Sunday, May 1, 2016

X-Files' Freezing Catalyst: Digging Deeper

A random Friday afternoon link at Chemjobber's place clued me into Mitch's post, about a random NMR encountered in an old episode of '90s sci-fi classic The X-Files. By some odd coincidence I, too, was watching the episode sometime in early April, though I didn't get my notes and pictures together in time. Alas.

(Before we get too hung up on the episode's premise - that in 1996 computational chemists at MIT were performing in silico calculations on a "catalyst" intended for rapid body freezing - let's also remember that this episode shows us protagonist Lisa, a wunderkind doctor / chemist / radiologist, strutting out of her lab sans questioning after her patient spontaneously combusts!)

Now, to the structure of "Compound X" - I took a close-up of the computer terminal Lisa's working on, right around 17:00. Yes, folks, that's 1,2-dichloro-1,1,2,2-tetrahelio-ethane. Carbon-helium bonds can't exist, shout the skeptics? Well, 1993 marked production of the first He@C60 clathrate (story here), and friend of the blog Henry Rzepa had a theoretical paper in 2010 discussing charge-shift C-He bonding. True, isolable heliocarbons are still at large, for anyone seeking a high-risk, high-reward tenure project [ducks].

Molecular modeling has always looked best on Macs. There, I said it.
Fox Broadcasting Corp.

In his post, Mitch calls attention to the NMR, though I found the second analytical spectrum more entertaining, since it has an actual reference printed across the top. Turns out the producers did their homework for this one - this spectrum is an example of spectral linear combination to quantify small amounts of metabolites in blood plasma - good call!

Real science! In a sci-fi show! Who knew?
Fox Broadcasting Corp.

Back to the (flimsy) plot: certain details are over-the-top cheesy, like the "hand scanner" Jason uses to access his facility - it looks like it was built from an old dot-matrix calculator screen screwed into a subway post:

State-of-the-art security for the "MIT Biomedical Research Facility"
Alternate caption: I spent a weekend building this prop, and they used it for 4 seconds of footage.
Fox Broadcasting Corp.

The writers have also presaged the warm-liquid-goo-phase meme from Austin Powers, as the antidote to the freezing catalyst seems to be epinephrine, DMSO, electroshock...and complete-body immersion in a human-sized deep fryer:

Warm liquid goo phase - Complete!
Fox Broadcasting Corp.

Spoiler alert - the concluding scene, a conflagration in the "MIT computer mainframe," would likely have set the Schrock and Buchwald groups back quite a number of years.

Finally, I'll leave you with a silly futuristic quote: "The technology to engineer [Compound X] is still 5, 10 years away..." Sorry, Dr. Lisa - it's been 23 years since this episode aired, and to my knowledge, we're still not making per-heliated small molecules. Maybe check back in another three decades.

If you enjoyed this post, try some of the others in the Chemistry Movie Carnival from 2013.

Sunday, April 24, 2016

Feng Zhang's CRISPR "Miami Moment"

I've spent a bit of time this week trying to grok the ever-expanding frontier where biology meets chemistry. RNA therapeutics, chemical probes, synthetic biology, protein engineering...I could go on and on. Of course, this list would be woefully incomplete without the new cool kid: CRISPR.

If you've read a few of the stories surrounding this field's origins, you'll recognize the names Doudna, Charpentier, and Zhang. An interesting story arc emerges in the countless biographies surrounding Feng Zhang, now at MIT / Broad. Here, it's retold through the lens of WIRED author Amy Maxmen:
"Soon after starting [at the Broad], he heard a speaker at a scientific advisory board meeting mention Crispr. 'I was bored,' Zhang says, 'so as the researcher spoke, I just Googled it.' Then he went to Miami for an epigenetics conference, but he hardly left his hotel room. Instead, Zhang spent his time reading papers on Crispr and filling his notebook with sketches on ways to get Crispr and Cas9 into the human genome. “That was an extremely exciting weekend,” he says, smiling."
Have you ever had a point in your life like this?  Perhaps Zhang truly found the conference boring, and researching CRISPR was his best escape. However, since this story crops up so often, I'd like to think it's an attempt to capture the "flow" state as it applies to crystallization of a new field of research or career direction. Hopefully you recognize the feeling - total immersion, loss of time, tuning out all external concerns while your brain opens up to the vast possibilities of something truly new.

Clearly, a computer algorithm with a scientific sense of humor printed this lotto ticket. 

From my own experience, I can remember a handful of flow moments that I sustained for longer than a few hours. In the first, I spent two or three days reading everything I could about a competitor's catalysis research - hoping not to get scooped - and encountering multiple exciting ideas about monodentate ligand binding left unexplored. In another, I tried to track the entire Vinca metabolism from Tryp to the few hundred polycyclic alkaloids like vincristine and ajmaline. Plant metabolism turns out to be much more complex than I'd ever imagined.

Readers, I'm certainly not alone...can you recall when you've experienced a version of Feng's Miami moment? What was it like?

Wednesday, April 6, 2016

WWWTP? Math Non-profit Edition

Saw this "promoted Tweet" go by on the Twitterz earlier this evening.
But something just didn't add up.

Can you spot the problem?

Sunday, February 21, 2016

WWWTP? Slate "slate" Edition

A slate on Slate, a frustrated man next to a frustrated organic structure. The title?
"Teaching the Teachers."

Judging by his chemical acumen - yes, this man needs teaching. Desperately.

 How did he manage to make the western 1,4 diene without it slipping into conjugation?
Inquiring minds want to know.

Saturday, February 20, 2016

What's that Crud in My NMR Sample?


The reaction finished in 20 minutes by TLC. You grabbed a quick aliquot for LCMS; one peak! Quickly, you quenched, extracted, perhaps pushed through a silica plug for good measure. After concentration, a gorgeous white powder formed, so you pulled high vac for 20 minutes and rushed down to "get your proton on." But, darn it! Still wet with traces of, well, something...

Friends, has this ever happened to you? Trace impurities in otherwise perfect spectra lead to much head-scratching and SI docs labeled "final product_spectrum 5." 

The three papers linked to this post should help.

The new chart offers recommendations (colored arrows) based on Chem21 assessments of environmental impact, safety, and toxicity. Shown above are chemical shift tables (1H) in deuterated chloroform, acetone, and dimethyl sulfoxide.

If I were joining a synthetic lab this year, or starting an internship / work-study, I'd download 'em all and thumbtack liberally to the back of my bench. Guaranteed utility.

Friday, February 19, 2016

Chemistry Bumper Cars: 2016-2017

Sometimes great science means changing the view outside your office lab windows.
(Bonus: This usually comes with a new title and some filthy lucre, too!)

The people have spoken: last year's list has grown ungainly, and so it's time for a new batch.
Same rules apply: If you hear of a move, tell me in the comments, and I'll post in the "Pending Confirmation" section. Escape from pending purgatory involves sending me a link or other documentation from the new institution. Fair enough?


Ryan Bailey (UIUC to Michigan)
Raychelle Burks (Doane to St. Edward's)*
Garnet Chan (Princeton to Caltech)  four sources + email
William Dichtel (Cornell to Northwestern)
Guangbin Dong (UT Austin to Chicago)  thanks to five sources!
Daniel Everson (St. Olaf to CSU Chico)
Keir Fogarty (St. Olaf to High Point)
Tendai Gadzikwa (Zimbabwe / Alberta to Kansas State)
Vicki Grassian (Iowa to UCSD)
Carlos Guerrero (UCSD to BMS)
Zhongwu Guo (Wayne State to Florida)  two sources
Stephen Heller (Willamette to Loyola Marymount)
Rigoberto Hernandez (Georgia Tech to Johns Hopkins)  two sources
Tijana Ivanovic (Colorado to Brandeis)
Lisa Kendhammer (Georgia to CSU Chico)
Bern Kohler (Montana State to OSU)  two sources
Kristie Koski (Brown to UC Davis)
Chad Lewis (Cornell to Pfizer)
Roger Linington (UC-Santa Cruz to Simon Fraser)
Aimin Liu (Georgia State to UTSA)
Pamela Lundin (Wake Forest to High Point)
Andrew Phillips (Broad to C4 Therapeutics)
Alexander Radosevich (Penn State to MIT)
Jerome Robinson (Axalta to Brown)  three sources
Tomislav Rovis (Colo State to Columbia)  four sources + Twitter DM
Stuart Rowan (CWRU to Chicago) three sources + email
Steve Soper (UNC to Kansas)
John Stanton (UT-Austin to Florida)
Alice Ting (MIT to Stanford)  many sources
Dave Thirumalai (Maryland to UT Austin, admin)
Angela Wilson (UNT to MSU to NSF)

Pending Confirmation

Anita Mattson (Ohio State to WPI)  one source
Eric Strieter (Wisconsin to UMass)  one source
Greg Verdine (Harvard to Fog or Warp or Eleven)


New Hires

Jonathan Barnes (Wash U St Louis)
Eric Bloch (Delaware)
Lauren Buchanan (Vanderbilt)
Jessica Brown (Notre Dame)
Michael Campbell (Barnard)
Saumen Chakraborty (Ole Miss)
Tai-Yen Chen (Cornell to Houston)
W. Seth Childers (Pitt)
Mita Dasog (Dalhousie)
Alexander Dudnik (UC Davis)
Daniel Everson (Cal State Chico)
Claire Filloux (UC Davis)
Aaron Frank (Michigan)
Nag Gavvalapalli (Georgetown)
Will Gutekunst (Georgia Tech)
Osvaldo Gutierrez (Marylandone source
Katharine Harris (Curry)
Adam Holewinski (Colorado)
Xiaocheng Jiang (Tufts)
Julia Kalow (Northwestern)
Aaron Kelly (Dalhousie, 2017)
Henry "Pete" La Pierre (Georgia Tech)
Frank Leibfarth  (North Carolina)
Brian Liau (Harvard)
Song Lin (Cornell)
Steffen Lindert (Ohio State)
Xi Ling (Boston University)  two sources
Charles Machan (Virginia)
Michael Marty (Arizona)
Karthish Mathiram (MIT Chem Eng)
James McKone (Pitt)
Sharon Neufeldt (Montana State)
Allie Obermeyer (Coumbia)  two sources + DM
Carissa Perez Olson (WPI)
Alison Ondrus (CalTechtwo sources + email
Maria-Eirini Pandelia (Brandeis)
Kathryn Perrine (Michigan Tech)
Myles Poulin (Maryland)
Hans Renata (Scripps Florida)
Brenda Rubenstein (Brown)
Justin Sambur (Colo State)
Alina Schimpf (UCSD)
Valerie Schmidt (UCSD)
Ginger Shultz (Michigan)
Jillian Smith-Carpenter (Fairfield)
Nick Stadie (Montana State) two sources
Pratyush Tiwary (Maryland)
Darci Trader (Purdue) one source
Gael Ung (UConn)
James Van Deventer (Tufts)
Jesus Velazquez (UC Davis)
Lela Vukovic (UTEP)
Jessica White (Ohio)
Travis White (Ohio)
Mark WB Wilson (Toronto)
Nathan Wittenberg (Lehigh)
Christina Woo (Harvardfive sources
Liz Wright (Barnard)
Min Xue (UC Riverside)
Michael Young (Toledo)  email
Bin Zhang (MIT)  two sources
Qiang Zhang (Wash State U)

Sen Zhang (Virginia)
Minjiang Zhong  (Yale)

Pending Confirmation

Mitchell Anstey (Davidson)  one very specific source....
Joey Cotruvo (Penn State)
Christopher Dares (FIU)  one source
Byron Farnum (LSU  Auburn)  two sources, awaiting site confirmation
Miles Johnson (Richmond)  two sources
Evan Joslin (U of the South)  one source
Pere Miró (North Florida)  one source
Cedric Owens (Chapman) one source
Ross Wang (Temple)  one source
Heather Williamson (Xavier)  thanks, Ian!
Lauren Zarzar (Penn State)  one source

List covers Feb 2016 - present

For 2015-2016 moves, click here
For 2014-2015 moves, click here.
For 2012-2013 moves, click here

*Bonus video!

Saturday, February 6, 2016

WWGS: What Would Gmelin Say?

Earlier tonight, I happened across a yellowed, dog-eared copy of The Rise and Development of Organic Chemistry, the 1894 opus* of Carl Schorlemmer, finished with help from his colleague Arthur Smithells. I didn't get a chance to read it cover to cover, but I appreciated a pithy quote in a postscript, purportedly an exchange between two chemistry heavyweights:
"When in 1829 it was found that pyro-uric and cyanuric acid were identical, Wöhler wrote to Liebig: 'Gmelin will say, Thank God, one acid less.'"
This, of course, in reference to Gmelin's attempt to gather the mid-1800s chemistry literature into a practical reference book. He would go on to create the Gmelin Inorganic Handbook, later to evolve into the Gmelin Database, part of modern-day Reaxys.

I appreciated the formal sentiment that pervades the text; certainly it's the first chemistry book I've seen that gives the reader a parting word after the index:

I'm sure I'll have more to say later on....there's some wild structures in this book, some that should give any serious bench chemist pause:

Aromatic endoperoxides? Egad.

*Just found out it's free online! Go here. Happy reading!