I’ll Miss Org Prep Daily

by James

in Teaching

I keep telling certain people that the “Master” in “Master Organic Chemistry” is a verb, not a noun.  I’m not , God forbid, a “Master of Organic Chemistry”:  Mastery is a journey, not necessarily a destination. That goes for me just as much as anyone who is studying organic chemistry for the first time. There’s always new things to learn.

However, there are people you come across every once in awhile who are singularly impressive in their breadth of knowledge and experience in the field, that the noun form of “Master” suits them well.  One of them essentially retired from blogging last month.  His handle is Milkshake, and for the past five years he’s run a little blog called Org Prep Daily.

Here’s what I’ll miss.

1. Reliable, detailed, well-written procedures

The “Prep” in the title doesn’t refer to preparing for organic chemistry exams or courses. In the field, a “prep” is a “preparation”, like a recipe. One recurring problem for organic chemists is in finding reliable processes for making certain compounds. With some journals (or research groups) there’s a nagging question: “do I trust this prep enough to invest my time in trying it?”.  The purpose of Org Prep Daily was to provide proven, reliable, well-written procedures for synthesizing organic compounds. Milkshake took all of his most reliable procedures over the years which had not been published,  wrote them up, and blogged them. That’s valuable. In addition, there were occasional insightful posts on practical lab matters, as well as on  studying, life in biotech,  and many more.

2. Insightful responses to obscure questions

On another level, Org Prep Daily was an advice blog. It was where Ph.D. level chemists went when they were stuck with their synthesis and are looking for practical insight on how to solve different synthetic problems.

A typical exchange:  (remember, organic chemists speak their own language: this actually makes perfect sense in chemistry-ese)

(commenter)  hi guys,

does here anybody know how to make acrylamide of poor nuclophile nitrogen atom, such as pyrrole, indole etc!acyl chloride and mixed carbonate (acrylic acid and isobutylchloroformate with NMM in THF)did not work well..

thanks!!

——

(milkshake) yah, this is a serious problem with acryloyl chloride and other activated forms of acrylic acid – they crap up very easily, for example by conjugate addition. I would try an experiment with a weak base like pyridine (or 2,6-lutidine) and acryloyl chloride. If this does not work I would suggest the N-silylation trick with acryloyl chloride and CuCl2 as a catalyst, as described in: Catriona Thom and Philip Kocienski: Synthesis (1991 or 1992, I am not sure) page 582-586

In addition, Milkshake is a handy guy to have around when you’re trying to figure out the compounds in your earwax.

(source: archive.tenderbutton.com)

Dylan   “So I co-spotted my earwax (EW) against cholesterol (C) and squalene (SQ). Both were in there, along with some unidentified component with an intermediate Rf that streaks a bit. No clue what that is…”

Milkshake FYI: the unidentified spot is probably lanosterol.

Dylan: milkshake: I am equal parts impressed and freightened by your predictivate powers. see update.

Milkshake I did not see the wiki entry but I knew lanosterol is on the path and it should be a little bit faster than cholesterol because of extra methyl. I figured if lanosterol is the major greasy stuff in sheep wool, it must be in Dylan’s ears too.

3. The best stories of near-death chemistry experiences you’ve ever read

Every organic chemist who’s been in a lab for long enough could probably give you a few war stories about fires, explosions, and near death experiences they’ve had. But how many people make tear gas on their balcony in seventh grade? Or have glass removed from their corneas – from two separate explosions, with two separate explosive reagents – before the age of 14?

Or do things like this in high school?:

 I was trying to synthesize papaverine, and this was completely above my ability (and the lab resources) but I was very persistent…. First I made lots of methyl iodide, from red P + iodine and methanol – refluxing and distilling it on the bench so I know how methyl iodide smells – but the methylation was messy. Next I tried to make dimethyl sulfate from sulfuryl chloride and methoxide in situ, and it worked to some degree – the vanilla smell of guaiacol was everywhere – but again I could not isolate anything from the mess. So my next idea was to use diazomethane made from nitrosomethyl urea…

Methyl iodide, dimethylsulfate, and diazomethane are all compounds that serious chemists will double-glove themselves for, since they’re such notorious carcinogens. To make them in high school, with a miniumum of protective equipment? Damn! 

Here are more stories. Read them. They are great.

For people starting out as chemists, there are great lessons here too. In the beginning you will make a ton of mistakes. Everyone starts from nowhere, and builds their way up – the hard way. In fact, as a young student in his native Prague, he had the nickname “Bořivoj” .  It translates as ”the one who tears down the places”.

So if you are just starting your chemistry career and if you think you are clumsy and inadequate, don’t feel that way. Everybody has a personal quota to fill – of dumb things to do, of fume hoods to set on fire and the labs to flood.  But remember to wear the protective glasses.  Never make acetonperoxide or iodonitride and never load up mol-scale preparations on the first run.

Shakespeare and Marcus Aurelius quotes. 

Can’t find any of his cited examples at the moment. But they’re out there. Here’s one that seems appropriate.

  • Have I done something for the general interest? Well then I have had my reward. Let this always be present to thy mind, and never stop doing such good. Meditations of Marcus Aurelius, XI, 4

——

I wish him the best of luck in his new job, but I hope that someday he decides to go back to sharing his thoughts on organic chemistry: there’s a lot of valuable stuff in his brain to learn from.  If there is a true “Master of Organic Chemistry”, in the chemistry blogosphere, Milkshake is it.

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{ 4 comments… read them below or add one }

Chemjobber July 6, 2011 at 10:11 am

My favorite lab disaster story from Milkshake:

But there was another like-minded highschool kid, repeatedly working on some chemistry involving acetone cyanohydrine, and he was making it from acetone and NaCN, in our little fume hood with a lousy fan-driven exhaust. I think he never finished his project either but I remember once we were going down the stairway and he was saying “I don’t know if this exhaust really works ’cause I was smelling hydrogen cyanide this time a lot” and then we got outside there were two dead pigeons on the grass and we looked up and the exhaust from our fume hood was looming right above us…

http://orgprepdaily.wordpress.com/2008/11/25/more-lab-disasters-2/

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mamid July 7, 2011 at 5:45 am

Yes, I hope milkshake will be back some time, sooner rather than later. I only discovered his blog this year, but, my God, what a treasure!

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BRSM July 9, 2011 at 4:50 am

A well written eulogy. I’m sure people will continue to read the org. prep. daily archives and hope. Unfortunately, I discovered the tenderblog too late, but still greatly enjoyed reading the archived material. A friend of mine only discovered it last week and is currently working through it. Milkshake’s Bořivoj (which I read as ‘demolition man’) stories are amazing, and remind me a lot of some of Max Gergel’s adventures from his classic book Excuse Me Sir, Would You Like To Buy A Kilo Of Isopropyl Bromide?

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Another chemistry graduate July 18, 2011 at 11:30 pm

He is a genius and gifted chemist. I discovered his blog when I started my graduate school. He will always be there to answer your chemistry inquiries :)

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