C'mon, Let's Twist Again, Like We Did (This) Summer

Dirk Trauner: natural products chemist, vision researcher, neuropharmacologist,
. . . carbon nano-tube enthusiast?

Apparently, it's "crazy saturated hydrocarbons" month here at JLC. An astute observer clued me in to the Trauner group's latest pursuit - polytwistane. Studied for five decades by organic chemistry pioneers such as Whitlock, Deslongchamps, Oka, and von Rague Schleyer, twistanes have been tricky to coax into existence, owing to their propensity to rearrange into more stable adamantane.

In a 'gedanken' (thought) experiment, Allen, Schreiner, and Trauner mentally "add" bridging ethane units to twistane, stretching it out into a pseudo-helical oligomer (Chem. Eur. J.):

Chem. Eur. J. 2014, 1638.

Some fascinating molecular motifs fall out of their modeling studies. For example, unlike adamantane, polytwistane has three distinctly different C-C bond lengths, a factor chalked up to strain energy. However, it's in no danger of falling apart - the researchers calculate a "very modest" strain energy (~1.6 kcal / mol CH). All the hydrogens occupy positions on the outside (convex) surface of the tube. Finally, note that polytwistane is formally a polymerized version of acetylene, which we'll come back to later.

Emboldened by these in silico  results, Trauner and team take to synthesizing a basic unit of polytwistane, so-called "tritwistane" (Org. Biomol. Chem.). Starting from laticyclic polyenes -- think bicyclo[2.2.2]octene, connected end-to-end -- the researchers try a variety of electrophilic conditions to form the bond in question. Eventually, a combination of bromination / radical reduction produces the simple tritwistane oligomer:

Org. Biomol. Chem., 2014, 108.

At the close of this paper, Trauner deadpans that "attempts to synthesize polytwistane . . .from acetylene itself are ongoing in our laboratory..." Sounds like a tough nut to crack, but if he succeeds, he and his collaborators will have access to a rather rigid, narrow, twisted new material certain to possess interesting properties.

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*Don't know the song in the title? Say hello to Chubby Checker!

Olympicene's "Top Secret" Final Step

Over in London, preparations for the 2012 Summer Olympic games continue apace. The torch winds its way through the countryside, the ticket printers hum along, and the British Army has mounted defensive missiles on local apartment roofs. But, for those who've been missing the synthetic chemistry connection, wait no longer: enter, Olympicene!

Olympicene
Source: IBM Zurich | BBC

Olympicene, a tight five-ringed structure, does indeed resemble the famous logo of the quadrennial international contest. IBM Zurich, who used specially-functionalized AFM tips to image pentacene in 2009, now brings us fantastic high-res images of this polycycle (see right). 

I won't go into the story behind the science, as that's been elegantly summarized in a number of places already. Instead, I want to highlight a perplexing 'teaser line' from yesterday's ChemConnector post: 

"You can see the Olympicene compound coming together step by step and yes, the final step is not yet reported!" 

OK. Let's see, we have the first few steps laid out for us, thanks to RSC's ChemSpider. Easiest way to make anything? Start with most of it intact! From commercial 1-pyrenecarboxaldehyde, a Wittig olefination, H2 reduction, basic ester hydrolysis, chlorination, Friedel-Crafts, and lithium aluminum hydride (LAH) reduction brings us to the 5-ringed alcohol (shown below). All the steps are greater than 89% yield, except the F/C (15%), which one imagines might make the "other" pentacene isomer preferentially.

I find the final "Top Secret" step amusing, because any organic chemist "familiar with the art" could think of at least five ways to do it! (Non-chemist readers: the molecule on the left needs a single C=C double bond, and standing in the way is just a molecule of water). That alcohol is fairly "activated" for elimination. My guess? A little strong acid, gentle heat, and some molecular sieves.

Pro Tip: Don't believe the hype declaring olympicene the "smallest 5-ringed structure," at just 1.2 nm across. Skeptics, cynics should check their bond lengths. Is olympicene smaller than cubane? (6 rings, ~0.6 nm). How about a ladderane? (5 rings, ~1 nm). Anyone know other molecules that might qualify?


Updates (04:18, 5/29/12) - ChemConnector mentions, via Twitter, that the step is less 'Top Secret,' and more not-yet-drawn-up for ChemSpider Synthetic Pages. Per Excimer's comment, fixed the position of the 'saturated' CH2 carbon. 
(21:10, 5/31/12) - Commenter (And U. Warwick Prof!) Peter Scott points out the new ChemSpider page, showing major isomer and detailing conditions.

Dirty Jobs: Why Don't Chemists Wear Suits?

“Clothes make the man.” – Mark Twain

For every occupation, a mark: grass stains on athletes’ socks, tar for roofers’ pants, or grease on mechanics’ smocks. But has Mike Rowe, host of Discovery Channel’s Dirty Jobs, donned a lab coat lately? Synthetic chemists work every day with substances other people use to dissolve metals, dye fabrics, or kill microbes. Naturally, we end up wearing some of it by the end of the day.

R.B. Woodward: Suit or bust!
Credit: nobel.se

A long-standing joke among bench chemists: you can tell a lab visitor straightaway . . . because they wear nice clothes! Looking at pictures of scientists from a few generations ago, one wonders why they chose to dress so sharply for an inherently messy, hands-on occupation: in the days of R.B. Woodward [1965 Chemistry Nobelist], de rigueur lab wear was a 3-piece suit, tie, and (maybe) a smock. Goggles or gloves weren’t strictly required. The counter-cultural ethos of the following scientific generation eschewed formal dress for button-downs, khakis, loafers, and lab coats, a change which may also have been driven by old-timers’ tales of neckties stuck in stirring rotors or acid-eaten sport coats.

Today, synthetic organic chemists just don’t wear really nice clothes, because they won’t stay that way for long. In every corner of the lab lurk wardrobe-destroying substances.

Color Changers - Nitric acid, hydrogen peroxide, and sodium hypochlorite – all strong oxidizers – leave dark-colored clothes with bright white or yellow marks. Solvatochromic effects, color changes brought on by solvent interactions with fabric dyes, show you shades you wouldn’t expect: green shirts can turn yellow, blue shirts turn purple, and yellow shirts appear orange. This tinge luckily fades over time as the solvents evaporate.

Mechanical equipment brings other laundry challenges. Grist and grime from high-vacuum pump valves stains blue jeans dark brown. Corroded metal clamps produce dark rust streaks. Silicone oil, a lubricant for glass joints, saturates fabric, leaving dark spots that look permanently “wet.”

It’s not just appearance under attack: ethanethiol, the odorant most people associate with gasoline pumps or natural gas leaks, leaches into hair and clothes, leaving a persistent sulfuric smell.

Indelible Metals - I once made a bright yellow ruthenium hydride complex, a trace of which spilled on my dark green T-shirt. No matter how many times it’s been through the wash, the compound stays firmly stuck in the fabric. Ditto dark orange stains from nickel complexes set into my white lab coat. Khaki pants develop purple-brown stains from silver complexes or iodine. Perhaps spills like these gave chemical company Johnson Matthey the idea for FibreCats, catalytic metals immobilized on fibrous strands for easy recovery.



Much closer to real life!
Credit: test-tube.org.uk



Scorched Shirts – Ever spill concentrated sulfuric acid on cotton? You won’t know until the spray-pattern of tiny holes shows up after washing and drying on high heat. Since cellulose and sucrose are both sugar-based, perhaps this is the clothing equivalent to the black carbon snake general chemistry demo. Be especially careful with that bottle of nitric acid; one of the first synthetic explosives, nitrocellulose or “gun-cotton,” was made accidentally in the early 1800s as cloths used to clean up spills would explode suddenly when left to dry.

Some pertinent advice for those who wish to look good in lab? Find a good dry cleaner.