Monday, May 28, 2012

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!

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.

From the Vault: Scientific Humor, Shameless Plugs

I've been dying to use this photo.
Source: Nichelle Nichols
Holidays give you a chance to relax and reflect. Here in the States, we set aside time at the end of May to remember those who've served in our armed forces, past and present. Thanks to them, I'm able to bring you this glance back on my official 13-month blogging anniversary. (Well, 2 days late, but who's counting? Wait, you are? Nuts.)

Yes, back on April 26, 2011, Chemjobber was kind enough to lend me a little space to get this whole 'writting 4 de internetz' thing moving along. Over at The Haystack, Car1`men and Lisa didn't balk when I suggested that my first guest post involve Michael Jordan and Back to the Future. Paul didn't mind me poking a little fun at Wender's expense, and somewhere in July 2011, I had the crazy notion to hang out my own shingle.

Fast forward to late May 2012 - what a ride! I've met a bunch of new friends through Twitter and commenting on other blogs. I've been fortunate enough to appear at, and post on, sites I could have only dreamed of a year ago.

But, best of all? It's been a lot of fun!

To parrot the Ig Nobels slogan, I hope to make you laugh, then make you think. CJ and I goofed around with inflated yields in methods papers. When Breslow published his latest origin-of-life tract, it grew new life in the chemblogosphere as #spacedinos. How about art? Off-the-cuff projects included messing around with #arseniclife, pushing drawing memes, stitching together Easter eggs, "rosetta stone" chemical scribbles, and the 'Leaning Tower of Septa.'

'Olympicene,' viewed by STM.
Just in time for London 2012!
Source: IBM Zurich | U. Warwick
Wordplay? We got you covered. How about cute pharma diminutives? Mobile phone games, the Big Pharma Apocalypse, new chemistry portmanteaux, or silly chemical names? I also love finding molecular inspiration out in the wide world, whether it be on gas stations, at concerts, or imposing iron gates. I've even mused about taking this show on the road, once or twice.

I know I promised not to say anything yet, I'm grateful every day that interesting, excited, friendly readers - like you folks - stop by for awhile. I'll keep writing 'em, if you keep coming back.

Sunday, May 27, 2012

Confusing Toxibbreviations

Dr. Freddy, over at Synthetic Remarks, presented an interesting problem: why do so many molecules have such confusing abbreviations? If you think of an abbreviation as a linguistic shortcut, a way to save time while communicating complex ideas, it makes sense to use something everyone can understand. Unfortunately, the simplest workarounds can also be the most confusing; when I write "RM," do I mean 'recovered material,' or just an alkyl group attached to a catalyst? Depends on your audience.

The strangest shorthands? Natural product toxins.
Batrachotoxin: "Nothing like Brevetoxin."

For convenience, when chemists isolate a new biocide, they assign it a name ending in "toxin," which inevitably shortens to "TX." Pop another letter on the front to differentiate, et voila! (This probably made sense back when we'd found just a small handful of these compounds, but they're getting crowded now.)

Here's a few I tracked down, listed alphabetically:

ATX: Antillatoxin, Anenome toxin, Ammodytoxin, Altertoxin, Aflatoxin, Anatoxin, Adriatoxin
BTX: Botulinum toxin, Batrachotoxin, Brevetoxin
CTX: Charybdotoxin, Conotoxin, Cholera toxin, Ciguatoxin
DTX: Dendrotoxin, Dinophysistoxin, Diphtheria toxin
ETX: Epsilon toxin, Erabutoxin, Edema toxin, exotoxin
FTX: Funnel Web Spider Toxin
Nereistoxin: "Don't call me  Noxiustoxin!"
GTX: Gonyautoxin, Geographutoxin, Gambierotoxin, Gila toxin
HTX: Histrionicotoxin, Hemitoxin, Horridum toxin, Homoanatoxin
ITX: Iota toxin, Paralytic insecticidal toxin, immunotoxin
JTX: Joro spider toxin
KTX: Kaliotoxin
LTX: Latrotoxin, Leukotoxin, Anthrax Lethal toxin
MTX:  Maurotoxin, Maitotoxin, Maculotoxin, Mosquitocidal toxin
NTX: Nereistoxin, Noxiustoxin, neurotoxin
OTX: Ostreotoxin, Orphan toxin
PTX: Pertussis toxin, Palytoxin, Pectenotoxin, Pumiliotoxin
QTX: Quinquestriatus toxin
RTX: Repeat toxins
Saxitoxin: "Will the real STX please stand up?"
STX: Shiga toxin, Saxitoxin
TTX: Tetrodotoxin, Tetanus toxin
UTX: Uraemic toxins
VTX: Verotoxin, Verrucotoxin
WTX: Weak toxin (cobra), Waglerin
XTX: None for business!
YTX: Yessotoxin
ZTX: Zetekitoxin, Zeta toxin

Readers - Have I left out your favorite poison or abbreviation? Let me know in the comments!

Wednesday, May 23, 2012

Close Enough for Chem - Guest Edition

Inspired by ChemBark's WWWTP series, I've asked friends of the blog to send me pictures of chemically-inclined art and logos from the wide world. Today, I bring you two more examples of so-close chemical structures.

Organo-'Catalyst' - This image, from a CT health center, contends that exercise can "catalyze" a better, healthier life. Well, that's a pretty strange-looking catalyst! Instead of your standard Pd or Ni, they've picked something approximating tryptamine. Honestly, the compounds that I think of when I see this structure don't necessarily encourage good health...

The "T" is for Texas Carbon - From a concert-goer in a college town comes this T-shirt (presented here without lifestyle endorsement). The tricyclic core of tetrahydrocannibol, an active component of marijuana, looks mostly OK, but the artist may have been under the influence when he drew that mixed-up hypervalent phenol ring!

Readers, have any more "almost" chemically-inspired photos? Feel free to send them my way!

Monday, May 21, 2012

Calimari Calligraphy: Same Ink, 160 Million Years Later

Old news: Geologists, digging up ancient British sea bed, unearth a fossilized cephalopod.

Big news: Its pigment sacs contain the same ink squid still use today!

Fossilized Ink Sac
Source: British Geological Soc. | Nat Geo
This archaeology, with a dash of chemistry for good measure, went to press in PNAS earlier today. As Nat Geo, Discovery News, and msnbc tell it, a stroke of luck brought the multi-national (Japan, India, USA, UK) team a fully intact ink sac, which still contained eumelanin, the ubiquitous black pigment found in skin, hair, and feathers throughout the biological world (for more on the structure and function of melanins, click here).  

Quoth the lead author, John D. Simon (UVA-Charlottesville), to Discovery
"Out of all of the organic pigments in living systems, melanin has the highest odds of being found in the fossil record" 
In other words, this collection of highly-oxidized tyrosine and indoleacetic acid residues, chained into polymeric pigments, stays preserved - and structurally sound - for 160 Million Years. Could we say that about most of the materials we make today? Moreover, by comparison of various spectral techniques, the authors wager that the ancient melanin composition looks nearly identical to what squid use today to scare off predators.

IR Data, "flipped"
Source: PNAS Supp Info
Well, I'd like to see some data, wouldn't you? Digging through the Supporting Info, I see loads of evidence: degradation studies, EPR, IR, Mass Spec, CHN analysis, Carbon-13 NMR, UV, pyrrolysis TIC, and X-Ray photoelectron spectroscopy (Whew!). 

Let's examine two of these a little closer. For the IR data, I've switched the view around 180 degrees, to present the peaks the way you'd normally see 'em in the lab. Note the top 2, calcium carbonate and hydroxyapatite, with their nice, sharp C=O and P=O stretching bands. When the researchers looked in the partially-fossilized sediment, they found mostly these two...but look at the dye! Even after all those millennia, the absorbances for the fossil dye line up almost perfectly with the modern-day sample.

Total Ion Chromatogram, Current (top) vs. Fossil (bottom)
Source: PNAS Supp Info
How about a little heat? If you cook the ink at 600 Celsius, then pass it quickly through a mass spec, plotting ion current vs. time, you get the next spectrum, the TIC. It shows the same breakdown products, a variety of small heterocycles and fatty acids, and something I wasn't familiar with: diagenetic products. These products, formed from reactions that occur during fossilization, show up here as sulfur heteorcycles. Since the samples have had quite a bit of time underground, they show much more diagenetic decomposition. 

Sunday, May 20, 2012

Sunscreen Chemophobia: Oxybenzone

(I wrote this for participation in the 2012 'Toxic Chemicals' Blog Carnival, over at ScienceGeist)

This 'suit' wants to sneak more chemicals into your sunscreen!
Source: EWG 'Hall of Shame'
Courtesy of Mother Jones and the Environmental Working Group (EWG), we can all breathe a bit easier. The eco-conscious nonprofit organizations have just released their recommendations for summer sunscreens. Unsurprisingly, the Top 20 are cut from the same cloth; words such as "natural," "clear," "garden," and "organic" abound. Ingredients, too: ~20% or so of 'micronized' (>100 nm) zinc oxide, some titanium dioxide for good measure . . .and just about every fruit oil, tea extract, or skin moisturizer you can think of.

Actually, I found myself much more drawn to the 'Hall of Shame.' These sunscreen outlaws represent all the nefarious tricks #BigChem might play on an unsuspecting public - sneaking in oxybenzone, "nano-zinc," and retinyl palmitate (synthetic Vitamin A) to make a buck off naive customers. I won't weigh in on the last two ingredients, but oxybenzone certainly caught my eye.

Oxybenzone, also called benzophenone-3, finds its way into sunscreen, lipstick, lotions, paints, and polymers. According to the Merck Index, it was first prepared over a century ago (1906), and patents from the 1950s show a simple one-step prep, Friedel-Crafts acylation of benzoyl chloride, which forms the new C-C bond between the "left" aromatic ring and the C=O group. Oxybenzone actually absorbs UV light over a wide swath of the spectrum, from 280-320 nm, meaning it offers sun protection from both UV-A and UV-B.

The EWG calls oxybenzone a "hormone-disrupting chemical." Like bisphenol A (BPA), another well-reported and contentious molecule, oxybenzone contains a free phenol group, and two aromatic rings linked by a central carbon bridge. These atomic features tend to crop up in compounds that mimic estrogens in the body.

Well, does oxybenzone pose endocrine risks? Where could you find that info, anyway?

I started where I usually do: TOXNET, the U.S. National Library of Medicine reference database. Oxybenzone triggers six references from the Developmental Toxin (DART) literature, which cover 18 years of studies on fish, mice, and cell cultures. I also checked PubMed, grabbed a 1992 National Toxicology Program (NTP) oxybenzone report, and the 2008 European Commission SCCP recommendations for consumer exposure.

What do the data show? At the highest doses - 50,000 ppm - all animals develop liver, kidney, and reproductive organ damage. But the dose makes the poison, and as you feed (oral) or rub on (dermal) less compound, the side effects fall off rapidly. No teratogenicity (fetal harm), no mutagenicity (DNA errors), and no unexplained deaths. The scientists did observe indications of "moderate reproductive toxicity," but, again, these showed up in the highest-dose groups. To replicate these effects in humans, you'd have to literally eat spoonfuls of the compound (For ongoing oxybenzone studies, see: NTP, CDC).

The European Union, exemplars for cautious chemical regulation, provide a convenient calculation for human exposure: for a standard 60 kg (132 lb) person, given skin absorption, sunscreen concentration (6% oxybenzone), and average application at 18 g (just over half an ounce), exposure = 1.78 mg / kg / body weight / day. That's ~2 ppm, fully 500 times less than the lowest doses currently testing at the NTP (see above). The 2008 EU panel assigns oxybenzone a Margin of Safety of 112; compounds above 100 generally meet their benchmark for safe use.

Delicious cup of low-dose,
 bioactive compounds
Source: Green Tea Health
But, hormones influence body chemistry at miniscule doses, right? And, these sunscreen compounds are ubiquitous! How can we be absolutely certain that they aren't toxic? Well, I'll counter with a simple observation: herbal, plant, and seed extracts - like the shea butter, aloe juice, camellia seed oil, jojoba, calendula, papaya, plantain leaf, starflower seed, linseed oil, green tea extract, olive oil, plankton, avocado oil, primrose oil, and bark extracts found in the "alternative" sunscreens - have just as many, if not more bioactive compounds!

For chemophobic consumers, the general (albeit, flawed) reasoning seems to go something like this:
Many small, aromatic, heteroatom-containing molecules may be endocrine disruptors.
Industrial companies produce many such chemical compounds.
Therefore, many "industrial" chemicals cause health problems.
Magically, however, this logical logjam clears if you mention "natural," "organic," or "chemical-free" formulations. I suspect the reasoning goes:
Many small, aromatic, heteroatom-containing molecules may be endocrine disruptors.
Natural product extracts contain dozens of compounds, some unknown, many untested.
But, since they're from plant extracts, they're probably safe.
Would consumer impressions of oxybenzone change if it were. . .a natural plant extract? Good news: it is.

That's right, the compound occurs naturally in various flower pigments, which chemically trained eyes might have detected in the "resorcinol-like" framework. To stretch the metaphor, given the eased FDA rules regarding dietary supplements, I wonder if one could employ this tactic to produce a "natural, plant-based sunscreen" that still contains oxybenzone!

Happy summer, everyone! Think clearly, ask questions, and challenge assumptions. And, wherever you buy it from, remember to always wear your sunscreen.

For a different perspective on EWG's sunscreen data, head over to Science-Based Medicine

Saturday, May 19, 2012

"Hot Rocks" Cause Injury, Mystery

As reported on Yahoo / GMA (video), and by the ever-vigilant Jyllian Kemsley over at Safety Zone, a real-life chemical mystery is unfolding. A few days ago, a California couple strolled the beach with their kids, and pocketed a few interesting-looking rocks they had found. Later that evening, the rocks caught fire while in Lyn Hiner's pants pocket, with a "...bright, intense flame," that, according to reports, couldn't be patted or smothered out. The resulting fire hospitalized both wife and husband with severe burns.

Source: AP
So, the question remains: what was on the rocks? The orange substance, found on green and gray surfaces, may indeed be "phosphorous" [sic], as mentioned by a mildly chemophobic (nearby nuclear plant, firing range?!) Associated Press report. A local geologist commented that the orange coloration is "...not natural, it's human made." With some imagination, you could probably come up with a few phosphorus alternatives (looking at you here, ExploSci!).

Pyrophoric Metals - Finely dispersed powders of magnesium, zinc, or thermite could certainly react with a little acid or moisture. However, these don't fit the bill as "orange substances."

Flash powder - Often used in special effects and flares. This blend of oxidizers and reactive metals would have to have been intentionally placed on the rocks, since they wouldn't have remained stable for long, out in the open air.

Reactive Groups - Many organic groups react with violent decomposition or exotherms when sparked, touched, or heated. Although certainly far-fetched, someone fooling around with picrates, nitrates, or perchlorates could have inadvertently doped the stones in question. There's at least a few dozen of these salts around, and many (iron perchlorate, mercury fulminate, ammonium picrate) may actually be orange or yellow-colored.

Exactly Like Cooking - Pancakes!

Continuing our series to put more money into grad student wallets, through the power of cheap -but nutritious! - leftover-generating food.

Well, it's never a bad time for pancakes. Just about 10 minutes from reading this, you, too, could be chowing down on a short stack...and it requires relatively few ingredients. You probably have them all just hanging around.

Fluffy Pancakes (Prep Time: 10 minutes)
Adapted from Kris, at

Equipment - Large pan or griddle, spatula, wooden spoon, measuring cup, measuring spoons, large bowl, small bowl.

Base Ingredients (about 6 pancakes) - 3/4 cup milk
2 tablespoons vinegar

1 cup whole wheat flour
2 tablespoons white sugar
1 teaspoon baking powder
1/2 teaspoon baking soda
1/2 teaspoon salt
1/2 tsp oil

1 egg
1 tbsp butter

Fun Part - vanilla, cocoa, cinnamon, nutmeg, cloves, ginger (to taste)
nuts, raisins, oats, other fruits or grains (to taste)

Procedure - Heat skillet / pan to medium heat. Pre-mix the milk and vinegar in large bowl, set aside 5 minutes; this simulates buttermilk, so if you'd rather, you can experiment with combos of kitchen acid / milk here: lemon juice, cider vinegar, etc. Now, add egg, oil, and butter to milk mixture, with stirring. 

Mix the first five dry ingredients together in a smaller bowl. Slowly add these dry ingredients to milk mixture, with stirring, over about 1 minute. Now's your chance to "personalize" your pancakes - spices, nuts, grains, chocolate chips, or fruits are all welcome. We at Just Like Cooking prefer combos like strawberry ginger, cinnamon pecan, raisin oat, or cocoa banana.

Remember that hot pan? Grease it lightly with spray or butter, and ladle on small portions (think about 1/4 c, or maybe 60 mL). The cakes will spread out slightly, begin to brown on the edges, and form small bubbles on top. After about 2 minutes, lift up a side - if it's golden brown, flip 'em all. Cook about 30 seconds on the other side, and transfer to plate for serving. 

But wait! Your pancake personalization hasn't yet ended...feel free to top these off with maple syrup, butter, peanut butter, Nutella, berry syrup, fresh fruit, powdered sugar, or black sesame seeds.

Total Cost: Dry ingredients ($1.00), Egg ($0.25), milk ($0.50), oil / butter ($0.25), spices ($0.50), additives ($1.00) = $3.50, or about $1.75 / 3 pancake serving.

Thursday, May 17, 2012

Breaking the Fourth Wall

Many readers have written to me lately, asking about the blogging process. How do you start out? How do you choose topics? How do you hook up with editors?

Without further ado, I'd like to lay bare my blogging 'process' for you.

1. Idea - Of course, this is the toughest part! One must sift through academic papers, newsreels, or the evening paper, seeking that elusive chemical angle. Failing that, just stand underneath a row of Edison incandescent light bulbs, until one of them shines brightly. That usually does the trick.

2. Composition - Blog posts, like all thoughtful writing, flow better when written out entirely in longhand. Make sure to liberally sprinkle in Twitter hashed tags, oblique in-jokes, and remember to include 'hyperlinks' by using the phrase "Dearest Editor: Do, please, insert after this word, the following: H.T.T.P <slash> <slash> <colon>..."
Source: Olmstead Soccer News

3. Pictures - If you have some upson board and charcoal, initial sketches are fine. Failing that, purchase a daguerrotype machine, or one of the brand-new Polaroid Company "instant" photograph machines. Remember, these require adequate time to develop, so please "shake it" well.

4. Upload - You wish to send a document, long-distance? Well, thanks to trans-Atlantic communications, the impossible can now be achieved! Simply bring your draft parchment to a local telegraph operator, and ask them for their post-haste rate.

Pictures will still have to be sent by mail, or by Pony Express. That's the rub.

Source: 20th Century Fox / Matt Groening
5. Transcription / Editing - Once received at the other end, a team of experts will typeset and format your opus, and suggest minor changes. Chief editors will ensure quality reproduction, as shown above.

Within a few fortnights, your brand new blog post should be "live," and you may feel free to start the process once more.

Wednesday, May 16, 2012

Spring Into Science Fair

Just a short little note about something dear to my heart - Science Fair. Over the past two days, I've been honored to judge projects from the "Physical Sciences" category. My charges ranged from 10-year-olds studying conductivity to high schoolers interested in artificial tissues.

Some observations:
Source: Philip Martin Clip Art

- What's Old is New Again, Right? The classics all made appearances. Fruit batteries, and kitchen sponges teeming with bacteria. "Green" cleaners, iron in breakfast cereal, and tooth-dissolving cola. And, of course, what would a Science Fair be without a baking soda volcano?
[Sadly, a fellow judge clued me in to a site that helps students, even those who start the night before, to quickly assemble a project, 'data' and 'writeup' included. Sigh.]

- TV Infiltration: Scientific 'reality shows' and crime scenes both figured prominently. Future forensic teams examined simulated blood spills with luminol, tested decomposition rates of flesh in various soils, and dusted for fingerprints. The Mythbusters might have enjoyed this fair; urban legends on display included fruit spoilage, fridge doors, car engines, memory tricks, and clothing stains.

- Back When I Was Your Age...Amazing to see how "high-tech" projects have trickled down into lower age groups. I watched third-graders isolating DNA, middle schoolers playing with Green Fluorescent Protein (GFP), and young adults - who couldn't yet drive cars - genetically engineering algae!

- Funny Titles: Double entendres and in-jokes won the day. On notice: a windmill project ("Who Broke Wind?"), a microbe digester ("Poop Power"), and a chromatography project ("Solvent Battles!").

All in all, it was a great experience, and I recommend all readers volunteer when the opportunity arises!

Monday, May 14, 2012

Baran Borole Begets Mess of Meroterpenoids

I know I'm preaching to the choir, but have you seen the latest from the Baran group?

Dr. Freddy probably said it best: Please, slow down, Phil!

In today's tract, Prof. Phil Baran and company search for a molecular linchpin, trying to stick a two-ring starting material onto an aromatic group. The resulting structures, dubbed meroterpenoids, show up in the framework of several marine natural products.

The group ID's a logical starting point: sclareolide, an essential oil isolated   from various species of sage plants. Long story short - the first few avenues (iodination, carboxylate degradation, BF3 salts) are all dead ends. The "Eureka!" moment comes when they try a cyclic borole (see right), which succeeds on multigram scale and produces a med-chem-friendly crystalline white solid. Using increasingly-popular radical conditions, Baran's team readily attaches this intermediate to benzoquinone (46-60% yield).

The result? A natural product, (+)-chromazonarol, formed in 34% yield... in only six steps! Mere mortals might have called it a day, but not Dr. Phil: he goes on to make nine more natural products, most of which had previously taken >12 steps to make on their own...not too shabby for a four-page Communication.

Boroles: All the things I've
come to remember...
Source: 1000 Eighties Blog
While reading this paper, I couldn't stop staring at the "borono-sclareolide" linchpin - now where had I seen that before? A-ha! It's the major attraction in all those antibacterial compounds Anacor recently developed. Perhaps, more entrepreneurial readers might consider calling to find out if Anacor's replete pipeline might suffer further functionalization, bringing forth even more wild drug leads.

Friday, May 11, 2012

What's that Molecule? U.S. NAEP Edition

I can be a bit rough on a few topics 'round these parts. Chemophobia. Unscientific rumors. Coloring-book abstracts. And, of course, the interesting Internet images of chemists - always white lab coats, intense gazes...and nonsensical atomic scrawls in the background. Up to now, however, I've tried to joke about it, and then offer small suggestions to improve them.

Her smile means she knows the structural joke...
Source: 2009 NAEP | U.S. Dept. of Education
Here's one that actually threw me: the National Assessment of Educational Progress (NAEP) has just released their 2011 National "Scientific Report Card" for U.S. middle schoolers (I'll comment more on what it says in a future post). Linking out from NAEP's site, I found this document, clocking in at 155 pages, which explains the scientific framework for this testing, and the methods used to assay student knowledge. Look at the cover image, of a young girl smiling as she discovers the joy of chemical modeling kits...

...What is that molecule, anyway? Anyone recognize it? It has a terminal "-CO3" group, and some sort of terminal methylene on the other end. I couldn't think of a reasonable answer, except the dreaded posed picture possibility.

High irony, that this picture appears on the front of a document about, education!

Thursday, May 10, 2012

"Holy Geez" - APM's Marketplace Interviews Dow (Chemical) CEO

"oh man, whatever they make is probably toxic. It's chemicals, it's hydrocarbons - holy geez, I don't want any of that stuff."

"Holy geez," indeed. The above quote, Marketplace host Kai Ryssdal's (KR) opening volley from today's interview with Dow CEO Andrew Liveris (AL), really sets the tone for the whole conversation. From there, to summarize: there's some kitschy Australia jokes, and a truckload of corporate newspeak about Dow's re-branding efforts and American manufacturing readiness. Without further ado, here's some choice quotes:
KR - "...if I say "chemistry," what do you think? People in white lab coats, right? Vials full of liquids, maybe?"
Sure, if you're into stock photos. Don't forget to include beakers, jokes about social awkwardness, and references to Breaking Bad!
Source: Busplug
AL- "But these days, you may have seen our ads on TV. We are really branding Dow. The word "chemical," of course, from a heritage point of view is still in our name." [Emphasis mine]
Again, when a major multinational conglomerate says these kind of things on syndicated radio, how can we ever hope to fight chemophobia?
AL - "So we've got to go out there and really re-educate humanity, because at the end of the day, 95 percent of all products out there have chemistry in them"
Dare I ask? What's the other 5%? Dark matter? Pixie dust? Aether? (This sounds like a job for Dr. Rubidium over at JAYFK, or our old pal Deborah Blum)
AL - "The word manufacturing, you know, even the word industry just doesn't sit well. People think about it as a smokestack, environmental, yesterday's era; that everything should be services."
I'm a proud member of the chemical industry. I make things. So do most of my colleagues, family, and friends. I'd like to say it's part of today's era. Anyone else?
AL - "We're re-branding what science, technology, engineering, maths mean to this economy and how we can transfer that into American jobs for the next generation."
Perhaps the most galling quote of all. I can hear Chemjobber sharpening his linguistic knives from all the way across the internet. Keep 'em ready, because the fight against mainstream #chemophobia continues...

Redox Champ: NHC Ipso, Facto

Bond density difference between electron-rich and -poor NHCs
Source: Cavallo, JACS  ASAP
On the surface, N-heterocyclic carbenes (NHCs) seem like dream ligands. They have strong, neutral dative electron pairs, steric bulk, and enough variants now exist that chemists can "dial in" chirality, control R-group rotation, or add them as salts.
Could we possibly improve them any further?

A new JACS ASAP answers: of course! Professor Luigi Cavallo, and KAUST / U. de Salerno coworkers, like to examine NHC ligands computationally. Using Gaussian '09 molecular modeling software, the authors toss in a variety of electron-donating (ex: NMe2, Me) or withdrawing (ex: Br, NO2) substituents on the aryl rings of mock NHC ligands. They then virtually "staple" them onto Grubbs, Grela, and Ir-COD catalysts, and calculate the redox potentials of the Ru and Ir metal centers.

These data trend like you might expect: electron-withdrawing groups on the NHC increase the redox potential, while donating groups reduce it. Well, what's driving these effects? The authors initially suspect σ/π donicity (that's a $5.00 word, right there), the ability of the NHC-M bond to directly influence metal properties. However, they note something odd: there's precious little change in the bond lengths between complexes, only 0.005-0.05Å; by contrast, in carbon-carbon bonding, moving from alkane to alkene shaves off 0.2Å! Thus, they suspect that the NHCs' influence isn't coming through their main bond.

Well, if it's not electronics, then what's changing these redox properties? Enter the 'ipso effect,' a long-observed, yet little-invoked, mechanism for ligand-to-metal charge transfer. The arene carbon directly connected to the heteroatom rubs up against the metal d orbitals, and charge can move through space. Perhaps the best known non-NHC systems to exhibit this effect are the highly-active Buchwald biaryl phosphines, which show ipso interactions with palladium and gold, among other metals. Cavallo and coworkers compare electron density maps (the trippy blue-and-red models, above R) between cationic and neutral metal states, and note a huge red splotch of π-to-d donation (see d) from the NHC orbitals to the metal.

NHC electronics lower intermediate energies
Source: Cavallo, JACS ASAP
But wait, there's more! The authors apply this model to previous observations in Ru metathesis chemistry, then extend the metaphor and tackle Pd biaryl coupling. As shown in the graphic (left), they calculate a ~3 kcal / mol difference for the first catalytic intermediate, depending on the electronic environment of the NHC used. For a throwaway closing line, they let us in on a final trade secret: this effect could be used to stabilize lots of high-valent metal I hear any calls for nickel (IV) chemistry???

Wednesday, May 9, 2012

Chemistry Words, with Friends

A recent discussion on Twitter brought some salient sci-comm discussion: Why aren't more chemical terms acceptable for play in the smartphone app Words with Friends?

(Not Really)
Source: Fake Science Tumblr
Unfamiliar with the game? Words, much like Scrabble, prompts players to place lettered tiles to form words on a 15 x 15 grid. The game rewards you for playing unusual letters (Q, Z, each worth 10 points) and for building words across certain labeled spaces, which confer extra points to certain letters and longer words (In fact, critics and fans both remark that WWF seems to be more like a "math game" than erudite word selection).

So, you'd think that WWF would allow submission of any legal word, right? Well, since language constantly evolves, the designers limited choices to a public-domain word list, ENABLE, containing ~173,000 words. Quite a lot, really, until you compare that to SOWPODS, the tournament Scrabble players' list, weighing in at 267,000 (and counting!).

The ENABLE list, ranging from "aa" (lava) to "zyzzyvas" (a weevil), represents scientific fields from anthropology to zoology. Large 'blocks' of terms deal with nuclear energy, geology, physics, and biology. So, what about chemistry?

I spent a few minutes trawling the list, then picking the brains of my colleagues. With this (very) minor effort, we found just a handful of terms missing: ipso, meso, fluorous, and chiron. [Words we guessed might not be there, but were, included: carbocycle, solute, solvent, catalyst, nucleophile, polydisperse, synclinal, catechol, aglycon, zincate, chiral, orbital, glycine, alkali, ketone, and bromide.]

All in all, more chemical variety than I had expected. Readers, I've obviously not covered the gamut of chemical terms, so if you find ENABLE lacking, let me know in the comments. Or, better yet, let Zynga know!

Stock Photo Fun - "Confused Scientist"

"Confused Scientist" (I can think of reasons why...)
Source: Royalty-Free Stock Photos
While searching for some stock photos to accompany an upcoming post, I found this gem. It's actually titled "Confused Scientist."

Well, let's start from the top, shall we?

- I've never seen anything labeled "Schematic Benzene Complex."

- I can't seem to draw a stable-looking, neutral compound from the formula she's considering. Five degrees of unsaturation, maybe a catechol or something? Anyone? Bueller? Bueller?

- You shouldn't eat chalk. Do you know where that's been?!?!

- Staring intently at the wall won't avail you. (ask Azmanam)

- The structure she's drawing, in addition to not having a benzene ring, just has valence errors jumping out from every which way. I count at least three.

Needless to say, I didn't opt to use this for my post. For more structure fun, check out ChemBark's WWWTP posts.

Saturday, May 5, 2012

Comic Homage

I've been a bit under the weather, so I've turned to an old stand-by: digging through the archives of my favorite webcomics. Bonus, when they contain scientific or chemical references.

So far today, I've made it through most of xkcd, and happened to finish Deborah Blum's Poisoner's Handbook last night. With some time on my hands, I figured a "mash-up" of the two might be in order.
(Cheat Sheet: check out this story about biochemistry, NASA, and "alien life" found here on Earth)

You never know what you'll find fishing around in Mono Lake...

Friday, May 4, 2012

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???

Thursday, May 3, 2012

Chemophobia Daily - NY Times (Again)

(This piece, by veteran Op-Ed columnist Nicholas Kristof of the New York Times, ran yesterday. It has been the focus of backlash and ire, from chemists on Twitter and other fora (#chemicalschangeus, #BigChem). Below, I've done some choice editing: to increase the alarmist hype, I've cut unnecessary interstitial words, focusing solely on inflammatory verbs and scary scientific terminology. Remember, this is only a 790-word column!)

"Chemicals Affect Us increasing alarm very common hormone-mimicking chemicals grotesque effects widely used herbicide female hormone feminizes male animals male frogs female organs male fish produce eggs contaminated chemicals male alligators tiny penises

growing evidence linking class chemicals problems humans breast cancer infertility low sperm counts genital deformities early menstruation diabetes and obesity congenital defect hypospadias misplacement urethra suspects endocrine disruptors wreak havoc endocrine system

Endocrine disruptors everywhere thermal receipts canned foods, cosmetics plastics food packaging Test blood urine human breast milk cord blood newborn babies

failure tackle Big Chem regulate endocrine disruptors
scolded Food Drug Administration failure ban bisphenol-A common endocrine disruptor
government vigilant threats grocery stores mountains Afghanistan
Researchers warn endocrine disruptors trigger hormonal changes DES synthetic estrogen cause vaginal cancer breast cancer decades later daughters now banned.
Scientists tiniest variations hormone levels influence fetal development female twin masculinized exposed hormones. Studies aggressive sensation-seeking eating disorders
worry endocrine disruptors hormones swamping fetuses analysis Endocrine Reviews
Fundamental changes chemical testing safety determination protect human health analysis declares chief environmental scientist toxicologist
nation’s safety system endocrine disruptors broken
endocrine disruptors data conclude chemicals not safe human populations developmental biologist
Worrying research long-term effects chemicals higher levels common endocrine disruptor, PFOA overweight PFOA unavoidable everything solutions.
Big Chem sensationalist science blocked strict regulation adopted tighter controls endocrine disruptors
Uncertainties scientists endocrine disruptors overwhelmingly protect families
microwave plastic pesticides refuse receipts"
*RECAP: That's 229 words there (29% of the article), including negatively-connoted words like "grotesque," "broken," and "aggressive," and even a bonus allusion to the U.S. military campaign in Afghanistan. Seven mentions of "chemical" (all negative), and a record 12 mentions of "disruptor."
And we wonder why there's so much extant public fear of chemicals?