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!
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)
Tijana Ivanovic (Colorado to Brandeis)
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

Rigoberto Hernandez (Georgia Tech to Johns Hopkins)  one source
Bern Kohler (Montana State to OSU)  one source
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
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)
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
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)
Christina Woo (Harvardfive sources
Liz Wright (Barnard)
Min Xue (UC Riverside)
Michael Young (Toledo)  email
Minjiang Zhong  (Yale)
Qiang Zhang (Wash State U)
Bin Zhang (MIT)  two sources

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
Alison Ondrus (CalTech) two sources
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!

Tuesday, January 26, 2016

Tough-to-Swallow Propargylation

As I thumbed through the recent Tet Lett abstracts, I encountered this title:
"Regioselective propargylation of aldehydes using potassium allenyltrifluoroborate promoted by tonsil"
Turns out, the authors were referring to Tonsil (R), an acid-treated calcium bentonite clay, not the fleshy pockets in the back of the throat associated with immune response. I guess BRSM  doesn't have to update his "Desperate Conditions" list quite yet...

So, in summary:

Source: Sud-Chemie

Not This.