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My Favorite Reaction’s Not A Reaction

As 7-Up was once called the “Un-Cola,” I am going to call my favorite reaction for CENtral Science’s Chemistry Blog Carnival the “Un-reaction.” When I was a graduate student and then postdoc, I wasn’t a synthesizer of things—I was a studier of molecular interactions: drugs sticking to DNA, proteins sticking to surfaces, lipids assembling into cell membrane mimics.

Behold, the power of the HeNe. Credit: Flickr user fcomartinezc


Some in the field might think this makes me an “un-chemist,” but I was indeed trained as a legitimate one. I was a physical chemist, which means that I still have books on my shelf with fun titles such as “Introduction to Electrodynamics,” “Symmetry and Spectroscopy,” and “Lasers in Chemistry.”

It also means that I spent a lot of time in the dark and used physics-based tools in my work. Lasers, for instance. Spectroscopists in particular couldn’t survive without ‘em. My favorite laser would have to be the “HeNe” (pronounced hee-nee).

That’s “helium neon” to all you synthesizers of compounds out there. In the lab, HeNe lasers are indispensible for their ability to help spectroscopists align optical tables. For instance, when you’re working with a high-repetition Nd:YAG laser, which puts out not-visible-to-the-naked-eye near-infrared light that can burn things (hair, especially, if you don’t tie it up in a ponytail while leaning over the optics), you want a visible, non-dangerous stand-in to put all the mirrors and lenses you’re using in place. Only then can you safely send the high-powered beam bouncing along down the optical pathway toward your sample.

HeNe lasers are great stand-ins. And they work by electronic excitation and collisional energy transfer. That might not be a reaction in the purest sense of making and breaking bonds, but you’ll have to forgive this un-chemist for bending the rules of the Carnival a little bit.

HeNe laser diagram. Credit: Wikipedia/Creative Commons

The first HeNe ever constructed was also the first available commercially—in 1962. It was then, and is still, composed of a small glass tube filled with, you guessed it, helium and neon atoms. An electrical discharge excites the electrons of the low-pressure helium atoms, which then collide with the neon atoms and their electrons, passing along the “excitement.” This energy transfer is possible because helium’s excited state is close in energy to neon’s.

Excited-state neon atoms accumulate, creating what’s called a population inversion, and eventually, with nowhere left to go but down, they emit light and drop to an intermediate energy level before bumping up against the tube walls, releasing further energy in collision and reaching ground state.

The burst of light the neon atoms emit is a red shade—632.8 nm—based on the difference in energy levels of their excited and intermediate states. Other weak energy transitions that cause lasing are possible—one of them makes green light at 543.5 nm—but red is dominant.

Aside from being great alignment tools, HeNe lasers’ claim to fame is that they were the original laser pointers before being replaced with diode-based varieties. But they’re still used to pop balloons in children’s science demonstrations and in Ig Nobel Prize promos. And they’ve also been known to scan a bar-code in a supermarket or two and make music by reading CDs in optical players.

The Ozone Zone

I chose my favorite chemical reaction based purely on aesthetics. Ozonolysis, wherein ozone—that tricky triumvirate of oxygen atoms—slashes its way through double bonds to make aldehydes, ketones, and carboxylic acids. Most synthetic organic chemists make things, but ozonolysis has a certain destructive appeal. Plus, there’s the pretty blue color that the solution takes on when the alkene is consumed, a sight not common to the largely colorless reactions of organic chemistry.

My graduate work involved making analogs of Vitamin D to fight, among other things, cancer. We started the synthesis of our analogs by taking commercially available Vitamin D2, and using ozonolysis to break it into its components like so:

I was after the molecule’s fused ring system. I’ll never forget when the senior graduate student teaching me how to use the ozonolysis setup placed a latex glove in front of the O3 stream to show me the potential hazards of not paying attention to her instructions. The air stream ripped the glove to shreds in a matter of moments.

The reaction also features a nifty mechanism bound to show up on O-Chem exams:

There’s the 1,3-dipolar cycloaddition (love to draw those leaping arrows), which leads to molozonide. Wikipedia shows this intermediate breaking into a carbonyl and a carbonyl oxide, which then undergo another 1,3-dipolar cycloaddition to produce a trioxolane (Or is it an ozonide? Nomenclature was never my strong suit). I, however, prefer the drawing that appeared in my O-Chem text (Morrison & Boyd), where an oxygen atom appears to shimmy its way through the C-C bond:


As an aside, you should know that “What’s your favorite chemical reaction?” is not a great conversation starter. I tried it last weekend with my husband and was met with ridicule.

Chemistry Cartoons For IYC 2011

For a little Friday afternoon fun, I thought I’d share some chemistry cartoons that came across the Newscripts desk recently as part of an International Year of Chemistry competition. Sponsored by the Physical & Biophysical Chemistry Division of the International Union of Pure & Applied Chemistry (IUPAC), the contest asked participants to submit

Merit prize winner "Degenerate Orbitals" by Bruno Demoro. Credit: Courtesy of IUPAC

cartoons illustrating a chemical principle “that would be clear and accessible to the general public.” The international panel of judges accepted entries from Jan. 1 to May 31 and awarded prizes during the 43rd IUPAC Congress in Puerto Rico in early August.

Even though my personal favorite (shown above to the right) among the six winners didn’t take home the grand prize, it did win a merit award for Bruno Demoro, a graduate student at Uruguay’s University of the Republic. As a physical chemist, I enjoyed the humor, although I suppose the general public might not get the reference to “degenerate” orbitals. Just us geeks here in the Newscripts gang.

Grand prize winner "Chemical Attraction" by Jessica Hough. Credit: Courtesy of IUPAC

Five students received merit awards of $100 for their entries, and one lucky winner—high schooler Jessica Hough of Valley Central High, in Montgomery, N.Y., took home $1,000 for her illustration entitled “Chemical Attraction.”

On the basis of the success of the contest, IUPAC’s Physical & Biophysical Chemistry Division says it plans to run an annual student chemistry cartoon competition. So check in with the organization early next year for details.

What’s In A Name? For Chemists, Their Field’s Soul

This post was originally published at Scientific American’s Guest Blog. Don’t forget to check out all the contributions to the Scientific American Blog Network’s Chemistry Day!

By 1992, the Soviet Union was formally dissolved, and the entire world’s political, economic, and military alliances were in the throes of transformation. But you could forgive officials at the International Union of Pure and Applied Chemistry (IUPAC) if they didn’t notice much of a difference.

At the time, they were still embroiled in a very Cold War-era standoff. At issue was one of the biggest prizes in the field of chemistry– naming rights for new elements in the periodic table. In the 1960s, American and Russian laboratories both laid claim to the discoveries of elements 104 and 105. And IUPAC had to play the role of arbiter. It took until 1997 to sort out the squabble, and along the way, several other new elements got dragged into the controversy, which some nuclear chemists dubbed the Transfermium Wars.

In the end, the Americans got their way on element 104, which was officially named Rutherfordium, in honor of British chemist and physicist Ernest Rutherford. Element 105, Dubnium, is named for the Russian town of Dubna. Belying the decades-long conflict, IUPAC explained its decision in rather understated terms:

Continue reading →

CENtral Science Represents at Scientific American Blogs’ Chemistry Day

Devoted CENtral Science followers may recall two posts about a big development in the blogosphere that went up at Terra Sigillata last month. There, my esteemed blog colleague David Kroll played host to a vibrant discussion about the shiny new Scientific American blog network– of course congratulating the massive effort on the part of Chief Editor and Community Manager Bora Zivkovic and many others that led to its creation, but also noting the paucity of chemistry blogs on the high-profile new network. The discussion spilled over into other prominent blogs, including those of American University chemist Matt Hartings and San Jose State U. professor of philosophy (and physical chemist by training) Janet Stemwedel. Well, SciAm’s blogerati were clearly listening. Today, in honor of the International Year of Chemistry and the IUPAC World Chemistry Congress in Puerto Rico, it’s all chemistry all day today at the Scientific American blog network.

What exactly does that mean? A smorgasbord of chemistry blog posts, both from regular SciAm contributors and guest bloggers. There’s even a Twitter hashtag, #SciAmChem. Bora has put together the master list of posts. I’m a bit biased, but I’d like to highlight two of them:

From CENtral’s own David Kroll: Drugs From The Crucible of Nature

Bora was even nice enough to extend me an invitation to guest blog with this illustrious group. It’s an honor to blog about one of my favorite topics, named reactions, for Scientific American.
From C&EN’s own Carmen Drahl: What’s In A Name? For Chemists, Their Field’s Soul

Of course, scores of other great posts are on the list, including writing from Hartings, Stemwedel, Ashutosh of Curious Wavefunction, Deborah Blum of Speakeasy Science, Antony Williams of ChemSpider/ChemConnector and SciAm blogger Michelle Clement, who works for the American Chemical Society.

It’s been a great day for chemistry blogging. But C&EN Assistant Managing Editor Amanda Yarnell put it best this morning on Twitter:

amandayarnell: Grt posts on @sciamblogs today by @discodermolide @sciencegeist @chemconnector & more. Here’s to hoping there’s not just 1 day of #sciamchem

Alan Alda Takes On Marie Curie

Alan Alda/Credit: alanalda.com

Marie Curie/Credit: nobelprize.org

Alan Alda, the actor and author, has added another credential to his CV: science playwright. Tonight his first play, “Radiance: The Passion of Marie Curie,” is being read as part of the opening night festivities of the World Science Festival at Alice Tully Hall in New York City. The play focuses on the eight years of Curie’s life between winning her Nobel Prize in Physics in 1903 and her Nobel Prize in Chemistry in 1911. Actors Maggie Gyllenhaal, Liev Schreiber, David Morse, Bill Camp, Allison Janney, and Mireille Enos are among those lending their talents to this evening’s reading.

“I’ve worked hard to make the science in Radiance as accurate as possible, and I’m always grateful when a scientist can help me make it even clearer,” says Alda in a Q&A over at DOE’s Energy Blog. “But I try not to have a single line of science (or anything else) in the play that isn’t dramatic, moving the story forward by having a character actively trying to achieve his or her objective.”

If any Newscripts readers are planning to check out tonight’s event, we’d love to hear what you think. The tickets, which start at $250, were out of the Newscripts gang’s budget.

Merkel Launches IYC In Berlin

Merkel at opening ceremony. Credit: Sarah Everts/C&EN

Obama, Sarkozy and Cameron skipped the opening ceremonies for the International Year of Chemistry in Philly, Paris and London, but props go to Germany’s head of state, Angela Merkel–formerly a theoretical physicist/chemist herself–for showing up at the IYC shindig here in Berlin today.

She said some things we’ve heard before, such as how chemists could help solve energy problems (with, say, nanotechnology) and how they already had (by developing energy efficient materials for improved housing insulation, for example). She also talked about Marie Curie as a role model, the promise of young scientists and the irony of the public’s not entirely positive perception of chemicals given that we’re all composed of them.

Merkel hands out awards. Credit: Sarah Everts/C&EN

But instead of rushing in and out, Merkel stayed around long enough to award three teams of very cute elementary students awards for a competition called Formula One. Effectively, the teams had to build a chemical battery and then race a home-made car for 20 meters. And again, instead of shaking everybody’s hand and moving along, she grabbed the moderator’s mic and started interviewing the kids about their projects. Pretty classy.

Organizers chose the lovely Radialsystem as their IYC launching site. The red-brick water pumping station nestles the Spree River right at the border of the former East and West Berlin. It was renovated in 2006 into a space for the arts and renamed Radialsystem. There’s lots of dance and theater to be seen here, but the last time I stopped by was to listen to some guy’s brain (alpha) waves as he sat on stage with headphones, himself listening to a sequence of conversations which ranged from boring bureaucratic negotiations to presumably more interesting bedroom dialogues. This is also where Merkel spoke at the 2009 Falling Walls conference, on the 20th anniversary of the fall of the Berlin Wall, where scientists gathered to discuss the ”walls” that needed to fall in science to improve the world. Continue reading →

Celebrating Chemistry in the Year of the Rabbit

Happy Chinese New Year! Or Gong Xi Fa Chai (if, like me, you speak Mandarin), or Gong Hey Fat Choy (if you speak Cantonese).

Credit: Shutterstock

People who are born in the Year of the Rabbit are said to be mild and generous, gracious and dignified. They are noted for their compassion and strong sense of sympathy. They are also alert and persevering, making for good work and life companions.

According to the Chinese zodiac, the Year of the Rabbit arrives every 12 years: 1831, 1843, 1855, 1867, 1879, 1891, 1903, 1915, 1927, 1939, 1951, 1963, 1975, 1987, 199, and, of course, 2011.

Chemistry Nobel Laureates who were born in the Year of the Rabbit include:

Ada E. Yonath (b. 1939)
Yonath shared the 2009 Chemistry Nobel with Venkatraman Ramakrishnan and Thomas A. Steitz for their studies of the structure and function of the ribosome.

Alan G. MacDiarmid (1927–2007)
MacDiarmid shared the 2000 prize with Alan Heeger for their discovery and development of conductive polymers.

Sir Harold W. Kroto (b. 1939)
Kroto shared the 1996 prize with Robert F. Curl Jr. and Richard E. Smalley for their discovery of fullerenes. Continue reading →

Cocktails, Dinner, and Chemistry

Posted on behalf of senior correspondent Marc Reisch.

Leading in to the U.S. kickoff of the International Year of Chemistry last night, about 175 chemical industry movers and shakers gathered at the Philadelphia headquarters of the Chemical Heritage Foundation (CHF). At his remarks just before dinner, Dow Chemical CEO Andrew Liveris got it right when he noted that lauding the benefits of chemistry to an audience including leaders in science and industry was like preaching to the converted.

And what an audience it was. Among the industry leaders present were Pierre Brondeau, CEO of FMC, Stephanie Burns, chairman of Dow Corning, and Craig Rogerson, chairman of Chemtura. Others at the dinner to welcome in the year of chemistry included Cal Dooley, president of the American Chemistry Council, and Nancy Jackson, president of ACS. Even the mayor of Philadelphia, Michael A. Nutter, made an appearance and professed his enthusiasm for chemistry, though he confessed that the effort to memorize the periodic table of elements in college pretty much ended his pre-med career path.

Earlier in the evening, guests were able to enjoy cocktails and meander about the spacious CHF building and its many science exhibits. They could also choose from among several lectures. One, by Washington Post columnist Jason Wilson, was a talk on the history of the once banned alcoholic beverage absinthe. Johns Hopkins University professor Lawrence Principe, discussed 16th and 17th century European books intended to make alchemy a respectable pursuit.

Continue reading →

International Year of Chemistry Opening Fiesta

After Thursday’s sequence of enthusiastic speeches that repeatedly declared that chemistry can solve all the worlds ailments (health, food security, energy etc), the second day of the opening ceremonies of the International Year of Chemistry at UNESCO headquarters in Paris got a bit more concrete on how this actually might happen, with talks from academics and industry leaders on how chemistry can improve nutrition, agriculture, medicine and materials for alternative energy.

But amidst the celebratory feeling in the main auditorium, a different kind of discussion happened at the press conference yesterday that is probably epitomized by reporter questions that went alot like: “So how do you address the criticism that this is all just a self-congratulatory jamboree for the chemical industry?” or “Exactly how is chemistry going to save the world?”  The answer IYC organizers gave was not precisely specific or clear, and it landed hard in the press room. I suspect this isn’t the last time similar questions will be voiced.

The IYC is an opportunity for chemists to celebrate their discipline, but it’s also clear that organizers also want to redeem the reputation of chemistry in the minds of a public that often sees the science as a source of pollution. IYC organizers said they want to remind the public that chemistry is the source of materials many people can’t live without—headache remedies and other drugs, toothpaste, iPhones or your favourite pair of sneakers.

To do so, there have been lots of launches in the past two days.  There was the video aimed to make 16-20 year-olds think chemistry is sexy. Or the announcement of  the world’s first and largest concurrent measurement of pH and chemical content of local water supply by elementary and high school students from Buenos Aires to Bombay. NASA is here promoting it’s earth observatory images. And of course many people were enthused about January 18th’s “Women Sharing a Chemical Moment in Time” (cue Whitney Houston) where female chemists met at 8 am in time zones around the world.

So chemists, celebrate and be joyous. But judging from the questions posed by the only non-chemists here at the opening ceremonies—the media—it might behoove you to be prepared to get specific about how chemistry benefits humanity if you want the excitement to spread outside the chemistry community. And don’t forget to temper those festive chemical soliloquies with some of the risks of molecular science, at the same time as you celebrate many of the benefits.