Saturday, December 3, 2016

Better Than Word of Mouth

Hello, dear readers. It's been...a while. I promise the blog is not dead, just sleeping for now. My 2017 New Year's resolutions include sculpting specific time out for all the sci-writing goodness. Stay tuned.

Enough maudlin overtures. Now, on to the fun!

Strem has, as any synthetic guru would attest, the highest-quality metal precursors in the biz.* Now, you could spend a weekend cracking ampoules to find out, or just open to the Supporting Information of one of Jeff Bode's recent publications in Org. Lett. Perhaps you remember this reaction - SnAP synthesis of saturated heterocycles - best from a cheeky Derek Lowe tweet:

That's in reference to the stoichiometric incorporation of tin** in the reagent, which serves as a linchpin for the eventual transmetalation to a copper species and ring closure, neatly without disturbance of the ipso heteroatomic group.

Well, much to my surprise, Prof. Bode has climbed on the recent trend of showing one's work through tactful inclusion of smartphone pics to buoy up procedure adoption. Especially with fussy transition metals, valency, contaminants, poor environment, and a whole host of other factors lead to catalyst poisoning and color changes. In the SnAP case, the litmus test seems to be formation of a correctly ligated Cu(II) ion in lutidine relative to the (probable) hexaaquo cuprate species formed as a blue heterogeneous train wreck.

The kicker? The fairly indiscreet preference for the Strem copper(II) precursor over all other suppliers. Look at the change! Night and day, and key to making these reactions work.

You couldn't buy better advertising than this....right, Strem?
Bravo, Bode group! I look forward to seeing your colorful coupling chemistry in future reads.


*Dear Strem: please send non-sequential $50 bills to See Arr Oh at Big City Company, USA
**SnAP. Get it? [drum kit]

Monday, August 29, 2016

A Tale by Mail

Long-time readers will no doubt be aware of my running affectation with the "Profiles, Pathways, and Dreams" series of books from ACS; books which, had I not read them in grad school, would probably cause this blog to never exist.

So I have a sneaky hobby: scouring the Internet's used book counter to assemble an entire set. Thus far, I've collected 17 of the 22 from the original 1990-1995 run. As I'm simultaneously trying for thrift, I'm proud to say the most I've paid for one of these books was around $25.

One of the best came in the mail only today - a first-edition, basically mint copy of Djerassi's Steroids Made it Possible. You know, the one with the picture of Nobelist R.B. Woodward going Mike Tyson's Punch-Out! on another esteemed chemist?

Steroids Made it Possible, ACS Books, p. 60

I open the plastic packaging, breathe in the old-book-paper smell.  But wait, there's no library markings. And the book is, what, 26 years old, and is basically undamaged? Curiously, I opened the cover, and realized that Djerassi himself had dedicated it:

To whom, exactly? Why, to Larry Lehmkuhl, the previous president of St. Jude Medical, according to Bloomberg. And is that really Carl's signature? I've compared it against two *for sale* on eBay and at Amazon - $89 euro and $39.85, as of this writing, respectively - it's the real McCoy.

This, of course, raises more questions: Did Lehmkuhl ever read his gift? Was he from a chemistry background? (I can't find much about him through the usual channels).

Did Djerassi mail out copies of his books, en masse, to anyone interested? If so, perhaps other signed treasures are out there, waiting to be found.

Sunday, August 21, 2016

ETC: Vonnegut, Djerassi, and a Mystery Polymer

I've recently finished the 1973 novel Breakfast of Champions, by acclaimed science fiction / humor writer Kurt Vonnegut. For those unfamiliar with Vonnegut's work, I enjoy drawing parallels* between him and "chemical provocateur" Carl Djerassi.

These two men share some odd similarities: born within 13 months of one another, each man suffered the Second World War - Djerassi as a refugee; Vonnegut as a POW - and had their personal lives scarred by young, tragic deaths in their families. Nevertheless, both became prolific writers of short stories, novels, and plays, and both lived to be elder statesmen in their chosen careers: Vonnegut to 85, and Djerassi to 91.

I'd even wager that they looked somewhat alike, with their bushy mustaches, well-coiffed hair, stylish clothing and impish eyes:

Novelist Kurt Vonnegut
Credit: Enotes

Chemist and writer Carl Djerassi
Credit: DLD / Stanford

Breakfast of Champions convinced me that Vonnegut may have had more than a passing fancy for chemistry, himself. Consider this hand-drawn rendering of a mystery plastic, ostensibly factory run-off that main character Kilgore Trout has unfortunately found stuck to his feet after wading through a river in Midland City, Michigan:

Credit: Kurt Vonnegut, Breakfast of Champions
Clearly, that's a cyanoacrylate co-polymer - think Superglue - and it seems to be drawn with a dendrimeric A-B-A architecture. I'm guessing that the ethylene glycol spacers (O-CH2-CH2-O) are meant to suggest the foaminess several characters encounter in the novel, that this mystery polymer is "...the stuff f***ing up Sacred Miracle Cave...", an in-book tourist trap overrun by large, odorous brown bubbles.

Incidentally, I love Vonnegut's inference for the continued polymer chain; where we chemists might write n, Vonnegut inserts his time-work "ETC."

Why? I'll let the author explain his philosophy:
"The man who taught me how to diagram a segment of a molecule of plastic was Professor Walter H. Stockmayer of Dartmouth College. He is a distinguished physical chemist, and an amusing and useful friend of mine. I did not make him up. I would like to be Professor Walter H. Stockmayer. He is a brilliant pianist. He skis like a dream.
 And when he sketched a plausible molecule, he indicated points where it would go on and on just as I have indicated them - with an abbreviation that means sameness without end.
 The proper ending for and story about people it seems to me, since life is now a polymer in which the Earth is wrapped so tightly, should be that same abbreviation . . .it is in order to acknowledge the continuity of that polymer that I begin so many sentences with 'And' and 'So,' and end so many paragraphs with '...and so on.' 
And so on. 'It's all like an ocean!' cried Dostoevski. I say it's all like cellophane."
Sometimes you encounter (surprisingly accurate) chemistry in places you didn't expect.
So it goes.

*Bonus: Here's Roald Hoffman interviewing both authors in a 1999 piece for American Scientist magazine

Monday, August 1, 2016

Enthusiasm Goes a Long Way

Earlier today, I watched a scientific speaker drive people out of the seminar room.

Was the person combative? Not at all; a well-respected mid-career chemist at a Top-5 school.
Unprepared? Nope; knew the slides backward and forwards.
Bad material? It was the linchpin talk of the session,
Perhaps haughty, egotistical, or rude? Still no - a model in professional conduct.

The talk was just, in a word...boring.

Source: Sydney Morning Herald

However exciting the science, you can't capture the audience if the delivery is dull as dishwater. Literally dozens of posts, listicles, humor attempts, even entire blogs (here, here) have been dedicated to the practice of scientific communication. So why don't these suggestions permeate into the wider community? Why do smart people not consider how their message comes across?

I won't go into the particulars of the talk I saw overmuch. Suffice to say that slumped shoulders, wooden expression, monotone delivery, and stiff arms will have your audience reaching for their smartphones in no time. Ditto: wordy slides, insider jargon, and attempts to somehow mash a 50-minute talk into a 30 minute time slot.

One wonders if, after a certain number of conferences, chemists have become inured to terrible talks. Perhaps we should consider installing a "canary" in the lecture hall "coalmine" - a speaking coach or senior faculty member, placed front and center, that can debrief the overall performance after the session, offer pointers, maybe even solicit feedback from the audience.

Optionally, what about Improv? Many fields - business consultants, customer service, construction, education - have benefited from comedy troupes teaching teams to think on their feet. Anyone have something like that occurring at their lab or university?

I'm not arguing that scientific talks be misconstrued as entertainment, yet I feel I could have learned more if I were actively on the edge of my seat, waiting to hear the next assay result or to see the next structure proof.

Anyone else agree?

Friday, July 29, 2016

Synthetic Endgame

Inspired by this paper from Melanie Sanford's rocking organometallic group at Michigan.

*Pun contest! I could also have called this post...

Gotta Make 'Em All
Poke-Ball and Stick Models
Chantix Charmander
Putting the Fun in C-H FUNctionalization
'All Thumbs' Synthesis

Friday Fun: Semi-Legal Starting Materials

I ran across this entertaining anecdote today while researching Lord Todd's research into vitamin B1.

From Todd's 1997 obituary in the Independent, written by fellow Nobelist "Kappa" Cornforth:
"[Todd] also worked on cannabis, and in his excellent autobiography A Time to Remember (1983) he tells with relish the story that, having naively imported 6 lb of distilled cannabis resin donated by the Indian police, he had to promise Customs that he would send 25 copies of any ensuing paper to their Bureau of Drugs and Indecent Publications."
Apparently, the "ask forgiveness, not permission" dictum applied in mid-1930s London. It bears reminding that this same choice, made today, would result the appearance of severe gentlemen in dark suits with thick briefcases and Summons in hand at the lab entrance...

Happy Friday,
See Arr Oh

Sunday, July 17, 2016

Undergrad Tech: Remember When?

Recently, I sat with a friend sipping coffee, watching passers-by hurriedly moving from one tall building to another. Remarks drifted back towards research - as they're wont to do when chatting with chemists - and she said: "Remember how hard it was just to order things?"

I knew exactly what she meant. Lab tech changes quickly, and you may not even notice until you take a step away from the bench. I'm not part of the generation who spent hours sketching molecules by hand from a rubber template pre-ChemDraw, but nor am I a grad student in the era of tablet computers that can access PDB or Aldrich from a free wireless connection in any lecture hall.

Maybe I'll take a quick stroll down memory lane to see how different things really were when I first started undergraduate research...

Planning: Then, as now, most projects kicked off using pen-and-paper or chalkboard sessions; whiteboards were in about 30% of classrooms and gaining ground, but my first experiences with drawing molecules for my coworkers covered my fingers in tacky powder. I can still smell lab chalk: musty, earthy, sometimes tinged with a faint amine odor if stored too near the reagents cabinet.

Courtesy of Dr. Freddy, at Synthetic Remarks, who seems to recall
chalkboards much more fondly than I.

Once you'd had the discussion, you transcribed it into a lab notebook - usually bound with black vinyl, perhaps featuring brown or maroon faux-leather accents and a bookmark string - and signed the page. Then it was time to dive into the literature. First, you staked out some territory at one of the few hulking beige monitors attached to your shared lab computers. Plan for coffee, since reboots and blue-screen crashes could usually be expected to last 10 minutes, with accompanying Windows jingles or goofy Mac cursor wheels.

(Why were operating systems always a generation behind on shared computers?)

Your 10-minute excuse to go grab a coffee.

Beilstein and SciFinder both offered installed systems with single-user seats. This meant you walked down your lab hallway, shouting "Does anyone need anything on SciFinder?" before logging in. The user interfaces were very Internet 1.0 - muted grey windows, inscrutable black text, fuzzy structures. Mostly, you would up transcribing the reference into your notebook alongside the idea. To get the paper, you usually brought a stack of dimes down to the reference library, and spent the next 20 minutes finding and then copying (don't forget to rotate every other page!) the journal article. The still-warm, toner-scented stapled copies were lugged back to your wooden desk to be pored over until evening. My fingers would often be tinged with more than one color of highlighter or colored pen after a night of intense study.

SciFinder Scholar, 1999. Source:

Synthesis: OK, you know what you want to make, so you need some reagents. Maybe first you glanced through the 2,000-row Excel file your lab has as its de facto "inventory" system. I remember some groups also had a dog-eared, yellowing notebook dangling from a rope of masking tape that listed all the chemicals no one needed any longer - hope you enjoy distillation! Failing these approaches, the trusty catalogs are all lined up against the single lab window, effectively blocking out 20% of the available visual real estate. Names of vendors I remember included Fisher, VWR, Aldrich, Sigma, TCI, and Columbia. Each one had different account reps, pricing, and delivery specs; you'd better believe your boss would ask if you looked up pricey, boutique reagents in more than one source. Someone had the lab job of calling these vendors every few days, providing the lab P.O. number or group credit card, and then taking delivery later that week. Collections of cardboard boxes large and small would be piled near the front door, and every week was Christmas (even if it was just your reagent-grade TEA).

The first and last physical Aldrich catalogs I remember ordering from.
Source: Alfred Bader, Sigma-Aldrich
At some point, you'd have everything needed to run your experiment. Hours passed, TLCs ran, and you scribbled long-hand in that same lined lab notebook. I'm fairly certain I spent thousands of hours hunched over, detailing exactly how the workup went, or scrawling single-line corrections (with initials!) for changes and errors.

Analysis: Instruments fell largely into two camps - things you ran and printed out to later affix into 3-ring binders, or numbers on an LED screen you hastily scribbled onto a Post-it note. UV-Vis and optical rotation fell into this latter camp; I still smile whenever I see a forgotten, tucked-away bookmark reading "+8.75 deg."

I worked in lab right at the death knell of chart-recorders - little red pens in threaded holders that traced a curve based on numeric readouts from an IR or GC. NMR, graciously, always emerged on an ink-jet printer in the corner of a sub-level lab. I was a Bruker shim-jockey for quite a while, bragging that I could shim, acquire, FT, pick, and integrate an 8-scan 1H in under 2 minutes. Of course, many academic labs now have robotic cherry-pickers and automatic data transfer, which must save tons of time (unless you're a biophysicist or monitor kinetics; we might as well chain you to the 600MHz).

Source: Cal State LA / Bruker Instruments

Presentation: My first lab group still owned an overhead transparency viewer, and we were encouraged to print or sketch acetate slides each week for discussion. As these smudged easily when warm or done hastily, there were many grumblings and thrown elbows at the photocopier from fellow labmates on group meeting day. PowerPoint was reserved for "big" talks - oral exams, defense seminars, or preparing a poster for ACS meetings. Once saved and laid out the way you wanted, these were burned onto a CD-R or stored on a 100MB USB flash drive your boss might loan you. The walk to FedEx felt tense, because you didn't want to lose this uncomfortable piece of plastic, which contained the only copy of your slides.
Just don't write on the glass itself, or the PI will get really angry. Trust me.
Source: Amazon

I'm sure that I'm missing more fun events from lab life and technology from the late 20th century. Readers, if you have a special memory from back in the day, please feel free to share it in the comments. I'll update the post if I've missed something vital.