Wednesday, July 23, 2014

"Cantrill-ing" Hits the NY Times

Apparently, U.S. Senator John Walsh has been accused of plagiarising a final assignment for his Master's degree. And how did the New York Times cover this story? Why, by literally "cantrilling" the paper!

Source: NY Times
Remember us all when you're famous, Stu.

Sunday, July 20, 2014

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!

Monday, July 14, 2014

JLC Turns Three!

Original Art Credit: Jon Lam (@tyrannos00r)
Wow, everyone. I feel so honored and humbled that you visit my tiny little corner of the Internet sometimes.

Thank you for your continued support and online interactions.

And now, some Salient Factoids from Year 3!
(Year 1 recap | Year 2 recap)


Pageviews: 724,000+
Total Posts: 458
Total Tweets (ongoing): 16,900+
Blog Carnivals: 1 #RealTimeChem

(Could it be that ChemCarnivals have dropped out of favor? Or am I just not playing along like I should be?)

Podcasts (4): Collapsed Wavefunction's Bad Science in the Movies, Chemjobber's Start-up Adventure, Calcium Redux, Plagiarism Roundtable

(I still owe you guys those chemical pronunciations...I haven't forgotten!)

Elsewhere: Carrie Arnold of Science Careers asked me about grad school. Still pinch-hitting at Food Matters. I spoke with reporters from Nautilus and Chemistry World, but I've not yet seen their stories.

R.I.P. The Haystack, my first blogging home.

Recurring Themes: Cool reactions (hydrogenation, peroxidesPauson-Khand, cyclobutanones, ghostly copper); start-ups, #MegaPharma, faculty moves, corrections, #chemjobs, activism, stock photo WWWTP?, book reviews, cool structures

Tuesday, July 8, 2014

A Chempubs Hat Trick

Slow down, Guangbin!
(said I, channeling my inner Dr. Freddy...)

Guangbin Dong of the University of Texas-Austin has just published three papers in three different journals with Impact Factors over three. What's more - he did it all in the same week.

Just think of them as buckyballs
The papers in question?

"Regioselective ketone alpha-alkylation with simple olefins by dual activation"
Science, published 4 July 2014; 2013 IF: 31.0

"Cooperative alkylation of cyclobutanones and olefins leads to bridged ring systems by a catalytic [4+2] coupling"
Nature Chemistry, published 6 July 2014; 2013 IF: 21.8

"Alkylation of rhodium porphyrins using ammonium and quinolium salts"
Organometallics, published 7 July 2014; 2013 IF: 4.1

I hereby institute the Chempubs Hat Trick - Three papers, Three Journals, IF > 3.0, one week.

Congratulations to Prof. Dong for winning the inaugural award! But, I'm sure I've missed others who've been so deserving. Readers, have you noticed anyone else - present OR past! - who made this many simultaneous "shots on goal"?

Leave awardees' names in the comments!

Monday, July 7, 2014

A Cage-y Déjà Vu

I love finding molecular "diamonds in the rough." Especially when they look, well, a bit like diamonds.

While strolling through the literature, I did a double-take at this polycyclic caged structure reported by Santiago Vázquez  (Universitat de Barcelonaand coworkers. Wow!

Source: ACIEE 2014, Vasquez et. al.

Spawned from a "highly pyramidalized" (nonplanar) olefin dimerization, it features three cyclobutanes, four "envelope" cyclopentanes, and four cyclohexanes locked in their "boat" conformations (Even worse? All those eclipsing methyl groups on each end . . .jeepers). One might expect a thing like that to fall apart in a minute with a little heat, but, amazingly, the compound remains stable up to 500 degrees Celsius.

Model of the "highly-pyramidalized" olefin monomer.
Phil Baran used to say that you could judge the strain based
on how badly your model's bonds bent...

A little reference digging proved that similar caged olefins were first produced almost half a century ago at Smith Kline & French, using a seven-step prep reliant on chloroketals and long-duration sulfuric acid stirs (yuck). A major step forward came in 1970, when Avila and Silva (San Fernando Valley State U) realized that blasting UV light at a double-Diels Alder adduct of acetylene dicarboxylic acid led to a symmetric anhydride precursor.

Vázquez extended this little gem of a starting material towards finding active antiviral analogues of amantadine. Using the imide version of Silva's anhydride, Vázquez produced a caged secondary amine (see right) that exhibits activity against mutant versions of the H1N1 flu virus. His compound also inhibits the influenza A wild-type proton channel; molecular dynamics simulations indicate that it performs a "flip" relative to bound amantadine that plugs up this pore more effectively.

Let's just hope that these new polycycles get an easier-to-pronounce nickname. 

Octopane? Rocketane? Congestane? I'm open to suggestions!

Friday, July 4, 2014

Friday Fun - Big Plans

Only five weeks to go until ACS San Francisco! Who's excited?

An Acme Labs product
(With gracious nods to the ACS and Dr. Leuenberger for their long-suffering patience and hopeful humor...)

Happy Friday,

Tuesday, July 1, 2014