Saturday, December 24, 2011

Christmas Break, Links, Survey

As we reach the end of Just Like Cooking "Year 1," I wanted to first and foremost thank everyone who dropped in to say hello. I hope you enjoyed it, maybe even learned something, and that my posts prompted some discussion among you and yours.

Brief Survey: What would you like to see as the Blog moves forward? More "everyday chemistry?" More reactions? More structures? More media diatribes? More "deep questions?" Or something I haven't mentioned? 

Please let me know in the comments...thanks!

In case you're up late during the holidays, and want something chemmy to sink your teeth into, here's some link love:

Synthesis of Halichondrin C (seriously, isn't Kishi like 125 years old? Still kickin' though!)
Scalable Enantioselective Total Synthesis of Taxanes (well, we're a few C-H oxidations away from curing cancer here, but it's a stab in an interesting direction)
Paul's "Chemmy" Nominations, 2011

Merry Christmas, Happy Hanukkah, and Happy Kwanzaa to all readers. Happy New Year, too!

Wednesday, December 21, 2011

Pharma Mascots - Cartoon Stand-Ins for Disease

Credit: Time Magazine

While glancing through some magazines yesterday, I came across a troubling ad for Abilify (aripiprazole). It’s not the drug that irks me, but rather the imagery - in the ad, depression takes the form of a sad, hovering blue bathrobe, stalking the nervous patient down the sidewalk.

I get it. Abilify helps a lot of people with severe depression feel normal enough to get outside and live. But the picture carries a menacing subtext: Without this med, depression will cover you and weigh you down, like a thick, fuzzy robe of gloom.

This is, of course, nothing new. Marketers make their livings playing on our subconscious reactions to colors, smells, and situations. But pharmaceutical marketing takes the message one step further. Many people recognize the signs and symptoms of disease: sore joints, skin discoloration, cough, fever, blurred vision. But do they know about the underlying condition, or anything about the drugs* used to treat it?

Well, cartoons to the rescue! Nowadays, each med gets its very own mascot, a stand-in for all the aches and pains brought on by the specific problem. For Uloric (febuxostat), a gout flare treatment, a man carries an Erlenmeyer flask full of green liquid meant to represent uric acid (which is actually a white solid). His obviously stunted gait and heaving effort evokes gout’s painful inflammation. Pristiq (desvenlafaxine), an antidepressant marketed by Wyeth before the Pfizer takeover, showed a sad, small wind-up doll, meant to show the effort needed to “get going” when depressed.

Lamisil (terbinafine) needed a mascot to represent a fairly common locker room ailment – foot fungus. The myco-avatar? Meet Digger, a small, spiky, yellow critter who represents discomfort and skin discoloration. His long claws are meant to simulate the scratching and burning brought on by infection.

Finally, Mucinex (guaifenisin) gives us Mr. Mucus, a hefty green glob used as a mucus analogy. He is, perhaps, the most over-the-top mascot, in that his only function seems to sit around as chronic congestion might.

Do these disease caricatures actually help someone, say, decide between two alternative treatments? Or appreciate the risks and side effects behind a certain treatment? Or are they just cute graphics to put on T-shirts and coffee mugs?

*In case you’re wondering, I didn’t forget: here’s the structure of the drugs

Update (12/24/11) - Added guaifenisin, generic name for Mucinex. The same generic drug is indeed found in several OTC medications.

Saturday, December 10, 2011

The Ad's the Thing - Science Draws 'Em In

Regular readers of Chemical & Engineering News might have noticed a rather rare, eye-catching advertisement in the October 17, 2011 issue. Takasago, a Japanese fine chemical supplier, took out two side-by-side full-page ads (p.40-41) to illustrate the catalytic ability of their new RUCY hydrogenation complexes. The layout suggests two pages of a scientific lab notebook, complete with hand-drawn structures, a font resembling personal handwriting, a table of reagents, even a digitized signature! (I hesitate to believe this is this scientist’s real signature; legal repercussions aside, many Japanese and Chinese scientists sign documents with a stylized kanji or ink stamp). 

A synthetic chemist captures the thrust of the ad immediately: high-turnover catalysts with high selectivity translate directly into time and material savings. But you don’t have to look far these days for “real-live” (staged) science at its best, selling everything from soaps to microprocessors.

Billy Mays: Oxidant Superstar
I’m reminded of the old dishwashing detergent standard, where a model with long rubber gloves dips a soiled plate into each of two basins, one containing the competitor’s soap, and one with New! and Improved! versions of the blue solution on the right. The grime falls reliably off the desired plate, but the scientific take-home message? Surfactants, formulation, perhaps even enzymatic degradation. It may be exaggerated to make a buck, but the pitch subtly makes you aware of the scientific development underlying the product. The same message pushes through with rust cleaners (solubility, transition metal ligation), or home fragrances (aroma chemistry, vapor pressure, sublimation). Billy Mays (RIP) and his OxiClean never made peroxide bleaching seem so efficient . . . or so sexy.

The real Ajay Bhatt....or Arthur Fonzarelli?
Source: The Oregonian
Don’t think that all these ads just shill for chemistry. Intel’s “Science Rock Star” campaign a few years back featured a strutting, smiling Ajay Bhatt (or his doppelganger), the co-developer of USB technology, proverbially fending off female fans and doting admirers while signing laptops and drinking from his Intel mug. Tongue-in-cheek, maybe, but this ad shines a light on the glaring contrast between the public worship of performers, and the relative ignorance of scientific figures. 

Update (12/24/11) - Added RUCY picture from C&EN

Tuesday, November 29, 2011

Quizás, Quizás, Quizás

Coming soon: More blogging.  Ciertamente.

(Although this is a lame excuse to buy time, try to think of it as my shameful placeholder until I can resume more science writing...just to tease, think startups, oxetanes, and science linkage)

((I'm also hard at work on more Haystack stuff...stay tuned!))

(((This parenthetical notation would drive a math major to Bedlam)))

Wednesday, November 2, 2011

Jobs I Could Do (And Those I Couldn't)

(An homage to Chemjobber)

I’ve spoken to lots of colleagues about the job market lately, and one of my favorite questions to ask them is always “Well, what would you do if you weren’t doing this?” Let me preface this discussion by saying that I love being a chemist; it’s the job for me. But, like everyone else, I have interests outside the lab: music, sports, food, and writing. Could one of these be my calling down the road somewhere?

As it happens, we’ve been in the midst of a move for some time now, and I’ve interacted with (too) many real estate agents. I walk away from most of these meet-‘n’-greets and fill-in-the-blank lease forms thinking “I could definitely do that job!”

Intense synthetic chemistry training draws on lots of skills: data mining, critical thinking, historical sense, motor memory, adaptation, public presentation, logistics, etc. Job promoters would call these transferable skills, and they open up a wide palette of career opportunities.  Below, I’ve run a thought experiment to see where I could contend, and where I might fall apart.

Could Do

Real Estate Agent – Really draws on the data mining and ability to forge contacts. Can you predict how a neighborhood will look in a few years? Memorize some tax and housing codes? Fill in lease and mortgage statements with names and dollar figures? Buy a GPS? You’re in!

But, how will they accept my tenure talk?
Struggling Musician – Some might say “Don’t you have to have talent and drive for this, and luck?” That sounds like an assistant professorship! You don’t make enough, you’re constantly self-promoting, and your most creative moments have to spill out in a 3-5 year period in your late 20s to early 30s (chemistry timeframe, people, I get that biologists are longer in the tooth).

Mel Brooks, he of Young Frankenstein and Spaceballs, once described his songwriting process for stage productions as humming into a tape recorder when the moment struck him, and having an amanuensis transcribe it into a song later (from It’s Good to Be the King: The Seriously Funny Life of Mel Brooks, by James Robert Parish). Food for thought.

Line Cook – Synthetic chemists ‘cook’ all day, and we use a much larger catalog of ingredients. Plus, I’ve read Kitchen Confidential, so I can answer Jimi’s question “Are You Experienced?”

Professional Gambler – Hey, it’s what you do with chemistry careers now anyway! (Bah-dump-CHING!)

Seriously, though, much of this involves critical thinking, learning about odds tables, house advantage, best times to play, and, if possible, how to beat the system. It also involves calculated risk, such as calling the bluff of that one-eyed, gruff man across the poker table from you.

Film Critic – OK, many readers have written a dissertation, right? How do you start? Read some literature, get a sense for where the field has been and where it’s going, learn central themes and players, then develop opinions about the work. Write.

"Boron? Yeah, like their whole show!"
"The movie's great: just change everything after the title!"
"Vitamin C? More like 'C you doing anything but this!"
Credit: Jim Henson Productions
Well, what do critics do? Watch a bunch of movies. Learn historical context and chart how actors and directors work together over time. Learn central themes. Develop opinions. Write. Dovetails nicely, wouldn’t you say?


Jobs that start with ‘Phys’ – Physician: what many scientists try first, perhaps due to parental input and a sense of social responsibility. For me, I couldn’t stomach the various fluids of every hue and smell that emanate from sick individuals. Trust me; I was an EMT once, long ago…

Physicist: Too much math. Anything that uses all the Greek letters, base e, imaginary numbers, and ever-stronger graphing calculators and computing clusters is where I get off the boat.

Phys-Ed Teacher: I was never a runner. To me, coordinating exercises for 20-30 young kids for an hour sounds like herding cats.

Let's see: loop[object bullet, n=0-25, IF fired(true), init stop(n)]
Credit: cinema sifter
Computer Programmer – Artists can “see” forms, shape, and color, like photographers can. Business types see emerging markets and opportunity, and musicians hear notes and rhythms where we cannot. I have personally tried (and failed) to be a programmer more than once, and I simply don’t think like they do. Iteration, nesting operations, classes, functions, describing how you want the program to function is, to me, “thinking about thinking.” Just not in my toolbox.  (On the other hand, check out these perks, courtesy of our bud CJ)

Readers, do you have any thoughts about your future career paths, and whether or not they include chemistry? I’d love to see some comments, or hoof it to Chemjobber and discuss there.

Sunday, October 23, 2011

The Chemistry Popularity Conundrum

Last week (October 16-22) was National Chemistry Week in the US. Did you celebrate? By all rights, it could have been the biggest one yet, since we’re deep into the tenth month of the International Year of Chemistry (#IYC2011). Did you see any news specials? Did Time or Newsweek run an exposé?

Probably not, but why not? When scientists cracked the human genetic code, front pages everywhere relayed the tense horse-race between Venter’s TIGR and Collins’s Human Genome Project. Whenever physicists flip the switch at the Large Hadron Collider, the public dreams of mini-black holes and cheating Einstein’s relativity. Chemistry, however, always seems to be the black sheep of the gang; DuPont’s slogan for nearly 50 years was “Better Things for Better Living . . .Through Chemistry,” until the final portion of the tagline was dropped in the mid-‘80s.
What creates the chemistry image problem? It’s true that many of the “pure chemistry” accomplishments of the last 30 years have gone largely unnoticed: ask someone at a local restaurant about triblock copolymers, organocatalysis, brevetoxin, or dye-sensitized solar cells. Applied chemistry fares a bit better, from polymers to paints, lasers to ligands, but the public still attributes many interface discoveries to other fields – drug chemistry gets lumped into “Health and Medicine,” or water-splitting tossed in with “New Energy.”
Don't let the test-tube on the front fool you.
The phenomenon even reaches general science books. On a whim, I opened up National Geographic’s The Science Book (bonus tagline – Everything You Need to Know about the World and How it Works) at a book store last week. A hefty volume, coming in at 432 pp., thus you might expect the “central science” to occupy at least 30% . . . right?
Wrong. Page count: biology, ecology, and sociology – 142 pages.  Physics, math, and ‘technology’ – 111 pages. Chemistry? 26 pages.
Does this all come down to poor public relations? Biology sells itself on some big questions: origin of life, evolution, ending disease, and genetic engineering. Physics moves out onto an even wider plane: does God exist?, fundamental particles, dark energy, string theory, and black holes. Ask most people about the word chemical, however, and their connotation is tangibly negative, associating the word with poisonous, pollution, ersatz stand-ins for “genuine” flavors or fragrances, artificial, corrosive, or toxic.
Prof. David MacMillan, Princeton
Not that none have addressed the issue – just recently, David MacMillan, editor of Chemical Science and accomplished organic chemist, called for increased outreach:    
‘One major thing chemists need to work on is their ability to promote their work to other scientists and the public. This is something we are really not good at in general and if we improved, it would really open doors for us and improve society’s perception of chemistry and its impact.'

ACS attempts much the same with their Chemistry Ambassadors program, and the Interactive Periodic Table of Videos surely adds some demonstration “Wow!” factor. But the days of science-themed programs (Mr. Wizard, NOVA, How it’s Made, even the tongue-in-cheek Look Around You) seem to have waned, and Mythbusters can’t save the whole genre single-handedly. Linus Pauling, Noam Chomsky, Carl Sagan, Stephen Hawking, Steven Pinker, E.O. Wilson, and Oliver Sacks have held down much of the science PR fort, but we still haven’t found the next great chemistry “populizer.” So, what are we to do?

Can these guys hold down the science program genre forever?
Well, I’m not the first to tackle this question. Luckily, many have gone before me: see Dr. Free Ride’s post on Scientopia (“navel-gazing” sounds so apropos) or the CHEMisperceptions Blog Roundtable from early 2011 hosted at ScienceGeist. Start there, and glance through the situations and stories these authors present. See where you stand.

And think. Just think.
Think about how you’ll answer the dreaded “So, what do you do?” question at the next holiday party. Think about a show you wish were on TV, DVD, or radio that covered breaking-edge reactions or materials, but isn’t. Think about how you might tell such a story. Think about what types of jobs you, as a chemist, might envision working in 10, 20 years . . . if they even exist right now! Think of the reactions, equations, elements, polymers, or drugs (heh) that really ‘get you up’ in the morning.
When you’ve thought awhile, narrow down your list to one or two things you truly enjoy. Write a short blog post or a newspaper article. Send an email. Take some pictures. Tell your kids. Teach a short course. Write a book. Produce a show. Anything you can do that creates new, high-quality content to help improve the stead of science in the world will do.
Idealistic?  Sure.   
Dreamy?  You got me.
. . . I’d like to think so.
(Note: You don’t have to start from nothing - there’s quite a few folks already working on the problem. For general chemistry blogs, start at CENtral Science. Work your way around to Chemistry Blog, Discover Magazine, SciAm Blogs, and Popular Science. Chemjobber, The Curious Wavefunction, and ChemBark help capture some of the current chemical zeitgeist, while Totally Synthetic and BRSM cover my favorite topic, chemical synthesis. For health and medicine, try In The Pipeline or The Medicine Show. Want books? Napoleon’s Buttons, The Poisoner’s Handbook, Mauve, and Uncle Tungsten are a few favorites. On a personal note, although he’s not formally a chemist, Surely You’re Joking, Mr. Feynman! and What Do You Care What Other People Think? helped me appreciate how one can use scientific curiosity to change the world.)

Wednesday, October 19, 2011

I'm Not Dead Yet

Good guess, but not where we're going...
Hello, readers . . .you may have noticed a lot of down time around here lately. Truth be told, we're planning a wee bit of "geographical displacement" brought on by "employment improvement" (Translation: a multi-state move is in the works).

More posts after the jump, I promise!

Friday, September 23, 2011

In Which You are What You Eat

I love food. Always have – both the process of making food (which may be why I’m a synthetic chemist) and the joy of consuming one’s labors (which lab work definitely doesn’t allow!). Recently, however, modern science blurs the line between the stomach and brain. “You are what you eat” no longer just refers to body weight or proper nutrient intake. We humans are superorganisms, meaning that our intestinal microbiology plays a huge role in our everyday lives. Turns out, where you were born, where you live, what you eat, and where you’ve travelled can all influence the metabolic phenotype (appearance) of the bacteria that inhabit your intestinal tract.
Hey baby, what's your gut microbiome?
Credit: Healthy Perceptions blog
Some microbiologists posit that humans can be grouped, not by race, creed, height, or sex, but by “gut profile.”  A recent multi-institution Nature paper, led by Bork and Ehrlich, disclosed three major enterotypes (gut profiles), based on DNA sequencing (of, well, poop) of 22 people from 4 different countries. The scientists try not to paint too broad a picture with this initial result, but note that gut bacteria influence key genes that regulate aging and body mass index, which may suggest microbial management of a wide variety of diseases.
Your gut bacteria also impact your emotions. WSJ’s Jonah Lehrer reports that yogurt – specifically the kind filled with “good” (probiotic) bacteria – can actually cause marked behavioral effects, at least in mice. Probiotic-fed mice showed fewer symptoms of stress and anxiety, even when placed in new situations. An ideal cure for modern social anxiety, right? Unfortunately, no: other scientists interviewed quickly point out neurological patients’ inability to feel fear or stress causes them to make even worse future decisions in similar situations, since they lack the negative feedback from the prior event.
Mmm, gene regulation!
Yogurt aside, your salad may also be helping to regulate your genes. Earlier this week, researchers in China disclosed new methods that can detect short strands of plant-derived RNA present in human bodily fluids. The researchers were especially surprised to find certain microRNAs actually inhibited the removal of LDL (low-density lipoprotein, the so-called “bad cholesterol”) from the bloodstream. Overall, the team found about 40 different microRNAs, from at least five different crops, and expects to find many more. Just more news to chew on, while you ruminate over your afternoon snack.

Saturday, September 17, 2011

Musings: Who are Chemists, Anyway?

When I’m performing a repetitive lab task (columns, iterative dilutions, etc.), my mind tends to drift. Yesterday, I began thinking about who I actually work with, where they come from, and why they’re in chemistry. Ever heard Jeff Foxworthy perform “You Might be a Redneck if…”? What if someone were to compile a similar list about synthetic chemists?
Thus, a few observations, from the subset of, say, 300 chemists I’ve worked with over the last ten years:
"It's OK, Dom, I'm leaving baseball for grad school"
Credit: AP
They tend to be older siblings: Perhaps there exists out there somewhere a biotech run entirely by younger sibs, but I haven’t found it yet! At my current job, all senior managers are the oldest siblings in their families, and I’m fairly certain most of the bench chemists have younger brothers and sisters. Maybe the old nature / nurture debate surfaces here, where parents encourage older children to pursue medical and scientific careers.
Folks come from all over: I hail from a town that the 2000 Census dubbed >95% Caucasian. Many of my friends went off to school, and then moved immediately back to town. After college, I moved 700 miles away, possibly to escape this exact fate! This "lifestyle inertia" has never occurred at any of the six labs I’ve worked in: the scientific population integrates well (math joke here?). My coworkers have hailed from all over the US, plus every continent except Greenland. It’s fun to watch Russian postdocs tell jokes to Indian coworkers, while French, Chinese, and Iranian labmates listen in and laugh.
Tech-savvy:  The first Blackberry I ever saw was wielded by a chemist. Ditto iPads, USB sticks, and noise-cancelling headphones. In grad school or college, you’ve probably used MacOS, UNIX / Linux, and most of the Microsoft Office suite, and you may have created .pdfs, manipulated graphics files, or solved crystal structures. It comes with the territory.

Merit badges = Future PhD?

Be Prepared? Four of my former coworkers were Eagle Scouts, and several more have EMT and First Responder training. Safety first.
Hobbies? Try second careers: Bench chemists live two lives: they’re passionate about their chemistry, but everyone has a hobby that they could fall back on (maybe a necessary practice in a bum economy). I’ve met semi-professional musicians, day traders, lay pastors, auto mechanics, authors, aerobics instructors, economists, coaches, show promoters, bodybuilders, shop owners, and even professional dancers.
World Travelers: Maybe this makes sense given their international background, but chemists travel all over. Many save up their whole vacation allotment for 2-3 years, and then go to China, France, Australia, or Argentina. Back when large chemical concerns had travel budgets (I know, a novel conceit), chemists could rely on at least one expedition per year, usually to attend a big conference in a far-flung locale.
Not Fashion Plates: You won’t see many chemists dressing like the men and women striding down docks in J.Crew, or taking nighttime strolls like they do in Ralph Lauren catalogs. Perhaps it’s thrift, or comfort, or maybe chemists just realize that their clothes have limited lifetimes in synthetic labs.
Office Pool?  Of course!  Chemists tend to jump at opportunities to participate in NCAA tourneys, fantasy football, or poker nights. Maybe it’s the competition? The odds? The logic? Who knows! I’ve worked in labs where two competing tournaments have been run simultaneously…and both found plenty of participants.
Wanna join our league?
One-Upsmanship: Many of the conversations I’ve had with older chemists invariably come down to competitions over how hard the job once was. Usually, they begin with “Oh yeah? Well, when I was your age, we had to recrystallize everything to purity, we didn’t have working fume hoods, and we actually used the (insert here name of old, dusty apparatus in the corner no one ever uses).” Maybe this speaks to how much synthetic chemists enjoy competition (see above).
War Stories and Battle Scars: No, I’m not talking about actual military service, although I’ve worked with a few chemists who have bravely fought alongside our troops. I refer to tales career chemists always tell at bars, stories where pump traps explode, flames shoot up from flasks, and injury was narrowly avoided. If you work in a synthetic lab long enough, you’ll have a few close calls, and you might even have something to show for it: a bald spot here, a burn there, even some stitches now and again.

Thursday, September 8, 2011

Come On, Allene! The Crabbé Reaction

Readers: This post was written in response to Rachel Pepling’s call for submissions to the IYC2011 Chemistry Carnival over at CENtral Science
Have you ever been in love?
Has a single, chance moment changed your outlook on life?
Did you ever have the burning desire to . . . add one little methylene group to the end of an alkyne?
I’m an organic chemist, and our emotions tend to track directly with the success of our bench work. In my third year of graduate school, I felt down in the dumps.  My methodology project had no traction; heck, I couldn’t even make the (relatively simple) allene substrates I needed in less than five steps! Such was life when, during my group meeting presentation, a voice chimed in from one of the postdocs sitting in the far corner of the room:
“I think there’s a reaction for this.  Haven’t you tried the Crabbé?”
(At first, I stared agog, since the name made it sound like he was ordering seafood in a fancy French restaurant, so I thought he was joking, but he wasn’t!)
Turned out, there was a “chemical shortcut” to do just what I needed: the Crabbé takes a terminal alkyne under Mannich-like conditions (di-isopropylamine, formaldehyde, dioxane) – with a dash of copper (I) bromide for good measure – and adds a methylene (=CH2) unit to form an allene (see scheme). Why make allenes, you ask?  The two alkenes in this three-carbon synthon are orthogonal (at a 90o angle), which twists their pi-electron clouds away from one another. Thus, each olefin can react independently in reactions like metal coordination or electrophile addition.
The reaction mechanism made me scratch my head for a while, just as it did Crabbé’s researchers working at U. Missouri in the early 1980s. These chemists propose that, after the initial Mannich adduct forms, a copper atom wiggles into coordination between the amine and the alkyne. When you crank up the heat, the amine kicks out a hydride (H-) from an isopropyl group, which then migrates to the copper. This copper hydride spins around, delivers its hydride payload to the alkyne, and kicks out an imine leaving group. 

Credit: Carl Sagan's Dance Party Blog

It’s a fairly chemoselective reaction, meaning you can use it late in the game in a synthesis (assuming your compound can survive heating in dioxane for a few hours with copper!). My favorite part? I enjoy watching the autumnal palette that evolves during the reaction, from birch-tree yellow to maple-leaf red. Different starting materials lend different shades. And, as most organic chemists will tell you, one-pot preps you can set up and forget about are the reactions we love.

Links and Such

A few recent internet chemistry items for your viewing enjoyment:

Paul is already hard at work predicting October's Nobel Prize in Chemistry.

Chemjobber waxes on vacation requirements (or not) in academic labs.

Hey look, nitrogen particles!  Wait, no, that's snow...
Over at Forbes, Matt has a profile of Peter Hirth, the man behind Sutent and Zelboraf.

Ivan Amato chats up horseradish and pain receptors in the Washington Post.

NPR's Morning Edition covered a recent Nature article, but what the heck is a "nitrogen particle"?

Saturday, August 27, 2011

Synthonix Rings Up an Advertising Coup

Gotta hand it to 'em: Synthonix sure can print a convincing ad!

One of these things is not like the others! Credit: Synthonix, Inc.
The Wake Forest, NC company has taken out a few full-page ads in C&EN: clean, simple black structures on white backgrounds, illustrating the wide variety of oxetane, azetidine, and spiro-heterocycles intended for stitching into med-chem lead molecules. But their latest ad, a portion of which is shown here, takes the cake.

As any Linnaean taxonomist can tell you (*Kings Play Chess On Fat Grey Stools, anyone?), classification runs deep in the scientific blood. When you consider the sheer number of organic molecules that can exist (10^60 potential molecules of 500 MW or less?!), please forgive the namers for getting a little punchy. Molecules garner nicknames based on their appearance (propellanes, cubanes), their smell (putrescine, cadaverine), or other chemists (bullvalene)!

The naming convention for small, 5-membered heterocycles proceeds thusly: start with Latin or English names of the heteroatom, and add "ole" to the end (rhymes with "pole" or "coal," not like Olé!).

Phosphorus? = phosphole. Sulfur? = thiazole. And arsenic...?

(I'll let you figure that one out)

 (*Kingdom, Phylum, Class, Order, Family, Genus, Species...Bio 101 FTW!)

Friday, August 26, 2011

Memes and Bandwagons

I'm interested in how internet memes get started; it's probably the same mob psychology that drives events like Black Friday or stock market bubbles. Either way, when I read Carmen Drahl's Haystack post with the handwritten chemical structures, followed by Chemjobber's homage, I felt the urgent need to actively participate in what is, undoubtedly, the next big thing on the internet: structure drawing!!!

Perhaps I should link this to a catchy jingle, or a flashing banner ad?
 So, there you go, now I'm part of the groundswell. Feel free to comment or critique, I'll even start you off: yes, I know my hydrogens look like "4's", and the persnickety demands of my postdoc advisor for exactness drove my desire to cap off those alkyl stereocenters with an actual group. 

'Til we all meet again on YouTube, 14,000,000 hits later...

Sunday, August 14, 2011

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!
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!

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.

Thursday, August 11, 2011

Interview: Prof. Eric Schelter, University of Pennsylvania

(A few weeks back, I posted about rare earth chemistry, and how insufficient domestic supply may hurt new-tech industries in the US.  Prof. Eric Schelter, a Professor of Inorganic and Materials Chemistry, graciously spoke with me about his research) 

SAO: How did you become interested in inorganic / organometallic chemistry, and rare earth / actinide chemistry specifically?

ES: I became interested in inorganic chemistry through interaction with my excellent undergrad mentor, Prof. Rudy Luck at Michigan Tech. Rudy set me up with a synthetic project on a dihydrogen complex of rhenium. This experience was quite formative as Rudy also got me interested in Texas A&M for grad school (he was a postdoc at TAMU). Also, the exposure to dihydrogen complexes introduced me to Los Alamos National Laboratory through the work of Greg Kubas.

In grad school at TAMU I did more synthesis and worked on electronic structure with Kim Dunbar. Working with Kim and her group was a great experience to learn X-ray crystallography, magnetism and electrochemistry. I had an interest in working with actinides so I pursued the LANL postdoc where I learned some uranium and thorium chemistry with Jackie Kiplinger and lanthanide chemistry with Kevin John. My interests in magnetism and f-block chemistry dovetailed nicely for starting my independent career in rare earths and energy science at Penn.

Prof. Eric Schelter (credit: UPenn)

SAO: We've read in National Geographic and Discover about rare earth usage in smartphones, hybrid cars, and military applications.  Can you give examples of other industries that rely heavily on these metals? 

ES: In general, rare earth magnetic materials are very important in many industries. Rare earth (RE) permanent magnets, primarily NdFeB, are used in the wind energy industry in large capacity turbine generators. The permanent magnets are also used in hard drives. Fluorescent lighting depends on phosphor materials that contain REs, especially europium and terbium. Neodymium is also used is lasers. Lanthanum and cerium are important catalysts in FCC [Fluid catalytic cracking] petroleum refining. Erbium is used in amplifiers for fiber optic communication. Yttrium is a critical component of high temperature superconducting materials. Gadolinium has an important use in medicine as a contrast agent in magnetic resonance imaging. This is by no means an exhaustive list.

SAO: Given the supply problem (the US currently does not produce enough rare earths for domestic industry), what is our long-term strategy to obtain more? Do we have a reserve, like the Strategic Petroleum Reserve, that we can operate from?  Or will new mining and separation techniques be the answer?

ES: There is currently no comprehensive long term strategy to address the US supply crisis and no strategic reserve of REs. A single supplier (Molycorp) of REs exists in the US, but rare earths are not rare - there are reserves of light and heavy rare earths in many places in the lower 48 [states] and in Alaska. There is a great opportunity here for scientists to help meet an important need by improving methods of obtaining pure RE materials.

SAO: How does your research address the rare earth supply problem?

ES: Much of the cost, time, and energy in obtaining rare earths is concentrated at the separations stage. We're working on new separations chemistry from several angles. In work sponsored by the DOE we're developing a new extractant strategy for use in liquid-liquid separations. We expect to contribute to a renewed domestic supply chain by targeting certain high value REs and improving the efficiency and reducing the environmental impact of their separations. We are also exploring fundamental redox chemistry of REs for application to separations.

SAO: Tell me something fun about yourself, your research, or your group.

ES: I am a complete /Lord of the Rings /enthusiast (freak) and am anxiously awaiting the film release of The Hobbit: An Unexpected Journey (SAO: Me too!)

Wow, much thanks to Prof. Eric Schelter for his preparation and willingness to be interviewed. Readers, if you (or someone you know) on the cutting-edge of chemistry would like to be interviewed, simply leave a comment here or contact me at

Update (8/11, 8:45AM): Carmen & CEN YouTube Channel recently covered Eric's chemistry