Thursday, January 29, 2015

Oxidase Toolkit: C-H Azidation

Do you ever stare at your late-stage molecules, thinking "They're almost perfect, but I really wish I could add an amine right over there." Thanks to a new reaction, you might soon be able to.

Reporting in NatureJohn Hartwig and coworkers have cracked the case: a mixture of iron (II), a tridentate nitrogen ligand, and a modified Togni reagent Zhdankin reagent reliably functionalize tertiary C-H bonds with an azide(N3 group). The selectivity, yield, and mild conditions match pretty well with White's C-H oxidation, which utilized a similar catalytic manifold.

Hartwig's initial targets for this new reaction include two modified steroids and a gibberellic acid derivative. Sadly, precious few heteroatoms exist in these molecules to gum up the ironworks, but I'm certain they'll address that in the full paper. I'd especially like to point readers to Figure 3, in which the group shows subsequent transformations: heterocycle formation, amine reduction, chemical ligation, and capping with fluorescent tags.

These two reactions together, along with a variety of C-H halogenations and sulfidations, seem to support the growing "oxidase phase" approach to total synthesis. One could imagine that, in a few years, a naked carbon scaffold could be suitably decorated with O, N, S, or X at positions of the scientists' choosing. Wow.

Tuesday, January 27, 2015

Another Year, More Chemophobia

Over the holiday break, a few people sent me pictures and links to demonstrate that we still have plenty to do to counter chemophobia in 2015. Here's a sampling:

1. U.S. FDA Cancer ad. Have you seen these pictures around airports, bus stations, and subways? This one - which I'm sure is equally supposed to simultaneously discourage youth smoking (while reminding them of Sauron from Lord of the Rings) appeared in my inbox a few days ago:

Nothing like some straight-up chemophobia from Big Government.

2. Health beans - now chemical-free!

Thank Goodness that 'omega fatty acids' or 'vital antioxidants' aren't chemicals!*

3. Microwaving'll kill ya. As a throwaway line in the Newsweek article interviewing famous futurists about whether or not Back to the Future Part II accurately predicted the future, Syd Mead, a "visual futurist" who designs sets for sci-fi movies, said this:
"No, I don’t remember [how the film depicted food]. I hope it wasn’t pills. [laughs] That was a fixture in future films. Popping steak or spinach or whatever in a pill. I hope it never comes to that."
"Microwave dinners are bad enough. Of course, microwave upsets the molecular structure of food, which isn’t too terribly healthy."
I've heard these arguments before, but neither one makes any sense. Healthy people routinely take all sorts of food supplements in "pill form" - vitamins, curcumin, antioxidants, essential oils - the list goes on and on. And as far as I'm aware, microwaves can't actually "upset" (change) the molecular structure of food.

Reminder: Syd consults for science fiction movies. We have a lot of work to do.
*Yes they are.

Chemistry Photo-Op

Carrying high-resolution cameras in our collective pockets has spawned a new age of lab photography. Witness Chemistry in Pictures, the official American Chemical Society Tumblr site. There you’ll find mazelike porphyrin crystals (below), glowing TLC plates, and ultralight aerogels poised atop fragile flowers.

Credit: Anna Slater | Chemical & Engineering News Tumblr

Want to dive even deeper into the laboratory? Kristof Hegedus has you covered: his aptly-named site Photos from an Organic Chemistry Laboratory brings forth reaction gifs, failed black tars, and icy fractals of crystalline intermediates. Perhaps your interests lean towards chemical education – the picture blog for you is Picture It… Based out of the University of Bristol, and freely available for re-use through Creative Commons, the authors overlay well-posed plants, foods, and common substances alongside their constituent molecules. 

Finally, for the effete artiste, we present Beautiful Chemistry. A joint venture of Tsinghua University Press and the University of Science and Technology in China, this site has it all: Priestly’s apparatus, HD videos of crystal growth, and animated DNA nanostructures. A true treat for the chemically and artistically inclined.

Chemistry Bumper Cars, 2015-2016

In the age of  Google and Glassdoor, hiring has become a year-round activity. Postdocs and grads alike should keep their ears to the wall, since nowadays any group meeting could list "Relocation" on the agenda...

From June 2014 - December 2014, comments, search engines, rumours, and tweets noted 50 faculty moves and 119 new faculty starts for academic chemists. I've started another page simply because the flow hasn't stopped; perhaps I should start up a database for next year?

**Know of someone missing? Let me know in the comments!


Orlando Acevedo (Auburn to Miami)  Facebook confirmation
Jane Aldrich (Kansas to Florida)
Jared Anderson (Toledo to Iowa State
Nasim Annabi (Harvard Med to Northeastern)
Valerie Ashby (UNC to Duke, admin)
Jeff Aube (Kansas to UNC)   thanks, Ziegler!
Mu-Hyun Baik (Indiana to KAIST)
Nicholas Ball (Amherst to Pomona)
Vahe Bandarian (Arizona to Utah)
Jack Barbera (Northern Colorado to Portland State)
Stephen Bernasek (Princeton to Yale-NUS, admin)
Wes Bernskoetter (Brown to Mizzou)
Stacey Brenner-Moyer (CUNY-Brooklyn to Rutgers)
Maurice Brookhart (UNC to Houston)  thanks, Maxxie!
BJ Chain (Hawaii to Delaware)
John Chaput (ASU to UC-Irvine)
Vadim Cherezov (Scripps to USC)  thanks, Marky!
Coray Colina (Penn State to Florida)
Jonathan Collins (Amherst to Whitman)
Matthew Cook (Belfast to Montana State)  one source
Sunil David (Kansas to Minnesota)
Juan del Valle (Moffitt to USF)
Mike Doyle (Maryland to UT San Antonio)
Dorothea Fiedler (Princeton to Liebniz)  thanks, Maxxie!
Fraser Fleming (Duquesne to DrexelLinkedIn
Valery Fokin (Scripps to USC)   thanks, Symmetry!
Boniface Fokwa (RWTH-Aachen to UC Riverside)
Malcolm Forbes (UNC to Bowling Green, admin)
E. Johan Foster (Fribourg to Virginia Tech)
Karl Gademann (Basel to Zurich)
Steve Granick (UIUC to UNIST)
Mike Green (Penn State to UCI)
Bartosz Grzybowski (Northwestern to UNIST)
Andrew Hamilton (Oxford to NYU, admin)
Andrew Harned (Minnesota to Texas Tech)  thanks, Ziegler!
Jason Hein (UC-Merced to UBC)
Ive Hermans (ETH Zurich to Wisconsin)  thanks, Marky!
Malika Jeffries-El (Iowa State to Boston University)  thanks, SJE!
Frank Keutsch (Wisconsin to Harvard)
Bryan Krantz (Berkeley to UMBC)  thanks, Marky!
Laszlo Kurti (UT-Southwestern to Rice)
Erin Johnson (UC-Merced to Dalhousie)
Nate Lynd (LBNL to UT-Austin)
Roman Manetsch (South Florida to Northeastern) thanks, Andrii!
Mahesh Mahanthappa (Wisconsin to Minnesota)
Michael Marletta (Berkeley to Scripps to Berkeley)  thanks, Maxxie!
Charles McCrory (DOE to Michigan)
Anne McCoy (Ohio State to Washington)
Alshakim Nelson (IBM to Washington)
Abraham Nitzan (Tel Aviv to Penn)   
Jiwoong Park (Cornell to Chicago)
Christian Paumi (Kentucky to Eastern Kentucky)
Jeffrey Rack (Ohio to New Mexico) thanks, Shawn!
Daniel Romo (Texas A+M to Baylor)
Daniel Savin (Southern Mississippi to Florida)  thanks, Marky!
Suzanne Scarlata (SUNY Stony Brook to WPI)  thanks, Shawn!
X. Michael Shi (West Virginia to USF) thanks, Andrii!
Yoan Simon (Fribourg to Southern Miss)
Herman Sintim (Maryland to Purdue)
Scott Snyder (Scripps to Chicago)
Raymond Stevens (Scripps to USC)
Arthur Suits (Wayne State to Missouri)  email confirmation
Renske van der Veen (Max Planck to Illinois)  thanks, Maxxie!
X. Peter Zhang (USF to Boston Collegethanks, Andrii!

Pending Confirmation

None right now!


New Hires

Drew Adams (Case Western)
Alexey Akimov (U Buffalo)
Leslie Aldrich (U. Illinois-Chicago)
Jared Allred (Alabama)
Robbyn Anand (Iowa State)
John Anderson (Chicago)
Carlos Baiz (UT-Austin)
Kyle Bantz (Virginia Military Institute)
Jeremy Baskin (Weill Institute / Cornell)
Jessica Bell (U of San Diego)
Timothy Berkelbach (Chicago)  thanks, TH!
James Blakemore (Kansas)
Marc Boudreau (New Hampshire)
Tim Brewster (Memphis)
Eleanor Browne (Colorado)
Francois-Xavier Campbell-Valois (Ottawa)
Patrick Cappillino (UMass-Dartmouth)
Carlos Castaneda (Syracuse)
Kelly Chacon (Reed College)
Julian Chan (Ottawa)
Ou Chen (Brown)
Danny Chou (Utah)
Shishir Chundawat (Rutgers)
Stephanie Cologna (U. Illinois Chicago)
Matthew Conley (UC Riverside)
Bruno Correia (EPFL)
Corrie DaCosta (Ottawa)
James Devery (Loyola Chicago)
Robert DiStasio, Jr. (Cornell)
Jack Dunkle (Alabama)
Keary Engle (Scripps)
Brandon Findlay (Concordia)
Polly Fordyce (Stanford ChEM-H)
Dan Fu (Washington)
Andreas Gahlmann (Virginia)
Isaac Garcia-Bosch (Southern Methodist University)
Joseph Genereux (UC Riverside)
Jason Goodpaster (Minnesota)  thanks, Bill!
Jeffrey Gustafson (San Diego State)
Eva Hemmer (Ottawa)
Basil Hubbard (Alberta)
Pengfei Huo (Rochester)
Todd Hyster (Princeton)
Nan Jiang (U. Illinois Chicago)
Chenfeng Ke (Dartmouth)  thanks, Maxxie!
Keith Keitz (UT-Austin)
Thomas Kempa (Johns Hopkins)  thanks, Maxxie!
David Lacy (U Buffalo)
John Latham (Denver)
Christina Li (Purdue)
Lingyin Li (Stanford ChEM-H)
Wei Li (Toledo)
David Limmer (Berkeley)  thanks, Maxxie!
Mike Marshak (UC-Boulder)
Ellen Matson (Rochester)  thanks, Organometallica!
Nicholas Mayhall (Virginia Tech)
Gabriel Menard (UCSB)
Maosheng Miao (Cal State Northridge)
Vlad Michaelis (Alberta)
Jeremy Mills (Arizona State)
Katherine Mirica (Dartmouth)
Jonathan Moerdyk (Seton Hill)
Mahmoud Moradi (Arkansas)
Katherine Mullaugh (College of Charleston)
Alison Narayan (Michigan)
Hosea Nelson (UCLA)
Eric Neuscamman (UC Berkeley)  thanks, Maxxie!
John Ngo (Boston University)  thanks, Li!
David Olson (UC-Davis)
Julien Panetier (Binghamton)
Alex Parent (North Dakota State)
Monica Perez-Temprano (ICIQ)
Michelle Personick (Wesleyan)
David Powers (Texas A+M)
Federico Rabuffetti (Wayne State)
Paul Raston (James Madison)  thanks, Marky!
Steven Ray (U Buffalo)
Sereina Riniker (ETH)
Aaron Rossini (Iowa State)
David Rubush (Benedictine)
Ian Seiple (UC San Francisco)  thanks, Palau!
Jon Sczepanski (Texas A+M)
Joan Schellinger (U of San Diego)
Nathan Schley (Vanderbilt)  thanks, Maxxie!
Adam Shuhendler (Ottawa)
Sarh Shaner (Benedictine)
Charles Sing (UIUC)
Ellen Sletten (UCLA)  thanks, Joel!
Christal Sohl (San Diego State)
Alexander Speed (Dalhousie)
Nicholas Stephanopoulas (Arizona State)
Sarah Styler (Alberta)
Manal Swairjo (San Diego State)
Samuel Tartakoff (St. Lawrence)
Ashleigh Theberge (Washington)  thanks, Marky!
V. Sara Thoi (Johns Hopkins)
Corey Thompson (Purdue)
Joseph Topczewski (Minnesota)  thanks, Bill! 
Gavin Tsui (CUHK)
Arturo Vegas (Boston University)  thanks, Sean!
Karl Voigtritter (Cal State-Chico)
Matthias Waegele (Boston College)
Dong Wang (Montana)
Jun Wang (Albany)
Ting Wang (Albany)
Masayuki Wasa (Boston College)
Kevin Welsher (Duke)
Florence Williams (Alberta)
Justin Wilson (Cornell)
Jaclyn Winter (Utah School of Medicine)
Cathy Wong (Oregon)
Judy Wu (Houston
Xiaojing Yang (U. Illinois Chicago)
Xin Zhang (Penn State)
Qiang Zhang (Albany)

Pending Confirmation

None right now!

List covers Dec 2014 - Jan 2016. For more, check out the 2016 list!

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

A Nudge Towards "Scrudge"

Last night, while I trudged through Alexander Shulgin's seminal work* PiHKAL, I came upon scrudge, a fantastic heretofore-unknown-to-me term for a very common phenomenon:

Here's the reaction Shulgin attempted:

And, in his own words (emphasis mine):
"The elephant labored and brought forth a mouse. A lot of work for a material without activity. 
I have used the term "scrudge" in this and other recipes, without defining it. With this aldehyde, as with most aldehydes where there is no ortho substituent on the benzaldehyde, the reaction progress should be carefully followed by thin-layer chromatography. As the aldehyde disappears from the reaction mixture, the nitrostyrene appears, but there is usually the development of one or more slower-moving components as seen by TLC. Such a wrong-product is called scrudge."
Scrudge just works. Not to judge, but any synthetic drudge could tell you they've experienced the same. On scrudge, I won't budge. Just look at the beautiful art inspired by just such a smudge:

Credit: Vittorio, who blogs over at Labsolutely

This post's a bit of a kludge, but I hope I've provided a nudge towards scrudge.
Feel free to use it in your next lab meeting or thesis defense!


*"Phenethylamines I Have Known and Loved"

Tuesday, January 20, 2015

2015 State of the (Scientific) Union

(Adapted from last year's post with 2015 data)

Did you watch President Barack Obama present tonight's 2015 State of the Union address?

I downloaded the text to the 2015 S.o.T.U. (Turning Point), and compared it against the text from 2011 (Winning the Future), 2012 (An America Built to Last), 2013 (Unfinished Tasks / Next Chapter), and 2014 (Opportunity for All).

I’m not a political pundit or a news analyst - I *am* a scientist (see below). So let's see how certain scientific themes grew or shrunk over the past 365 days.

Breakdown (# of each word in full text):

Energy – 2011: 9, 2012: 23, 2013: 18, 2014: 8, 2015: 2
Oil – 2011: 2, 2012: 10, 2013: 5, 2014: 6, 2015: 4
Gas - 2011: 1, 2012: 9, 2013: 7, 2014: 4, 2015: 2
Wind / Solar - 2011: 4, 2012: 3, 2013: 4, 2014: 2, 2015: 3
Nuclear – 2011: 5, 2012: 3, 2013: 3, 2014: 5, 2015: 5
Batteries - 2011: 0, 2012: 2, 2013: 1, 2014: 0, 2015: 0
Biotech / Biomed / Biofuel – 2011: 3, 2012: 0, 2013: 0, 2014: 0, 2015: 0
Chemical – 2011: 0, 2012: 1, 2013: 0, 2014: 1, 2015: 0
Tech / technology – 2011: 12, 2012: 9, 2013: 8, 2014: 6, 2015: 3
Science / scientist – 2011: 7, 2012: 2, 2013: 4, 2014: 1, 2015: 6
Engineering – 2011: 3, 2012: 1, 2013: 3, 2014: 1, 2015: 0
Math – 2011: 3, 2012: 0, 2013: 2, 2014: 1, 2015: 1
Research – 2011: 9, 2012: 4, 2013: 4, 2014: 4, 2015: 2
Development – 2011: 1, 2012: 2, 2013: 1, 2014: 0, 2015: 2
Carbon – 2011: 0, 2012: 0, 2013: 1, 2014: 3, 2015: 1
College / Universities– 2011: 12, 2012: 15, 2013: 8, 2014: 12, 2015: 14
Health – 2011: 8, 2012: 5, 2013: 5, 2014: 8, 2015: 8
Internet  2011: 6, 2012: 1, 2013: 1, 2014: 0, 2015: 3
Cyber  2011: 0, 2012: 1, 2013: 2, 2014: 1, 2015: 2
Jobs  2011: 25, 2012: 33, 2013: 32, 2014: 23, 2015: 19

Interesting 2015 one-offs: "I'm not a scientist", universal child care, $0 community college (?), "Google, eBay, and Tesla", Precision Medicine Initiative, solar fuels, Instagram from Space, stopping hackers, opening Cuban relations, Pope Francis' "small steps."

Is there a take-home message here? Does word count relate to the overall direction of the country? Probably not. Each speech is different: 2015 brought middle-class values, international relations, and Presidential legacies; while 2014 spoke to middle-class unemployment, higher ed, and equality issues

Still, I'm saddened that, in a speech many journalists billed as a push for education and technology-based jobs, the time spent on those subjects by this President appears to be dwindling.

Readers: Did I miss anything? Let's discuss it in the comments!

Friday, January 9, 2015


Presented for your enjoyment: a tapestry of structurally-related alkaloids, which take up their very own page in a recent Tetrahedron article. Beautiful.

[click to enlarge]

Happy Friday,
See Arr Oh