “We show wavelength in the condoned (italics) unit of nanoMeter  . . . “  It may be condoned, but this chemist thinks in Angstroms, and my guess is that most chemists do, because atomic radii and diameters are small numbers in Angstroms, not fractions of a nanoMeter.

p. 939 — “Absorption of two photons or multiple photons . . . does not occur, execpt with special equipment . . . “  True enough, but the technique is now widely used in biologic research.   This is not new      [ Nature vol. 375 pp. 682 - 685 '95 ] In contrast to conventional microscopy, two long wavelength photons are simultaneously absorbed in two photon fluoresence microscopy (multiphoton microscopy)   < [ Science vol. 300 p. 84 '03 -- actually within a few femtoSeconds -- I thought simultaneity was asking too much > and combine their energies to excite a fluorophore not normally absorbing at this wavelength.  This permits the use of infrared light to excite the fluorophore. By using low energy (near infrared) light rather than higher energy visible light photons, light induced degradation of biological samples is minimized.  

p. 939 -- Manifold probably really refers to the potential energy surface associated with the different energy levels, rather than the numeric value of the energy level. 

p. 940 -- Look at transition dipoles very hard if you want to understand Forster resonance energy transfer (FRET), whch is widely used in biology to determine how proteins associate with each other. 

p. 944 -- How in the world did they get enough formaldehyde in the excited state to measure it -- or is this calculation? 

p. 947 -- Nice exposition on GFP (Green Fluorescent Protein) which has revolutionized cellular biology.   But the organic chemist should ask themselves, why don't chemical reactions between the hundreds of side chains on a protein happen all the time?  For more on this point see http://luysii.wordpress.com/2009/09/25/are-biochemists-looking-under-the-lamppost/

p. 951 -- How do you tell phosphorescence from fluorescence -- the lifetime for phosphorescence is much longer (.1 - 10 seconds), but is this enough. 

p. 970 -- The chemistry of photolyases, which repair thymine photodimers is interesting.  Here's a bit more information.        [ Proc. Natl. Acad. Sci. vol. 99 pp. 1319 - 1322 '02 ] Enzymes repairing cyclobutane dimerase are called photolyases.  The enzymes contain a redox active flavin adenine dinucleotide (FAD), and a light harvester (a methenyltetrahydrofolate < a pterin > in most species).    It has been proposed that the initial step in the DNA repair mechanism is a photoinduced single electron transfer from the FAD cofactor (which in the active enzyme is in its fully reduced form — FADH-) to the DNA lesion.  The extra electron goes into the antibonding orbital of one of the C C bonds of the dimer.  (The electron donated is on the adenine of FADH).  The entire process takes less than a nanoSecond.   Electron transfer to the dimer takes 250 picoSeconds.  The dimer then opens within 90 picoSeconds and the electron comes back to the FADH cofactor in 700 picoSeconds.  This all happens because the dimer has been flipped out of the DNA into a binding pocket of the photolyase (how long does this take?).

       Interestingly, photolyases use less energetic light than the natural absorption of thymine dimers (2500 Angstroms).   Photoexcitation of the enzyme culminates in electron donation from the excited state flavin directly to the thymine dimer. 

p. 973 –> The photochemical reactions are impressive synthetically, and represent a whole new ball game in making fused rings.   The synthesis of cubane is impressive, and I wouldn’t have though quadricyclane could have been made at all. 

p. 980 — Caged compounds and their rapid release in incredibly important in biological research, particularly brain research.  Glutamic acid, is the main excitatory neurotransmitter in brain, and the ability to release it very locally in the brain and watch what happens subsequently is extremely useful in brain research.  

p. 987 — Sinbce the bond dissociation energy of O2 is given (34 kiloCalories/Mole) and C=O bonds are stated to be quite strong, why not just say the BDE of C=O is 172 KCal/M?