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, W√∂hler 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.

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*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:

This.
Source: Sud-Chemie

Not This.

Monday, January 11, 2016

The NMR Laundromat

Source: OPRD / CNRS
The simplest, most practical solutions* are often the best.

I'm reminded of classic papers for pragmatic lab procedures, like Clark Still's on flash chromatography, or Gottlieb & Nudelman's on detecting trace NMR impurities. Everyone has encountered their lab's version of the Kugelrohr setup - run by an old electric kettle and a windshield-wiper motor!

From the ASAP of Organic Process Research and Development comes this handy one-pager: a how-to on cleaning dozens of NMR tubes simultaneously, using glassware readily available in just about any synth lab.

Seeing this instantly triggered a "Well, duh!" moment for me - the amount of time I've stood before a stoppered 500mL vacuum flask impaled with a cannula, washing single tubes by hand...I'm sure it reaches into hours, if not days.

If you try this, leave a comment; I'm really quite interested to see how it turns out. I'd also wonder if OPRD might be angling for other quick one-offs. Couldn't hurt to try, right?

*Of course, I'd be remiss if I didn't point unfamiliar readers to the treasure trove that is Not Voodoo.

Sunday, November 29, 2015

xkcd Quiz in the New Yorker

Source: Randall Munroe, for the New Yorker
If you haven't taken Randall Munroe's Thing Explainer quiz in the New Yorker, click on over for 5 minutes of fun.

I'm sure anyone reading this blog'll get a perfect score, but it's an interesting approach to scientific outreach all the same.

Click here to try your luck!

Molten Salt Bath, Anyone?

While paging through Organic Reactions, Vol 1 in the chemistry library*, I encountered some unusual conditions in a review of the Elbs reaction. If you're not familiar, it's a high-temperature pyrolysis** of ortho-tolyl ketones to produce polycyclic aromatic hydrocarbons (PAHs). Products produced from the reaction find use as analytical standards for oil processing, in studies of DNA intercalation, and as molecular wires.

PAH prepared by heating at 500 oC
Bonus: Roman numerals in older reviews? Classy, but confusing.
Source: Organic Reactions 1, p. 154
As alluded to above, the chemistry itself wasn't what caught my attention, but rather this sentence:
"The flask is charged with 152 g of the crude ketone and heated in a nitrate-nitrite bath (care!) a430 ± 5 oC."
Four hundred degrees! During all my years in lab, I can't remember heating reactions past about 300, and those were with machined blocks of aluminum on an ancient Thermo hotplate.*** 

I realize that pyrolysis technologies have advanced in 70 years' time - FVP permits higher temperatures for much shorter residence times - but the concept of a molten mixture of sodium nitrate and potassium nitrite seemed both dangerous and alluring.

This is either Hawaii's Mt. Kilauea, or a molten salt bath. Or both.
Source: thelandofshadow.com

Looking through SciFinder, it seems that molten salt baths still find regular use in case-hardening and nitriding of steelwork, along with applications in cleaning organic residues off polymer extrusion dies. For extreme data-philes, the Molten Salts Research Center thoroughly analyzed a variety of salt mixture properties in a 150-page reference. Park Thermal International has published what seems to be a very conservative safety manual for nitrate-nitrite baths, and with good reason: aluminized leather aprons, tinted visors, and gauntlets help protect workers from glowing pools of salts at temperatures just below "decomposition...with extreme explosive violence."

Though I've never worked with molten salts, that doesn't mean none of my readers have. I see Milkshake has softened a 2L round-bottom flask by heating up to 380 with a graphite flake dry bath. How about you, Chemjobber?

Or are molten salt baths potential entrants in Derek's "Things I Won't Work With"?

Update (29 Nov): A commenter points out some previous Milkshake high-T campaigns.

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*Real books! Complete with yellowing pages, musty smells, and indexes full of names like Fuson, Fieser, and Bachmann.
**Can't get enough Elbs? Curious readers are directed to Name Reactions for Carbocyclic Ring Formations, 2010, Jie Jack Li and Timothy T. Curran. Review starts on p. 324.
***Obviously not counting use of a butane torch to pull pipettes, heat sieves and salts, etc.

Friday, November 27, 2015

Chemistry from the Deep: Geomimicry

Hydrothermal vent
Source: Geotimes.org
Lots of fascinating chemistry occurs in places humans can't routinely visit. Deep-sea hydrothermal vents, super-hot fissures formed from volcanic activity below the ocean floor, produce plumes of minerals and organic compounds. Through "geomimicry," researchers hope to harness similar conditions for use in labs here on dry land.

A team from Arizona State University - a geochemist, a biogeochemist, and a physical chemist  - report in JOC ASAP some interesting oxidation conditions using only copper salts and hot, pressurized water. With cupric chloride as an additive, benzyl alcohol and phenylacetic acid are oxidized to the corresponding benzaldehyde and benzoic acid in water at 250 Celsius and 40 bar (580 psi). The researchers speculate that the copper ions form different chloride species at high T and P, capable of promoting a series of single-electron transfers out of the organic substrates.


The article closes on an intriguing, somewhat humbling note:

"The vast majority of the organic material on Earth does not participate in the familiar, conventional surface carbon cycle because it is located deep within the crust and therefore undergoes chemical reactions under hydrothermal conditions. In contrast to the majority of reactions close to ambient [temperature and pressure], which tend to be controlled by enthalpic and kinetic factors, reactions...under geochemically relevant conditions tend to be controlled by entropic and thermodynamic forces...this suggests that much new useful organic chemistry may be inspired...by geology."

In other words, the reactions and catalysis we tend to study in labs "above ground" are just the tip of the organic chemistry iceberg....err, volcano?

Monday, November 16, 2015

3D Recipe: Drug Design Meets Virtual Reality

I still remember the distinct sense of wonder upon seeing the first immersive chemistry visualization environments in pharmaceutical companies' hiring brochures. These culminated in CAVEs*, where groups of scientists could congregate, done special glasses, and be surrounded by room-size, manipulable molecules. Now, the promise of bringing virtual reality to every bench chemist seems a little closer, thanks to the Molecular Rift.

Source: UIC CAVE virtual environment

In last week's ASAP issue of the Journal of Chemical Information and Modeling, a team of researchers from Lund University (Sweden) and AstraZeneca teamed up to deliver a relatively inexpensive ($500) virtual reality setup based on the Oculus Rift, a VR headset, paired with the Microsoft Kinect, a motion sensor popularly used with the Xbox. The paper prescribes a collage of open-source software - including the video game engine Unity and the chemistry informatics package Open Babel - that the Swedish researchers utilize to model metal complexes and a CB1 receptor, complete with undulating ribbons of secondary structure.

Source: Lund University / AZ

So, what's the big advance here? It's all in the control: the Kinect sensor watches the user's hands, allowing navigation of the molecular model using intuitive hand gestures. This way, the chemist doesn't have to intrude on the immersive VR with keyboards, joysticks, or mouse clicks.

Hoping to "...stimulate further development in a collaborative fashion," the authors have released the source code to the public** through the open-source code repository GitHub. If you're among the first to try it out, drop me a line!

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* Cave Automatic Virtual Environment. It wouldn't be software without a good recursive acronym...
**VR headset and Kinect sensor not included : )