Hail and farewell to the New Clayden pp. 1169 – 1181

Finished at last, in just over 6 months.  A magnificent introduction to organic chemistry (for the future chemist, not for the pre-med.  Far too much detail). As noted in some inserts on the last few posts, the book enables you to read organic papers appearing currently in Nature and Science. Hopefully the authors will get whatever they wanted (fame, glory, money?) from the tremendous effort it must have taken to revise the first edition. Bravo and Thank you all ! ! !

1169 Glivec (imatinib) is Gleevec in the USA

1170  Fluouracil doen’t modify uracil. It inhibits one of the enzymes in the thymidine biosynthetic pathway (thymidylate synthase), resulting in a deficiency in one of the 4 nucleosides making up DNA. 

1171 “Blocking HIV protease inhibitors means mimicking the proteins they  slice up.”

What you are trying to block is the (single) HIV protease with an inhibitor.

The sentence should read 

“Blocking the  HIV protease means mimicking the proteins it slices up.”

1172 “This stops the drug being hydrolyzed, but the drug also has to stop the viral protein being hydrolyzed”
The sentence should read
“This stops the drug from being hydrolyzed, but the drug also has to stop the viral polyprotein from being hydrolyzed”  or (if you don’t want to explain what a polyprotein actually is)

“This stops the drug from being hydrolyzed, but the drug also has to stop the target of the viral protease from being hydrolyzed”

1172 There has been a lot of commentary that research into synthetic organic chemistry and the synthesis of large molecules is more an art form than useful science.  The emergency large scale synthesis of indinavir in gram quantities described here puts the lie to that.  No “Manhattan” project to make it in large quantities could have succeeded without a lot of synthetic reactions developed purely for their interest previously.  – Of interest that the last section “The Future of Organic Chemistry”  pp. 1179 –> makes exactly this point (but I hadn’t read it before writing the above). 

1177 The clever synthesis of oseltamivir by Corey (birthdate 1928) in ’06 shows that he hasn’t resting on his laurels.  As a mathematician said about a difficult problem he threw out for all to solve in 1697, which was solved anonymously.  “I recognize the lion by his paw” — the lion was Newton of course. 

1178 — Not clear why the attack of N bromoacetamide in the presence of SnBr4 results in a bromonium ion on the same side as the NHBoc group.

1181 — Nice ending to the book, but it would have been helpful if they actually recommended books they like on “orbitals and chemical reactions, NMR spectroscopy, molecular modeling, physical chemisty, photochemistry, enzyme mechanisms, biosynthesis, organometally chemistry, asymmetric synthesis (assuming there are any), supramolecular chemistry and polymer and materials chemistry.”

So what’s next?  PChem (not physical organic), statistical mechanics (particularly Molecular Driving Forces as recommended by WaveFunction).  Why?  Because so much of what goes on in the cell is determined by the physical interaction (not chemical) of the cells components (proteins, lipids, metabolites).  We wouldn’t be alive without enzymes and chemical transformations, but there’s far more going than that.  One example:  The processes which determine where and when a given protein coding gene is expressed are purely physical, involving binding of proteins to DNA (and each other), and changes in conformation as they do so.  To be sure, RNA polymerase II is a magnificent molecular machine which involves a good deal of chemistry, but the factors determining where and when aren’t chemical.

So there’s a lot of molecular biology I’ve put aside to write about later, and later is now. I’ve got 6 PNAS’s and 1 Cell sitting beneath my desk with tags in them marking very interesting molecular biology.

Here is where teleology raises its head.  As soon as you ask what something is for, chemistry is silent.  It can only tell you how something happens, not why.  It’s the Cartesian dualism all over again — see http://luysii.wordpress.com/2011/05/11/the-limits-of-chemical-reductionism/

Of course I plan to continue reading organic chemistry thanks to the background Clayden has provided.

Then there’s relativity and the mathematics behind it — a very long term project, hopefully not longer than my 74.5 year old brain holds out.  For why see http://luysii.wordpress.com/2012/09/11/why-math-is-hard-for-me-and-organic-chemistry-is-easy/

Happy thanksgiving to all ! ! !  My son says he likes it because it’s probably the most inclusive holiday we have.
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Comments

  • Curious Wavefunction  On November 16, 2012 at 5:48 pm

    As you probably know, the mathematician was Bernoulli, and the problem was the brachistochrone or the curve of fastest descent.

    Well-done.

  • luysii  On November 16, 2012 at 5:52 pm

    I did. However, putting it in would result what one son (a web designer and information architect) calls TMI (too much information).

  • Curious Wavefunction  On November 20, 2012 at 3:02 pm

    Happy Thanksgiving to you two by the way!

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