Friday, September 28, 2012

Friday Fun: Chem Swords

As Stuart Cantrill pointed out on Twitter this morning, today's xkcd comic hits all the right receptors for chemistry geeks:

xkcd #1114, c. Randall Munroe
So, in four short panels, we have jokes about Sb and Ac, role-playing games, LoTR, even an olde tyme word for "spooky." Perfect!

Here are my humble attempts*

- I forged a blade from iron oxide, but it just rusted away.
Source: Ted Wolf / Rankin-Bass

- Next, I made a silicon dioxide scimitar; it shattered like glass.

- My 'Einsteinium Excalibur' shrunk every three weeks.

 I have high hopes for my Osmium Sword of Omens; it roars, and dihydroxylates everything it touches!

- Magnesium Masamune: Victor Grignard's house blade.

- The neon lightsaber? Went over like a Pb balloon.

*I tossed some of these on Twitter before I sketched out the post. Please don't "Lehrerize" me for it! (Sounded better than "Breslowize")

Thursday, September 27, 2012

Methylamine Pseudoscience

Please see updates, posted below original piece. Thanks!

Pseudoscience strikes again. About a month ago, over at Slate's Brow Beat culture blog, Mr. Daniel Lametti - he of 'Ph.D.-Waste-Of-Time' fame - wrote a piece analyzing a recurring Breaking Bad plot device: the theft of large quantities of methylamine for the characters' illegal methamphetamine operation. The meat of the post:
"As a post on Reddit asks, since Walt is a brilliant chemist, couldn’t he just synthesize the stuff himself?
Yes, and pretty easily. There are many different ways to make the compound; with little more than an introductory organic chemistry class, you could probably synthesize it in your kitchen sink. (Brow Beat doesn’t recommend trying to make methylamine in your kitchen sink). Chemically speaking, methylamine is just ammonia with one hydrogen atom swapped out for a methyl group—a carbon atom and three hydrogen atoms. Without getting into too much detail, an easy way to achieve this swap* is to “bubble” ammonia (a gas) through methanol (a liquid) that’s been laced with a dehydrating agent like Silica gel. You could probably buy these chemicals at Home Depot and CVS. Silica gel packets are often packaged with new shoes and electronics to keep them dry."
Wait, huh? Let's start from No.

As a practicing synthetic organic chemist, I agree with the statement that silica gel dehydrates solvents by water absorption. Sure. But I've heated plenty of alcohols in the presence of silica gel, and 99% of them don't spontaneously lose water! (That would be a rocking olefin synthesis, if it worked...)

Methylamine: Easy as hooking up five pressurized reactors in your kitchen sink.
Credit: Albermarle
Let's put this on firm scientific ground. The reaction in question, a nucleophilic substitution, could theoretically occur by two mechanisms: SN1, where the -OH group of methanol dislodges to form a methyl cation (?!?!), followed by subsequent ammonia bonding; or SN2, where the ammonia directly displaces the -OH, one step, no intermediates.

In this scenario, both are extremely unlikely, especially at room temperature and pressure.

Now let's talk practicality: which company will sell you a cylinder of ammonia gas for 'home use?' (Not Home Depot). How will you get your methanol? What's the plan to isolate the (volatile, stinky) methylamine from the complex mixture of compounds this theoretical reaction produces?

Well, how do companies make methylamine? Albemarle technical documents to the rescue! Seems that mixing methanol and excess ammonia at 300-500 degrees Celsius, under pressure, over a zeolite catalyst will produce an equilibrium mixture of methylamine, dimethylamine, and trimethylamine (favored). After fractional distillation, the trimethylamine can be streamed over an amorphous silica / alumina catalyst to disproportionate it back into methylamine.

Not a kitchen sink in sight.

Update, 8/17/13 - This piece jumped back into the spotlight as Breaking Bad winds down its 5-season run. Thanks to Dylan at WaPo's Wonkblog for linking back here.

Commenters have taken issue with my description of the reaction, so I've slightly changed the text for clarity (methods / mechanisms, "forms" cations, oxidation...)

8/19/13 - Arguments have cropped up, in multiple forums, about reagent availability, feasibility of the chemistry at small-scale, mechanism, purification, etc. I blame myself for not refining my argument well enough in the original post. Very directly, I'll re-state the major arguments:

1) The silica gel + methanol + ammonia route will not produce methylamine as stated
2) Although an experienced chemist *could* produce methylamine using different reactions in a kitchen sink, he will by no means produce enough to support a burgeoning criminal enterprise which manufactures methamphetamine at multi-kilo scale.

*Curious - Appended at the bottom of the essay is a thanks for Prof. Adam Braunschweig, faculty at NYU now UMiami.. To what extent did Prof. Braunschweig proofread this post? Did he sign off on the "kitchen sink silica gel" concept in the middle? I can't possibly imagine that he thoroughly vetted this essay.

Wednesday, September 26, 2012

The Simpsons: Just Like "Cooking"

Ever have that feeling like you somehow missed the boat? 

Back in 2011, TV sitcom stalwart The Simpsons aired Episode #491 (NABF20), entitled "The Food Wife." I caught it in reruns for the first time tonight. Aside from the hilarious send-ups of celebrity chefs and uptown foodies, the episode turned a truly dark corner when it compared molecular gastronomy methamphetamine

Really, it's true - Gothamist and Esquire both scribed pieces about the show last year.

Credit: Simpsons Wikia | 20th Century Fox
Breaking Bad gives its swan song later this year. We know Walter and Jesse's lab work has truly permeated pop culture when references pop up on prime time comedy cartoon shows.

And how often do you get to see Homer Simpson stumble around a garage lab*? Priceless.

*(Even one that doesn't make any practical sense; are those goofy cones supposed to be filters? And why do TV writers always think we connect reflux retorts with 'mad scientist'-esque glass tubing?)

Welcome, Akirium?

Researchers at RIKEN in Japan announced today that they had most likely synthesized a few atoms of Ununtrium, or Element 113. Despite previous detections of the element by both RIKEN and a Russian group, further investigation by various international scientific agencies did not award naming rights to either party.

It'll never happen, but I can dream...
c. Katsuhiro Otomo
Now, I'm neither a physicist nor a nuclear chemist, so I'll leave explaining of atomic decay patterns to Phillip Broadwith over at Chemistry World. But I do love a good periodic table naming story, so I kinda hope that the Japanese group wins out. Not to disparage Russian nuclear research - it's top-notch - but they've named a few already (Dubnium, Flerovium), and most of the rest have come from Europe, the U.S., or come up through antiquity.

So, what would a Japanese-discovered element be called? Researchers at RIKEN have suggested some fairly bland entries: "rikenium," or "japonium," reflecting tradition in naming the new element after its place of discovery (wouldn't that second one be "nipponium?"). Names can also honor the researcher, which here might mean "Moritum."

Of course, I like to dream about names just slightly further afield. Akira, one of the more successful manga and a cultural touchstone, would make an excellent eponym: "Akirium."

Readers, what would you name a new element, if you had the chance?

Update, 9/27/12 - Readers from the Twitterverse suggest a few more candidates: "Nintendium," "Friday13eon," "Sonyicum," "Unlukium," and "Sushinium."

Saturday, September 22, 2012

Abstract Coloring Champion

I can find no words to adequately describe this picture. It's just so....fitting.

That's rainbow-colored Taxol in the background, for those unaware 
Image courtesy Rice University, Union-Tribune, San Diego

Friday, September 21, 2012

Friday Fun: Kevium

Kids, come closer, so ol' Uncle See Arr Oh can tell you about life in the '90s. See, back then, a postage stamp only cost $0.29, and "the Net" was still something you connected to with a modem!

Kevin French, from Mission Hill
(Warner Bros, Oakley / Weinstein)
I recently came across my Amazon dream sale: the entire Mission Hill series - all 13 episodes - for only $9.00. You may remember Mission Hill as the quirky, colorful cartoon show that was part of the [cough] original Adult Swim lineup on Cartoon Network, almost 15 years ago.

I had completely forgotten about the wacky uber-geek younger brother, Kevin French. He's the foil to cool older brother Andy, a struggling cartoonist in Boston. But, as the series progresses, you learn that Kevin's pretty cool, especially by today's standards: he loves science and math, plays online computer games, and gets into hilarious scrapes by trying to view the world through a rational lens. Kind of like The Big Bang Theory...but animated.

I also forgot that Kevin has a huge poster in his bedroom of "Kevium," supposedly element 108; this really shows the show's age, since 108 wasn't officially Hassium (Hs) until 1997! (I'll assume the producers did enough background research to notice Fr was already taken). As for those numbers on the bottom? Beats me. I guess they're supposed to be ionization energies or isotopic masses, but I think they just scribbled 'em in.

R.I.P. Jerome Horwitz, Medicinal Chemist

Multiple news outlets (NYT, SciAm, Karmanos) now report the passing of Jerome Horwitz, 93, a career medicinal chemist behind AIDS drugs such as AZT (1964), stavudine (1966), and dideoxycytidine (1967). Most obituaries focus on two facets from his life:
  1. His invention of AZT, a drug so synonymous with AIDS treatment that it's been mentioned in raps, novels, and Broadway shows.
  2. His perceived failure to patent his antiviral molecules, thus "costing" him and Wayne State University millions in revenue realized instead by Burroughs Wellcome (later GSK). 
First report of AZT, J. Org. Chem. 1964, p. 2076*
I want to take a slightly different tack on Horwitz's career. For my money, he met all the criteria for a successful career in organic chemistry. He published >100 articles and book chapters; not a one-trick nucleoside pony, Horwitz's work covered sterols, acridines, tetrazoyl ylides, epoxide rearrangements, and analogue development of anticancer drug XK469. He had a fifty-year career as a professor at two universities. His work led to (at least) three approved drugs.

He even has a statue installed at Detroit Medical Center.

Even more interesting, he accomplished nearly everything in his career while staying in one place: Michigan. He jumped outside (briefly) to Illinois for a postdoc at Northwestern, but all other schooling and professional work came from in and around Detroit. It's amazing to me, given how much I and others have moved around for a career in science, that his tenure in one metro area lasted for a lifetime.

*Side note: When I look up old papers, I enjoy seeing who else I recognize among the authors in the same issue. 1964 must have been quite heady - in the same issue with AZT, we have papers by Nakanishi, H.C. Brown, Bill Dauben, Alfred Blomquist, and John Baldwin.

Thursday, September 20, 2012

Nicolaou to Rice - Official!

KCN, all smiles, after confirming
what we all knew anywa
(Click here for the Rice Press Release, issued Thursday, Sept. 20)

Some interesting tidbits about the move:

- The $6 Million** Dollar Man: No, not Col. Steve Austin...KCN! The figure is accurate, as first reported in the comments of Derek's blog.

- "Formidable Alliance against cancer." K.C. is apparently the crown jewel for an as-yet-unannounced super-team* of scientists. Probably doesn't hurt that M.D. Anderson, a leading Houston hospital, is down the street. The CPRIT file that listed Nicolaou includes funds for 8 other "Established" professors; if Rice gets 'em all, they'll be a force for biomedical research.

- Family Connection: As stated elsewhere (and mentioned through personal communications earlier in the week) the fact that his daughter Colette, a Psychology lecturer, works at Rice certainly factored into the decision.

- Timeline: Looks like the move won't happen immediately. Having announced the move, K.C. now waits for his new lab space to be custom built in the Rice BioScience Research Collaborative. Perhaps he'll have time in the intervening year to write "Classics IV - A New Hope"

*(Update, 9/20 - This presser has to have some of the best superlatives ever used to describe a chemist. In sixteen paragraphs, it calls him "great leader," "legendary," "cancer drug pioneer," "formidable," "prodigious intellect," "distinguished," "super-star researcher," "transformative," and "devot[ed] to the craft of teaching." Wow. Whomever wrote this release, I want them to do my obit someday!)
**(Update, 9/22 - The author of this article points out that K.C.'s total compensation will be closer to 9 million dollars, after Rice raises a $3 million matching fund. Ye Gods.)

Dirty Hood = Good Hood

Ever worked in a completely new chemical fume hood?

I have. Actually, due to moves and new facility construction, I've been (lucky?) to have three completely new hoods - hoods devoid of any smells, stains, or funny noises. All still had working baffles, legible installation labels, functioning flow meters, and bright white walls.

I ruined them all.

Chemjobber's latest post, referring to a "stinky walk-in hood," along with Pauling's lab notebooks got me thinking: How many times have I had to strip everything out of my hood, and start from scratch? I counted at least three; each one occurring in a beautiful, unsullied space.

In graduate school, I set up a sodium-mediated halogen exchange / rearrangement a few weeks after our move. After carefully flame-drying the apparatus, I greased and clamped all the joints, and set it to heat in an oil bath. I lowered the hood, and walked the ten feet or so to my desk...boom! We had a motley crew of older hot plates that didn't always heat up like you'd hope. Best I could piece together, there was an autoinitiation, followed by a massive exotherm I hadn't observed on smaller scale. Best part? After splattering my hood with compound, the flying glass cracked the oil bath, and little pieces of flaming sodium rained down around the pool of oil forming below my stir plate. Good times.
Total cleanup time: 3 days

As a postdoc, I had the "honor" of installing my own monkey bars, manifold, and otherwise arranging my virgin hood exactly as I pleased. Fast forward about a year, when I decided that a fairly exothermic borohydride reduction would go much better with a solid addition funnel. I'd covered all my bases - passive N2, massive cooling bath, flame-dried everything, the works! Except for one tiny variable: the borohydride particle size was too fine for the funnel's Teflon screw. One turn led to accidental addition of about half the reactant. Upon solution contact, the sudden gas release blew backwards into the solid addition funnel, which commenced to shoot a fine dust of borohydride onto every hood surface, including my arms.
Total cleanup time: 2 days

Later into my career, I had another heated reaction fail in stupendous fashion. The compound, a gummy orange solid, coated every surface of my hood: behind the sash, inside the light ballast, up the baffles, even down into the storage cabinets underneath. When I was finally done with that cleanup, my lab coat had been stained so thoroughly orange that we just bagged it and sent it out as waste.
Total cleanup time: 2 days

Look, all of these incidents would have been much worse if my sash had been up, or if I hadn't been wearing correct PPE when they occurred. We think about fume hoods as big vacuum boxes, but they're also great for containment of runaway reactions.

Readers: I know I'm not alone. Have a spectacular story of a reaction gone wrong? Share it in the comments.

Monday, September 17, 2012

A Few More Thoughts on Faculty Moves

While looking back at the map I made for my earlier post today, I had a few "deeper thoughts" about the faculty moving process.

- Is it just me, or do all the moves seem to be to warmer places? Even funnier, some mention it in the press releases following their moves. Take this gem, from Greg Fu:
" does not hurt, [Fu] adds, that he gets to leave those cold Cambridge winters behind."
A future Prof practices
for his first faculty move
- Although I claim that the moves are often prestige-based, i.e. to move into a highly-ranked university, several of these moves buck the trend. Finn moved from Scripps (#7) to Georgia Tech (#26), and Woerpel from Irvine (#26) to NYU (#67). If Nicolaou does indeed move to Rice, he'll be moving from #7 to #33. Now, I realize there's other rankings in town (see Chronicle, Times), and the "big fish" mentality suggests these rankings will improve once the new recruit sets foot on campus. But I'd still argue that some of these were lateral moves at best.

- What's up with the Pacific Northwest? The South? The Rockies? How come nobody from these places seems to move around? Either everyone in these locations is completely satisfied with their lives, positions, and income, or there's some dynamics between the East and Left Coast that I haven't yet figured out. 

Readers, what do you think?

Chemistry Bumper Cars

By now, most folks on the chemblogosphere have heard the rumbles about K.C. Nicolaou's possible departure from Scripps. His landing spot looks to be Rice University, in Houston, aided by a generous multi-million dollar "golden parachute." Followup comments posted on Chemjobber and In the Pipeline saw speculation run rampant regarding other Scripps synthetic chemists, including M.G. Finn, Jin-Quan Yu, Phil Baran, and Dale Boger.

Wow. Does everyone have the moving bug?

I seem to recall Kyle over at The Chem Blog drawing us a convenient map a few years back, during another busy moving season (2005, I believe?). The past two years have proven quite busy as well, with no less than an entire ChemBark post entitled "Nocera to Harvard!" (vide infra).

Without further ado, I present my highly-researched, but definitely not-to-scale, map of synthetic faculty moves, 2011-2012.

Legend (Updated 9/20):
1.  Keith (purple) Woerpel, Irvine to NYU
2.  John (Berkeley blue) Hartwig, UIUC to Berkeley
3.  Vy (green) Dong, Toronto to Irvine
4.  Dan (crimson) Nocera, MIT to Harvard
5.  O(maroon) Yaghi, UCLA to Berkeley
6.  M.(Goldenrod) Finn, Scripps to Georgia Tech
7.  K.(Cyprus orange) Nicolaou, Scripps to Rice (confirmed!)
8.  Greg Fu(schia), MIT to Caltech
9.  (Rust)em Ismagilov, Chicago to Caltech
10. Paul (cyan) Chirik, Cornell to Princeton

I've been searching for a chemistry faculty movement metaphor. At the end of the NFL season, reporters write about the "coaching carousel," where coaches switch jobs circuitously, trapped on an employment merry-go-round. Well, that's not quite right here. Chemists usually move away for good, and there's clearly a directionality to the moves: towards more money, higher prestige, or warmer climes. Perhaps a Ferris wheel? Nah: it implies "up" or "down," a good view of the situation...and far too smooth a ride. Negative on the Gravitron, though grads and postdocs might feel like they're smashed by the pressing gravity* of an upcoming move.

I've got it: Bumper cars! Everyone starts out hesitantly, driving around in circles, hesitant to make first contact. After a few minutes, though, it's a free-for-all, everyone bouncing off each other, crashing, laughing, sparks flying off the ceiling. In the end, no one ends up where they started, and everyone has headaches. (Bear with me, it's a work in progress, doesn't yet have the oomph of a "Manifest Destiny" or "fiscal cliff.")

Faculty jostle for top spots like, well, you get it...
Credit: UK Telegraph

Are faculty moves unavoidable? It's true that the grass is always greener. But, if you're already a professor at a Top 20 institution, you likely receive the lion's share of grant monies, decent media coverage, and your pick from top-shelf graduate students. So why go? Some moves are nostalgia-driven - the Prof. wants to return home to a welcoming parade, having "done good." Some moves try to fix the two-body problem. Some happen because of missed tenure, or a feeling that it's "just time." Maybe in today's uncertain economy, it's just best to assume you won't be in any job longer than ten years...with a handful of exceptions.

Readers: Know of any more high-profile U-Hauls being loaded this academic season? If the "Chemistry Bumper Cars" trend persists, this might yet become an annual post.

P.S. Heard about a move I missed? Email me at seearroh_AT_gmail, and I'll add it here!

*I completely understand, having been involved with two moves in grad and postdoc.

Thursday, September 13, 2012

Hall Pass Top Ten

Apologies for my recent blogging absence. I've been...

1. Trapped in a cargo crate on the high seas, eating bugs and crackers, with only gull cries and typhoons to amuse me. Help!

2. Entering development data into an Excel spreadsheet by hand, from 70 years of targets.

3. Abducted by aliens. I haven't been probed or dissected, but they really, really want me to tell them about organocatalysis and NanoPutians.

11. Messing with the bull, and got the horns.
4. Sleeping (not).

5. Furiously scribbling down every potential idea for a major grant renewal.

6. Stuck in traffic.

7. Eating my way out of a giant cake.

8. Downloading, scanning, printing, "borrowing," recording, and photographing disparate data for a very looooong document.

9. LMAO.

10. Working.

Regular posts [should] resume next week. Stay tuned!

(P.S. Cheat sheet - Nos. 2, 5, 8, and 11 are pretty much true...)