The Old Days at Org Syn

Thanks to a bevy of used book stores, I'm slowly completing my collection of Profiles, Pathways, and Dreams, the biographical essay series from editor Jeff Seeman. I recently re-read four of these: Cheves Walling, F.G. Stone, Raymond Lemieux, and the indomitable Jack Roberts' colorful collection of biographical anecdotes. Never one to pull a punch, Roberts wistfully recalls his first involvement with Organic Syntheses in the mid-1950s, then led by famous organic chemist Roger Adams:

"The modus operandi of Organic Syntheses is relatively simple. Much of the work is carried on by mail, and the editors meet twice a year for much of a day to assign preparations, work out difficulties, plan for future volumes, choose new editors, and the like, with the current editor-in-chief presiding. Following that meeting, the editors join with the editorial board for cocktails and dinner at one of the best (and most expensive) restaurants in town. In the old days, the dinner would be followed by . . .an Adams report on whatever was on his mind at the time. He often ribbed his colleagues, without malice, but nonetheless, severely. After Adams finished, the meetings often degenerated into the semblance of a stag smoker, with rounds of off-color jokes, the most tasteless of which usually came from the representatives of the publisher . . .Rather prodigious quantities of spirits, wines, and brandies were consumed, and some of organic chemistry's most renowned practitioners had to be helped off the scene. My first encounter with these bacchanalian festivities was in Atlantic City, in the spring of 1956. I made it back to my hotel under my own steam, but I spent the next day in bed, a lesson I did not forget."

This recollection sounds uncomfortably close to how I felt each time someone in my graduate group passed their oral examinations. Some things never change.

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.

Review: ChemBioDraw 14.0

Dear ChemBioDraw* Ultra 13.0,

Listen, we had a good run together. But I've fallen for another: ChemBioDraw Ultra 14.

My good friends at PerkinElmer (PKI) were kind enough to grant me trial access to their spiffy new chemistry drawing software. As an avid user since, oh, say, ChemDraw Pro 4.5, I feel confident in stating that this version wins all around for smoother operation, better templates, easier file export, and better shortcut keys.

So, I figured what PKI really wanted me to do most was to try and BREAK ChemBioDraw 14.0
 . . .if I could. Did I succeed? Let's talk a walk through the software and find out.

CBD 14.0 means NEVER seeing this screen again (hooray!)

Starting at the top, I figured I'd check the "What's New?" link in the help menu. One thing I appreciated more than I thought? ChemBioDraw 14.0 directing "Help" queries into the appropriate section of the User Guide. Version 13 still spawned its help window inside Windows help, with the infamous purple booklets leading you down wild goose chases of clunkily-presented information.

Drawing hasn't changed much since 13.0. At least the text direction auto-correct -- which drove me batty in former iterations -- seems to have been tweaked; the system now opens my older drawings the way I typed 'em in originally (hence, below, attaching pasta sauce to a scaffold in place of a sugary placeholder).

I promise this made sense in earlier ChemDraw versions...

The CBD 14.0-to-SciFinder jump works much more smoothly than I had anticipated. For those of us who shuddered through dial-up desktop versions of SciFinder in the late '90s, this version feels like the sleek Lamborghini of the search world. After drawing (or importing) my structures of choice, I lassoed them up and pressed the little "SciFinder diamond" on the top toolbar. Within about 5 seconds, a new window opened with the standard exact / substructure motif. Two clicks later, I'd be deep into the primary literature.

So, my goal was to break the system, right? Here's a logical place to try - I attempted to load each and every complex structure I had drawn since starting my fledgling blogger's career, around 2009 or thereabouts. Again, I was amazed by the speed and accuracy of the SciFinder pop-out, which returned roughly 90% of the correct molecules I'd searched for (below):

From this 2011 post

From this 2013 post

From this 2014 post

However, it's not all bubbles and sunshine. Two of my molecular queries bore no fruit**; perhaps they're too new to have been uploaded into CAS's databases yet. But one thing remains tricky: drawing and searching for metallocenes. Along with their new push into biology clip art, ChemBioDraw has a renewed focus on making sure you've got those sandwich compounds properly aligned.

Sigh. If only I remembered what they were all supposed to be...

Now, even after aligning my query using the proper template, SciFinder makes a mess out of it.

From this 2012 post

So, obviously I went looking for things to break, and found some rather limited examples. Honestly? The rest of the program works pretty well. And writing this review gave me a wonderful opportunity to poke and prod at the product in ways I hadn't in far too long.*** I finally realized you could change the solvent on the NMR predictor! I played around with expanding and collapsing peptide and RNA strings. And the post-drawing mods to more complex peptides, like disulfide and lactam cross-linking? Much better.

Found on p. 126 of the User Guide. (Get it?)
I'd like to shake the hand of the person who slipped this in...

R.I.P., Optimizing Octopus

I will take this final moment to remember a long-lost piece of ChemDraw lore. Once upon a time, to "clean up" one's structures, the icon looked something like this (right). I've heard it referred to as a jellyfish, a squid, a broom (no!), but I always knew it as a friendly little octopus. With CBD 14, any doubt about its brushiness has been cast aside with a full-out icon redesign.


Looks great, guys. Now let me think about more ways to use it for actual work!

Thanks again to Philip Skinner and PerkinElmer for the chance to review the software.

---
*For other blog reviews of ChemDraw products, see Jess The Chemist, Andre the Chemist (no relation), or Chemjobber.

**Here's the structures that returned empty SciFinder searches. Both compounds (left, right) were first reported in 2014.

***P.S. I never knew you openly solicited beta testers for these products...gimme a call sometime, PKI!

Who Would YOU Invite to the NOS?

Plans for the 2015 ACS National Organic Symposium (U. Maryland) have ramped up recently. The Division of Organic Chemistry sent out some feelers last week, requesting nominees for speaking invitations.

Source: University of Maryland, 2015 NOS website

Judging by early suggestions, I think they'd especially like to hear about up-and-coming* chemists, both in the U.S. and abroad. So, readers, I'll put two questions to you:

1. Which early-career (<10 years' experience) U.S. organic chemist would you recommend?

From the comments: Jeff Johnson (UNC), Guangbin Dong (UT-Austin), Chris Vanderwal (Irvine), Rob Knowles (Princeton)

2. Which international** early-career organic chemist's work most excites you?

From the comments: Masayuki Inoue (Tokyo), Weisheng Tian (SIOC), Nicolai Cramer, Michael Willis, Shu-Li You (SIOC), Jerome Waser (EPFL), Nuno Maulide, N. Yoshikai (Nanyang), M. Niggeman (EWTH Aachen), Ang Li (SIOC)

Please leave your thoughts in the comments. Thanks!

*Presumably, this serves to generate a more inclusive environment, and also (hopefully) helps NOS to reverse the steep declines in attendance. 

In 2003, 1081 chemists traveled to Bloomington, IN; only 636 made it to Seattle, WA in 2013.

**Bonus points if they're from outside the U.K. or Europe.

Photochromic Blast from the Past

While digging through some old ACS party favors, I came across this wallet card, which I obtained at an ACS "Kids in Chemistry" event ca. 2001.  A check-in with Mr. Google brings back this 2004 Celebrating Chemistry outreach pamphlet, where the PULS (Photochromic Ultraviolet Light Sensor) card helps budding chemists understand the virtue of UV-blocking sunscreens.

What's missing for us big kids? An explanation of the inner workings of the cards' photochromic dye!

Does anyone with long-toothed ACS volunteer experience happen to know the answer? When did these cards hit the scene? Who manufactured them? What dyes were used? Are they still in use for outreach today?

Coaching Science

Scrolling through my ACS Matters newsletter, I came across an interesting program I hadn't seen before:


The ACS Science Coach Program.

Participants in the program volunteer with a local elementary, middle, or high school, visiting at least six (6)
times, helping to plan labs and mentor young scientists. ACS even chips in a small grant ($500) to support the effort. Sounds like a cool program to me!

Just one question: Do you suppose the admins ever read the #ChemCoach carnival? [crosses fingers]

Update: Apparently, this dates back to pre-2011, so perhaps *I* subconsciously used *their* idea!

DOC Detective Work

I'd like to send some good vibes and a hearty hello to attendees at the 43rd Annual National Organic Symposium in Seattle. Wish I could be there with you guys; maybe I can 'save the date' for #44 in 2015.

While browsing around on the Division of Organic Chemistry website, I stared at the logo for one second too many, thinking "What molecule is that, anyway?"

Have you ever wondered that?

I figured that SciFinder would know best, so I searched for the exact carbon framework: Zero hits! So, it's not actually a molecule anyone's worked on. I poked around through ORGN's historical archives*, including the first N.O.S. program (1925, Rochester, NY). I perused the excellent recent review of the conference in JOC - no explanation there, either.

Let's examine a few of the other ACS Division logos. Fluorine chemistry stands out - some hand-drawn goodness representing a closed ampoule of the highly reactive gas:

Inorganic chemistry lays claim to the entire periodic table, with a lens flare for added emphasis:

My "Aha!" moment came upon viewing the coiled chain of the Polymer Division, suggestively curled back on itself to create a "P":

Go back to the DOC website, and have a peek at the tiny icon at the top of your browser tab. Here's how mine looks:

Get it? The graphic spells out the letters "D-O-C" (How had I not seen this before?!?)

Clearly, we've lost the thread of the joke due to better understanding of molecular structure. At its founding (1909), most Division members were still drawing what I lovingly refer to as the "Monopoly hotel" version of the cyclopentane ring - one bond artificially elongated to ease printing (or stenciling):

Over time, of course, we realized that a regular pentagon was a closer representation, and conformational analysis teaches that we ignore 3-D structure at our own peril. Nowadays, the more streamlined DOC logo - though structurally correct - loses the "D" flavor of the older generation's five-membered ring.

Challenge: We're still two years out from the next NOS meeting. In the spirit of olympicene, created to honor the 2012 London Olympics, perhaps someone could synthesize "ORGNANE," the presumptive hydrocarbon of our beloved logo. It's C12H22, so I doubt it's that volatile (ChemDraw predicts bp >200 deg C).

Hey SURF fellows, want to be famous? This might be the summer project for you!

*Fast fact: ORGN only claimed 1,014 members in 1948. This swelled to 16,800 by 2010, presumably due to the explosion in medicinal, polymer , and industrial chemistry research.

The Periodic Table of Mugs

Another big thank-you to the ACS for my brand-new set of periodic table mugs!

This is exactly how they came to me, colors and all... Honest!

I realize I'm one of the lucky ones, and that my earlier agitation may have forced someone's hand. But I'm serious here: Keep up the program, ACS! By membership year, I'm deep into "Row 3" of the table, and I'd love to see some beautiful transition metal mugs. Wouldn't you?

Killer Schwag from ACS

I feel like I've seen a snow leopard, a yeti, a dodo bird, Bigfoot, and a giant squid simultaneously.

This piece de resistance arrived by first-class mail today. Behold, the elusive ACS Five Year Mug:

Oh. My. Gosh. 

I am grateful to whomever at ACS / C&EN heard my griping a few weeks ago:

@apgoldst -In that case, I'm holding out for my "Mugnesium" next year #snerk @chemjobber
— See Arr Oh (@SeeArrOh) May 21, 2013

Kudos to ACS for quickly addressing the situation. Now, about those next 8 elements...*

*Seriously, ACS, I would be most willing to build a periodic table of mugs. I promise to stay alive / renew membership at least long enough to get to the transition metals. For an extra goof, you could send me a "tin cup" on my 50th Anniversary (Sn). 

Who Gets Hired Where?

Not to steal Chemjobber's thunder, but I can't resist the question: Does anyone know a reliable data set for industrial chemistry hiring?

Taking my cue from Paul's incredibly exhaustive list of 2013 moves and hires in the academic world, I baited Twitter with the question. CJ opined immediately, with an apt football analogy:

Snerk. 

Dan weighed in with a tantalizing bon mot:

Is there a massive, unseen data set out there somewhere? [scratches chin, head...]

Straightaway, I can only think of LinkedIn, which suffers from being 1) voluntary, and 2) noisy data. Other sources might include faculty web pages (infrequently updated) or the C&EN Careers page (accurate, but limited). The ACS Employment and Salary Survey could track this, but I don't think it's granular down to the specific position and company. 

Readers: Does anyone know of a better way to collect this data? 

Update: CJ (correctly) points out that 'ACS Career Survey' isn't a real thing. Fixed, thanks!

'Tis the Podcast Season

So, whatcha doin' for the next 30 minutes?

Want to listen to three chemists cynically dismember the ACS grad report? Sure you do!

Head on over to CJ's place, and criticize our critique.

Frost Flowers
Source: Matthias Wietz | NPR.org

#Chemjobs: Fellowship Freefall

Back in graduate school (*cough* ages ago), I distinctly recall looking forward to the annual announcement of the Division of Organic Chemistry (DOC) Graduate Fellowships. The competitive awards, which require advisor recommendations, essays, and a pretty slick research record, granted the lucky few a full year's stipend along with travel funds to attend the National Organic Symposium.

When I clicked for the 2012-2013 crew, I felt something was missing...where's all the fellowships? I counted only eight grantees. Not to condemn them; their research certainly merits the award, but didn't the DOC used to give out a whole pile more?

In a word: yes. Here's the historical data for the grantees, taken from this website. 

Talking points:

1. Lines, lines: It's not an accident that the trend mirrors the overall economy generally, and employment in Big Pharma specifically. Note the huge uptick in awards between 1997 and 2001, when the average was ~18 per year. Boom times. It's since settled down to just about 8 annually, around the average of the recession-era '80s.

2. Visits: Those last seven years (2006-2012) match the corresponding decline in corporate recruiting (see MIT, Harvard graphs via Chemjobber).

3. Strange birds: Since graduate school enrollment has dramatically increased, at the same time as fellowships have decreased, these awards become even more prestigious, if only by dint of rarity.

4. Peak Perfection: Let's look at the top year: 1997, when 19 fellows were named. Who sponsored the awards? Take a trip down memory lane...

Wyeth-Ayerst

Abbott

Pfizer

DuPont Merck

Hoescht-Marion Roussel

Org Syn (x 3)

Organic Reactions

Boehringer Ingelheim

Zeneca

Bristol-Myers Squibb

Procter and Gamble

Pharmacia-Upjohn

Eli Lilly

Smithkline Beecham

Merck Research

Rohm and Haas

Schering-Plough

Wow, how many of those guys even exist anymore? Contrast this list with the 2012 crop:

Merck / Division of Organic Chemistry

Org Reactions / Org Syn

Genentech

Boehringer Ingelheim

Org Syn (x 2)

Amgen

Troyansky (family endowment)

Pretty slim pickins.

5. Winners? Losers? Some auspicious names have been missing from the DOC Fellows' list in recent years: Harvard, MIT, Scripps? Actually, the trend improves for state schools, with 5/8 in 2012 going to the public universities. Compare this to 1995 ("boom times"), when the list included Harvard (x 2), Stanford (x 2), Johns Hopkins, Northwestern, MIT, Yale, USC, Chicago, and the publics represented by Berkeley (x 2), Wisconsin (x 2) and Utah.

Note: Thanks to Chemjobber for the inspiration.
Update (11/8/12) - Fixed USC, not a public uni! Thanks, Anon commenter...also Chicago..

Friday Fun - Scientists at Play

Source: Bill Nye, Facebook

I'm constantly amazed at how much interesting, relevant science stuff comes down the Twitter feed. As I've said before, in very short order I've become a total convert. The online community of friends and contacts keeps me motivated, blogging, and perhaps a half-step ahead of many traditional news outlets.

Well, all work and no play makes SeeArrOh a dull boy, so here are a few hand-picked images that have crossed my path in the past few weeks:

1. Bill Nye (who I really need to do a post on!) and Neal deGrasse Tyson, two grizzled vets of science outreach, obviously game for appearing X-Men style for a satirical post-apocalyptic movie poster.

2. In my imagination, all of my colleagues from across the pond - Stu, Freda, B.R.S.M., Neil, TotSyn - dress like this every day for work.

Source: Sony Pictures / Aardman

This shot, from a Sony Pictures promotional site, actually ruffled feathers when the U.S. release team decided to chuck the original title, used for (more science-friendly?) U.K. movie audiences.
Does that animation style seem familiar? Thank Aardman studios, the clay stop-motion filmmakers who've created wonderful characters like running chickens, dashing mice, and, of course...Gromit.

Source: 2012 ACS San Diego

3. Finally, the ACS Mole hams it up with current President Bassam Shakashiri at the 2012 conference in San Diego, proving once again that "Science is Fun!"

I just have to know...who gets to wear the Mole costume? And, where do I sign up???

Chemistry "Hacks" (The Good Kind)

My hackathon drink of choice, coffee!
(And hey, ACS, why no more mugs?)

Last week, a fascinating article, "The 48-Hour Startup," appeared in Wired magazine. It explored the world of hackathons - events where pizza and Red Bull fuel two straight days of programming, hacking, and rebuilding code to create a functioning, marketable smartphone app. The upshot: some prize money, and sufficient street cred to attract more through angel investments. This article made me wonder . . .why don't more chemists have hackerspaces, like programmers and engineers do?


Let's go all the way back to the beginning of chemical research - who were we? Alchemists, who worked after hours, scribbling in secret languages; some hoped for profit, and some just loved the thrill (Sound familiar?). They didn't follow the implicit hegemony we do today: school student -> university trainee -> graduate study -> postdoc -> junior professor -> original ideas? By the time you're done jumping through hoops, you might have left your sense of curiosity and wonder behind.

Early Chemical "Hacker"
Alchemist with Scale, Johannes Weiland
Credit: Chemical Heritage Foundation

Well, how do we discover anything? If you believe much of the popular press, either by accident (saccharine, guncotton, Velcro), or by deep thought and monastic contemplation (relativity, total synthesis, calculus). I'd add a third avenue: cross-fertilization, the genius behind Bell Labs' design for their "idea factory."


Ever beat your head against a research problem, only to find the answer at a neighboring department's seminar? Borrowed something the next lab down the hall had on the shelf? Not to wax all Zen and the Art of Motorcycle Maintenance on you, but I subscribe to human quality precognition, a subtle mental undercurrent that guides you toward the right reaction or correct conditions. Others might call this gut instinct, and I've heard process chemists chat about initial optimization ("lucky on the first try!").


So why not speed this process along? Could we take a page from the video game designers, the hackers, and the dorm-room dot-com stars?


Here's my proposal (which, incidentally, might work pretty well at a large, national chemistry conference, just sayin'): What if visiting chemists had access to an open lab space, replete with all the latest catalysts, equipment, and reagents? One could imagine equipment dealers sponsoring this space, much like Cuisinart and KitchenAid sponsor cooking shows. 

Picture this, but with more fume hoods and Buchwald ligands

Access to a well-shimmed NMR and tuned LC-MS, along with a few high-speed internet connections and journal subscriptions, would complete the experience. Professors, hearing about a fantastic new reaction, wouldn't have to brief their lab groups. International scientists could mingle, and compare lab technique. Best of all? You could just play, try experiments for fun, on a whim, or because you were just curious about the result.


Who knows? Maybe, in time, the phrase "chemistry hack" might mean something good!