ChemBark

In his third post, Retread looks at some of the physics and math needed and used by chemists.

Now that the answer book to Jones has arrived (23 May) I’m going to start over from the beginning, this time doing all the problems.  Mathematicians are fond of saying that it isn’t a spectator sport, and that problems must be done to really grasp the material.  I’m not so sure that is true for chemistry, but I’ll take excimer’s advice.

I’d gone through the first 300 or so pages of Jones and it’s apparent the two textbooks are wildly different in the way they approach the beginner.

English & Cassidy start out with hydrocarbon structures.  Molecular orbitals make their appearance on p. 63 (remember the book only has 442 pages of text). They are introduced as follows: “A somewhat more easily visualized physical picture of a double bond is given by a relatively recent theoretical development known as the molecular orbital theory.”  Recall that there are only six three dimensional drawings in the first 100 pages of E&C.  Four of them involve orbitals.

Jones drenches the reader in atomic and molecular orbitals using all the graphics at his disposal.  One needs to step back in time to realize the mathematical armor the high school graduate possessed in ‘56 entering college.  Outside a few of the great academic high schools in the USA (Central High in Philly, Bronx High School of Science) calculus was simply not taught in US public high schools.  The thinking was that is was so hard that it would destroy the brain of anyone under 18.  There was a giant dose of anxiety on taking it for the first time.  Just about all the undergraduates in the math courses I audited had a year or two of calculus in high school and some were exposed to it in the 8th grade.

So junior chem majors back then didn’t have the apparatus to tackle the Schrodinger equation etc.  Formal quantum mechanics wasn’t taught to us back then.  Even though the department had Walter Kauzmann, who wrote the influential “Quantum Chemistry” in ‘57, and who taught physical chemistry (which we all took), quantum mechanics wasn’t really discussed in the course.

The department did introduce us to quantum mechanical thought.  As juniors we were required to read a book “The Logic of Modern Physics” by P. W. Bridgman, written in 1927 in the early heyday of quantum mechanics.  I found it extremely irritating.  It argued that all we could know was numbers on a dial reporting the results of a measurement.  The notion of particle trajectory was to be abandoned, etc. etc. Jones skirts the issue on p. 10 where he talks about the node in the 2S orbital, a place where an electron is NEVER found.  An electron following a trajectory as we know it macroscopically could never pass through the node.  If you like thinking about such things, I recommend just about anything a physicist named Mark P. Silverman writes.  In particular, Ch. 5 “And Yet It Moves: Exotic Atoms and the Invariance of Charge” in his book “A Universe of Atoms, An Atom in the Universe” deals with the issue of the ‘motion’ of an electron in an atom.

I have a friend, a retired philosophy prof from Columbia, who dismisses all biology and chemistry as ‘anecdotal’.  The only thing he regards as solid is Godel’s proof.  I told him he better hope he’s wrong if he ever gets sick.  In a similar vein, Bridgman is as wrong as he can be when it comes to chemistry.  Why?  Because the theory behind chemistry may have its origin in numbers on a dial, but it gives rise to gazillions of successful predictions about reactions, structure and spectra.  Theory is immaterial, but it guides chemists (it’s the old Cartesian dichotomy between flesh and spirit).   Following chemistry in a peripheral fashion during my years in medicine by reading what appeared in Nature and Science (on a superficial level), it seemed that the work in gas phase kinetics was just confirming (always good) what we ‘knew’ back from ‘58 – ‘62.  The one surprise was the reversal (p. 245) of the acidity of primary, secondary and tertiary alcohols in the gas phase.

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In the second part of his series, Retread lays out his first impressions of Jones vis-à-vis his previous orgo text in grad school, English & Cassidy.

The book for my first Organic Chemistry course (’58 – ‘59) was English and Cassidy, 2nd edition, ‘56.  Jones is the 2004 edition.

………………………………………English & Cassidy            Jones

Pages (text only)                442                          1323
Page size  (inches)            9 x 6                         10 x 8
Text width                          4.5                           5.25
Text height                         7.0                           8.50

The most striking difference is the graphics.  There were only six 3-dimensional representations in the first 100 pages of Cassidy, while Jones has TNTC (too numerous to count).  It is hard to find a page in Jones without one.

The tone is completely different.  Jones is chatty and conversational.  “Remarks for the Student” in E&C begins as follows:   ”It is usually taken for granted that the student who  takes up the study of organic chemistry has a thorough knowledge of first-year college chemistry.”  Not too warm and fuzzy.

One of the very best things about Jones, is that he tells you what is hard, and what you must learn. “The (R, S) convention looks a bit complicated.  It is easier than it appears right now, but it just must be learned and cannot be reasoned out.”   Repeat this advice 50,000 times and you’re through med school.  There is no reason the appendix is on the right, the heart is on the left, speech is usually in the left hemisphere  etc. etc.  Jones also tells you what looks  hard but really isn’t — drawing cyclohexane in the chair form for instance.

Another very good thing about Jones (which may seem rather trivial) is that when he points you back, he gives you a page number to go to.  On retirement from medicine, I indulged a lifelong taste for math by auditing some math courses (number theory, abstract algebra,  algebraic geometry) at the local colleges.   Math books almost never repeat anything.  You are referred back to theorem 10.3 (and have to hunt for it).   There are hundreds of theorems, corollaries etc. in the average upper level math book.  It gets irritating unless you have a completely flawless memory.

Also, math books don’t usually tell you what’s really important, and what will be used later.  Not all results are equally crucial for the argument.  On reading it for the first time, you can’t tell the wheat from the chaff.  Jones is excellent at this.

In one sense, the two books can’t be compared, just as stereos back then and now can’t be.  I worked all summer as a supermarket checker at $1/hour before entering college in ‘56 and bought an RCA Victor record player to take with me for $140.  The richest man in the world back then could not buy sound of today’s quality no matter what he was prepared to spend.

However today’s convenience store worker would have to work considerably more hours to buy Jones (167.74) and the answer book (80.59) than I would have had to for English & Cassidy back then.  I asked the student checking me out how anyone could afford books like
these.  He said that often students bought a single textbook and shared it.  Shades of the 19th century Ghetto.  My grandfather told me how there were people who could only read Hebrew upside down, or at a 45 degree angle, because 4 – 6 students would sit around the  same table and study the same page at the same time.

One final point.  Despite the dryness, formality, lack of graphics etc. etc. not much harm was done.  I liked the book back then as did most of us.  This includes Jones himself (Yale ‘59), who almost certainly used the book, as English and Cassidy were Yale professors and the first edition came out in ‘49.

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What’s all this about?  Well it started like this when I posted the following on The Wall:

24 Apr ‘07

Let’s say you were a graduate student in organic chemistry at Harvard ‘60 – ‘62 (I was), and that you passed 8 of the first 9 cumes (I did) and that you talked Woodward into letting you work on you own idea 9 months after you got there because passing 8 cumes was all you needed to start your PhD work (also true) and were remembered by most concerned as arrogant unfortunately true) and that you were god-awful in the lab (true) and left organic chemistry to go back to medicine. Further suppose that organic chemistry always seemed natural and fun, and that you happened to see a squib in the 12 April Nature about the total synthesis of Lyconadin B, Googled it and found the structure and commentary in TotallySynthetic.Com and fell back in love with organic chemistry, and wished to get up to speed so you could enjoy reading about the field again..

How and where would you start? What are the best introductory texts for organic chemistry, physical organic chemistry? Are there still texts, or is everything on the web now? What is the best place to read about NMR and structure determination (just beginning back then), computational chemistry (practically nonexistent back then — they were still sweating H2+). Also is Debye Huckel theory still what we used to think about it — good for slightly impure distilled water, but not much else. Something better is needed for cell water which is 0.3 molar..

I love the irreverance of the chemical blogs. Have at it folks.

and

Thanks

I got this back the same day from Excimer:

I’ll bite: my favorite introductory chem text is by Jones- it has pretty widespread use throughout undergraduate classes still, and I like Anslyn and Dougherty’s “Modern Physical Organic Chemistry” for that subject.

and from Paul:

Excimer mentions my two favorite undergraduate organic texts. I would also consider ordering the solutions manual to Jones, then working out some of the problems. There are few things more satisfying than being able to solve problems to convince yourself you understand what’s going on. If you’re super-excited, what about enrolling in an orgo course at a local community college? Taking courses on a subject always gives me extra motivation to learn things, since you have to stick to a schedule.

So I bought the above (the solution manual hasn’t arrived yet) and started working through Jones ‘04.  Anslyn looks like something I should read after Jones.   I was impressed with how different Jones is than how I remembered my first Organic text (English & Cassidy 2nd Ed. ‘56) so I managed to find a copy on the net and it arrived today.  The next post will contrast the two books.

So this series will be sort of “Rip Van Winkle meets Modern Organic Chemistry”.  Why should you bother reading what’s coming?   Just imagine quitting grad school with what you know and spending the next 45 years reading molecular biology and biochemistry with the background you currently have (in your spare time while going to med school and practicing neurology that is).  I guarantee you’d find it primitive and rather simplistic but would have no problem understanding what’s going on.   So there will be tidbits here and there that you’re unlikely to find elsewhere (such as why Jones is wrong about Strychnine poisoning — I saw a case, and how the cell lets potassium inside while excluding the smaller sodium ion — if you don’t know the answer think of how you’d design a protein to do it — MacKinnon won a Nobel for it — if you can’t wait.  I can assure you that no one had a clue until the structure was solved.  There was a lot of handwaving about differential absorption of Na and K to proteins, and that great fudge factor that no one could calculate — the activity coefficient.

Stay tuned,

Retread

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