Clayden through p. 175

Clayden, Greeves, Warren and Wothers is a fabulous textbook of organic chemistry  (if you’re serious about organic chemistry).  I started it 2 years ago, found a few errors and wrote  Clayden asking if there was an errata page and if he wanted any further errors found as I went through the book.  

He wrote back saying — “this is fine by me but much prefer if you send them all at once!  I’ll try and answer – we have lots of ideas for the revision anyway; you may well give me some more. Time always presses though so it’s easier for me to spend a couple of hours sometime than a dribble of minutes every few days.” 

I got sidetracked after getting up to about p. 400.  In particular, I wanted a better grounding in quantum mechanics, so I wouldn’t just be mouthing incantations about orbitals, bonding etc. etc.  The QM course I audited last fall was a good start, and I’m currently pushing on through “Molecular Quantum Mechanics” by Atkins and Friedman and “Modern Quantum Chemistry” by Szabo and Ostlund (the latter recommended by Michelle Francl). 

Clayden et. al.  is now 9 years old, so before starting over, I wrote Clayden again asking

“Any idea when the 2010 Edition of Organic Chemistry will be available?”

and received

Not in 2010!  We’re working on a second edition at present, but publication is not likely before 2012.”

I’d already come up with tons of questions brought up by the text, some more errors, and some suggestions for improvement in the next edition. If I were Clayden and received all this stuff at once, I’d chuck it.  So what to do? 

The plan is to put them in a series of bite sized posts.  This is where you come in.  If you own Clayden, get it out and go through my comments, questions, suggestions (they all refer to specific pages).  If you know  answers to any of the questions, put them in a comment.  If you find other errors let me know and I’ll add them to the post.  If something in the book is confusing to you, speak up.  If you also have suggestions for improvement let’s hear them.  It’s a great book, but nothing’s perfect.

I’ve been posting here now for about 6 months, and it’s time to put the 40+ posts into categories, so they can be found more easily rather than scrolling through the whole mess. Each Clayden post will have the page numbers it covers in the title and be in the Clayden category.     Hopefully, you’ll find this series of posts of some interest and use.  Perhaps Clayden et. al. will as well.  They certainly didn’t put me up to this and don’t even know I’m doing it.  Consider it a freewill offering and a way of saying thanks for writing a great organic text. 

Here goes

There should be a lot more problems at the end of each chapter.

p. 55 1.1% * 1.1% is 1.21 * 10^-4  not 1.32 * 10^-5

p. 55  You might put in that there is a greater than 50/50 chance of a single 13-C atom showing up with a 63 carbon atom molecule as .989^63 = 49.8% — or, better — ask them to figure out just when this happens

p. 71 “The strength of an IR absorption varies with the change of dipole moment when the bond is stretched.”   The more the dipole changes the more radiation is absorbed. True enough, but why is this the case? 

p.91  What does the radial node and the nodal plane of a 3p orbital look like? 

(2 Nov ’10) p. 96 — Organic chemistry is a visual subject, and the orbital diagrams have great power because of this.  It is unfortunate that the split of antibonding and bonding orbitals appears symmetrical — antibonding is increased in energy from the isolated atomic orbitals as much as the bonding is decreased. This of course is not true.  Fleming “Molecular Orbitals and Organic Chemical Reactions” (2010) p. 5.  I realize you aren’t writing a quantum mechanical tome, but some sort of statement should be put in the next edition to this effect, and all the diagrams changed slightly. 

p. 100 — Amazing that I didn’t realize this before — BUT the lone pair of electrons on each nitrogen in N2 are found one in a 2s sigma MOLECULAR orbital (bonding) and one in a 2s sigma* MOLECULAR orbital (nonbonding) — this is why they don’t contribute to bonding.   The two energies cancel but my question is     ” is the bonding sigma molecular orbital electron to be found between the nitrogens (as opposed to being on the other side of the atom as it is usually drawn :N triple bond N:) ” ?

p. 102  — probable mistake, middle column under red line “antibonding MO is raised in energy by only a small amount relative to AO on atom B (this should be atom A).

p. 132 — “Most organic reations are ionic”  — as opposed to what? 

p. 133 Answer to problem #3 — you snuck in an extra carbon in the ring with the nitrogen. 

p.136 (30 August ’10)  The term coefficient in  “The greater coefficient of the pi* orbital. . .  ” isn’t explained until p. 159. It should be done here.

p. 139  — Burgi Dunitz — 107 degrees is pretty close to the tetrahedral angle, why not just say the nucleophile comes in at or close to angle at which the new bond will form?   I’d trust the theoretical calculations much more if they weren’t post hoc. [ 30 Aug ’10  Later on (p. 888) you explain its utility in the reaction of chiral aldehydes.  A pointer to that discussion should be considered in the next edition ].

p. 139 – 140  The small hydride filled 1s orbital should be nearly covered by either the antibonding sigma orbital of H in H – X or the 2p of the antibonding pi orbital.  The difference must be the percentage of the antibonding which overlaps with hydride 1s orbital.  Correct? 

p. 140 — Why is the BH4 anion stable in water?

p. 144 — If you want to add further background in Clayden10, you might mention paraldehyde, a cyclic trimer of acetaldehyde which I used as a sedative and an anticonvulsant in the 60’s and the 70s’ for DTs (until better drugs 

p. 144 — If you want to add further background in Clayden10, you might mention paraldehyde, a cyclic trimer of acetaldehyde which I used as a sedative and an anticonvulsant in the 60’s and the 70s’ for DTs (until better drugs 

Problem #5 — Chapter 7 — what about strain relief by making the middle carbonyl sp3?  If all 5 atoms are planar, then (assuming equal C-C bond lengths) the angles at the carbonyl groups are 108 rather than 120.

 p. 158 gives as an example combining three 2p atomic orbitals in the allyl system.  The lowest one is where they are all in phase and a pi orbital over all 3 atoms is created.   The highest one is antibonding — all 3 are out of phase and there are two nodes.  The middle one is nonbonding, with just two p orbitals on carbons 1 and 3 and NOTHING on carbon 2. What happens to the middle carbon in this case?

p. 159 — “From relative sizes of the coefficients”  — what coefficients ??  as far as I can see coefficients for combining atomic orbitals into molecular orbitals were never discussed. (30 August ’10)  The term coefficient IS explained in the side bar, but it should have been explained on p. 136 where it appears toward the bottom of the page “The greater coefficient of the pi* orbital. . .  “

p. 161 — the bottom diagram is missing a dot for the electron in the structure on the right. 

p. 163 — Interesting that the difference between C-C (154 pm) and C=C (134 pm) is 20 pm the same difference as between C-0  (143) and C=0  (123) — any significance to this? I looked up N-0 and N=O on the web and a 19 pm difference appears (121 and 140 pm)

p. 165 — “This amount of energy (e.g. 88 kJ/mole) is not available at room temperature”.   Well, how much energy is available at 300 K?   This is very hard to find. 

p. 168 — “The overall energy of the two bonding butadiene molecular orbitals is lower than than that of the molecular orbitals for ethene”    I think I know what you mean, but the diagram shows psi2 (a bonding molecular orbital) at higher energy than ethene.  Perhaps — when the two bonding molecular orbitals of ethene are put in butadiene they have lower energy.

p. 169 — “The wave length at which a compound shows maximum absorbance”  — shouldn’t this be the longest wavelength at which the compound absorbs light — or does absorbance of light increase as the energy levels get closer to each other?  Also the compounds absorb light in the infrared red region (if they have bonds with a dipole moment) which is of much longer wavelength.  Something is missing here.

p. 170 — “If a compound absorbs one colour, it is the complementary colour that is transmitted.   The glass of a red light bulb doesn’t absorb red light; it absorbs everything else letting only red light through.”  Really?  are you saying that compound exist that absorb EVERYTHING in the visible region except one frequency which gets through?  On the next page you say what I think you mean “Yellow light is absorbed by this pigment and indigo–blue light transmitted” — Just absorbing one colour of light produces the appearance of the complementary color as the other two primary colors get through.  

pp. 172 – 173 — Great way to introduce aromaticity — clearly a lot of neat chemistry has happened since 1962.  Reading the book is a real pleasure.  What is SbF5/SO2ClF oxidized to?

p. 175 — “It turns out ” — possibly too complicated to explain here, but there should be a reference to where you could see where the polygon rule comes from (I assume there is).   We got into the Huckel approximation in the QM course I audited — it is amazingly crude and simplistic, yet it works ! 

That’s it for now

Advertisements
Post a comment or leave a trackback: Trackback URL.

Comments

  • Wavefunction  On March 4, 2010 at 9:17 am

    Retread, in a single sentence, Clayden et al. changed my life. You might notice that I wrote the first Amazon review of it in 2002 and have literally ‘evangelized’ it on blogs. I pitched a condensed form of it as an introduction to OC to sophomores in graduate school. They loved it. However when I was intensely reading it I was 21 and was much more interested in ‘practical’ organic chemistry and therefore worked through the important reactions and problems. I also found a few errors but I unfortunately misplaced the notebook where I noted them. You have an excellent list. I shall take a look at my dog-eared copy and check it out.

    By the way, predicting Burgi-Dunitz is not necessarily very easy for theoretical calculations; the difference between 107 and 109 can be substantial for force fields and theory since modern force fields are usually supposed to be accurate to 1 degree when predicting bond angles (along with 0.1 A in bond lengths and 10 degrees in dihedrals). Plus, a difference of 2 degrees can probably translate to a difference of a kcal or so among transition states, and you know how that significantly affects equilibrium constants. (In a recent JACS communication, Houk et al. rationalized two different TSs for pi-pi stacking by noting that one was more favorable than the other because the stacking distance was closer by 0.1 A)

  • luysii  On March 4, 2010 at 10:16 am

    Well, it’s great that modern force fields are that accurate. Hopefully I’m on my way to understanding how they are done. I’ve got the time — assuming my brain holds out. My father’s lasted into his late 90s (he passed away at 100).

  • Yggdrasil  On March 4, 2010 at 2:42 pm

    Regarding your comment on p 165 (how much thermal energy is available at room temperature), let’s take a naive approach and assume that there is a simple conversion factor between temperature and energy such that energy = constant * temperature. This is reasonable because it assumes that temperature and thermal energy are directly proportional. You should be able to justify this based on the definition of temperature.

    What units would such a conversion factor have to convert temperature (in units of K) to an energy (in units of, say J or J/mol)? Do you know any fundamental constants that have the units you determined above?

  • luysii  On March 4, 2010 at 3:07 pm

    Sacrebleu ! ! It’s the gas constant. Thanks.

  • Wavefunction  On March 4, 2010 at 4:12 pm

    Oh, you should get through force fields before you are 90. It’s just a bunch of equations with a bunch of parameters…

    A slightly old but excellent reference would be “Molecular Mechanics Across Chemistry” by Rappe and Casewit

    Another way to think about energy at room temperature is that it’s 0.025 eV, since that’s the energy of thermal neutrons. Multiply by 23 kcal/mol to get about 0.6 kcal/mol.

  • Yggdrasil  On March 4, 2010 at 4:19 pm

    Correct. This is why in many equations in chemistry (for example, the Arrhenius equation), energies are compared to kT (or RT if you prefer to measure energy per mole).

    It’s amazing how useful dimensional analysis can be. I remember many times in stat mech working out a derivation and finding proportionality constants popping up that conveniently have the units of J s or J/K.

  • luysii  On March 4, 2010 at 7:54 pm

    Gas constant 8.3 Joules/Degree Mole * 300 / (4184 Joules/Kcal)

    = .595 kiloCal/mole

    Touche !

  • Allergy and Immunology resources  On September 23, 2010 at 7:20 am

    Retread, in a single sentence, Clayden et al. changed my life. You might notice that I wrote the first Amazon review of it in 2002 and have literally ‘evangelized’ it on blogs. I pitched a condensed form of it as an introduction to OC to sophomores in graduate school. They loved it. However when I was intensely reading it I was 21 and was much more interested in ‘practical’ organic chemistry and therefore worked through the important reactions and problems. I also found a few errors but I unfortunately misplaced the notebook where I noted them. You have an excellent list. I shall take a look at my dog-eared copy and check it out.

    By the way, predicting Burgi-Dunitz is not necessarily very easy for theoretical calculations; the difference between 107 and 109 can be substantial for force fields and theory since modern force fields are usually supposed to be accurate to 1 degree when predicting bond angles (along with 0.1 A in bond lengths and 10 degrees in dihedrals). Plus, a difference of 2 degrees can probably translate to a difference of a kcal or so among transition states, and you know how that significantly affects equilibrium constants. (In a recent JACS communication, Houk et al. rationalized two different TSs for pi-pi stacking by noting that one was more favorable than the other because the stacking distance was closer by 0.1 A)

  • monk  On November 6, 2010 at 9:16 pm

    p. 133 Answer to problem #3 — you snuck in an extra carbon in the ring with the nitrogen. + double bond is missing in the first ring.

  • Peter  On November 28, 2011 at 6:33 am

    This is an incredible effort.

    I am a third year undergrad student. Clayden is the prescribed textbook from first to third year at my school.

    I appreciate its depth, but it feels slapdash in places. Having said that, the main problem I have with it, is that each chapter has references to earlier chapters – and so its almost like you have to read it from start to finish, rather than say with McMurry or Carey or Ege, where you can skip the chapters you know, and move on to those you don’t.

    For an undergrad text, there are too many unnecessary details. There are no end of chapter reaction summaries. Too many little boxes, and distractions. Even the chapter names are less clear than they could be.

    On the other hand, I can see why people like it – I only wish there was a summarised form! I have analytical, physical and inorganic chem, and genetics to study as well: reaction summaries at the end of each chapter would be a huge help for undergrads (see every other undergrad organic chem textbook).

    I don’t mean to knock the book too harshly. I even have a copy signed by Dr Wothers, who came to Australia to do a serious of chemistry shows…if they gave us more time to study it, I think I might like it more – rather than 2 x 12 weeks to read the whole thing while studying three other subjects and writing lab reports.The chapter on Retrosynthesis was great, one of the best things I’ve read in any textbook.

    And to the author of this blog and this effort especially, thanks alot – really, what an incredible and worthwhile effort, I can tell you as a student, that you’re helping so many future chemistry students by posting this stuff: lets hope that any problems are fixed, and your suggestions (all of which I agree with) are incorporated,

    Thanks again,

    Peter

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s

%d bloggers like this: