Category Archives: Molecule of the Week

Snow: the marvel of frozen water

Credit: Electron and Confocal Microscopy Laboratory, Agricultural Research Service, U. S. Department of Agriculture

From my unplowed street in New York City last week, two feet of beautiful fluffy white stuff morphed into frustration if you actually needed to leave the house. But secretly snow still reduces me to an 8-year-old child every time I see a few flakes. I grew up in Florida where I rarely saw a few pellets and never made a snowman or snowangels until sometime in college. Nor did I have to shovel  the disappointing aftermath, gray ice-slush hunks of industrialism on asphalt.

Snowflakes form six-sided moments of magic that come and then waft away, forcing us to slow down, whether we want to or not.

I’m not the only one who got swept away with the snow this week.

For the final truth about snowflakes is that they become more individual as they fall—that, buffeted by wind and time, they are translated, as if by magic, into ever more strange and complex patterns, until, at last, like us, they touch earth. Then, like us, they melt.

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MotW: Nobel Prizes all about the carbon

Carbon is the big star among the science Nobel Prizes this week. Sure, IVF is a big deal, too. But, today, I’m all about the element that ruled my life as an organic chemist. Carbon more than math is the universal common denominator of ‘O-chem. “As my undergraduate professor once quipped , “You just have to be able to count to four: four bonds to carbon.”

, from Wikimedia Commons”]But otherwise the two prizes aren’t all that similar. The physics prize for the discovery of graphene— sheets of carbon the thickness of a single atom– recognizes a discovery just a handful of years old. It’s superstrong, transparent, incredibly dense– fascinating properties that have scientists excited about what we might be able to do with it. But what has it done for the world lately? Not much, at least not yet. Some scientists think the award is premature.

The chemistry prize was awarded for classic organic synthesis: using palladium, a matchmaker metal with the remarkable ability to help chemists link together complicated patterns of carbon atoms. Although the enzymes between living cells are gifted at making these types of connections,  stringing carbon atoms together in precise ways  within a flask in a traditional chemistry lab is both art and science (and often an exercise in frustration).

But this is one elegant solution. The scientists discovered the reactions in the 1970s, but the chemistry that had come into its own by the time I started graduate school in the late 1990s.  As a result, my chemist mind thought, “oh, really, they haven’t awarded a Nobel for this yet?” But there’s no question that this science has touched people all over the world.  The pain reliever I took yesterday (Naproxen, the active compound in Aleve), cancer drugs, plastics,  compounds in TVs and other displays and flexible screens all result from chemists using these techniques on an industrial scale.

Naproxen structure via Wikimedia Commons
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Winter Olympics (Ice and Physics) Mania

American bobsledders in 2002 Olympics, Photo by Petty Officer 1st class Preston Keres, USN, American Forces Press Service News Articles

From a science perspective, the great frozen stuff is the unsung hero in all these sports. Its slick surface (and low friction) allow skates, skis, snowboards, sleds, and curling stones to slide smoothly, with a lot of help from some talented athletes, who have trained for years. Of course, it also creates all kinds of problems under suboptimal conditions: bad surfacing thwarted speed skaters yesterday. And warm weather made skiing a slushy mess.

I’ve also collected a few links related to Olympic science:

P.S. As I’m glued to my television and pondering ice and physics, I’m also thinking of the family of Nodar Kumaritashvili. A horrible crash and a tragic loss.

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Practical phase changes: more carbon dioxide

I get to talk about an interesting application of carbon dioxide today in my latest article for Scientific American: sterilizing transplanted tissues such as tendon and bone. Before I heard about this technology, I certainly wouldn’t have suspected that the ubiquitous gas that we exhale could become a super-scrubber with a little heat and a lot of pressure.

I’ve ended up playing with a lot of carbon dioxide over the years. Like most kids, I had ghoulish carbon dioxide bubbles from dry ice that fizzed my Halloween drinks. As a chemist, dry ice became almost too “normal.” As an undergrad, I made my own bricks of the stuff from a tank of compressed CO2, and in graduate school, I’d weigh it out by the tens, if not hundreds, of pounds. Mostly, I used it to cool things down.

But though it’s easy as a working organic chemist to think  it cliché, watching the supercritical fluid form and dissipate is amazing. That sense of wonder within a high pressure chamber– and the practical applications that come from it– keep me coming back to work everyday.

Speaking of clichés, this professor probably fits the stereotypical scientist image a little too well. But I love his giddy enthusiasm when he talks about how he uses the demonstration to see whether a prospective student might be a good fit for his research group.

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MotW: Happy T(ryptophan)-day!

Tryptophan, via Wikimedia Commons
tryptophan structure via Wikimedia Commons

Though the tryptophan rush from turkey is more hype than reality, Thanksgiving is the perfect time to put up the most structurally complex of the amino acids, tryptophan.

The body uses it to make serotonin, and biochemists use its absorbance of ultraviolet light to determine concentrations of proteins in their samples.

Today I’m thinking that it’s much more esthetically interesting than most of its amino-acid pals, at least the naturally-occurring ones.

Happy Thanksgiving!

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MotW: Acetaminophen (and House’s Vicodin habit)

Acetaminophen structure via Wikipedia (benjah-bmm27)
Acetaminophen structure via Wikipedia (benjah-bmm27)

More FDA warnings for cold sufferers– and really anyone who takes pain relievers– to keep in mind. Acetaminophen– the molecule at the left– is found in Tylenol and a whole host of other pain relievers, cold medicines and prescription drugs. At lower doses, it’s safe, but at higher doses can cause liver damage and even liver failure. The tricky thing? The molecule is included in so many different medications that it’s possible to take too much without realizing it. If you’re sick and have a headache, that Tylenol combined with acetaminophen in a cold remedy might have just tipped the dose over the recommended levels.

An FDA advisory committee issued the warnings, but  it will be interesting to see what the agency decides to do to help prevent further problems. It’s possible that some prescription painkillers such as Percocet and Vicodin, which mix acetaminophen with narcotics, might be taken off the market.

I must admit that the Vicodin tidbit led me to more frivolous thoughts about Gregory House, the fictional doctor from the TV series. Considering everything else that has managed to go wrong with him, I’m a little surprised that the  producers haven’t written liver failure into the plot line considering his Vicodin problem. Or did I miss it? Will the writers have to find a new painkiller addiction? Will he finally kick the habit?

So– I guess I’m wondering out loud– could the FDA wind up changing both our pharmacy shelves and the plot lines of TV? My brain is lurking somewhere in that nebulous space between pop culture and medicine today.

The practical stuff, news stories and FDA info:

The fun stuff: I couldn’t find a good video clip about House’s Vicodin habit, but this video/song montage was the next best thing. Enjoy!

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Molecule of the Week: Carbon dioxide (part 1 of many)

Carbon dioxide (via Wikipedia by JacekFH) carbon atom in the middle flanked by two oxygen atoms
Carbon dioxide (via Wikipedia by JacekFH) carbon atom in the middle flanked by two oxygen atoms

This small molecule is too big for a single post, so I’ll probably revisit it at different points in this blog. It’s the most oxidized form of carbon, often thought of as waste product: both of fossil fuel burning and of the energy reactions that fuel life. But it’s also an essential component of photosynthesis to generate food and natural fuel sources.

But today I’m thinking about one of the many environmental impacts of rising atmospheric levels of carbon dioxide: the acidification of the oceans.

Changing the acidity of the oceans alters a delicate balance. Science suggests that this growing acidity may be dissolving carbonate in corals and releasing metal ions that would normally be wrapped up in carbonate minerals. (See this article in Chemical & Engineering News about the disrupted chemical balance).

The ocean has always been a giant sink for carbon dioxide, water absorbs it forming carbonic acid. Cooler water absorbs more carbon dioxide, but higher concentrations in the atmosphere are the primary force in pushing more of the gas to dissolve into the water, turning the ocean more seltzer-like (in terms of pH, not fizz).

coral reef in Red Sea, copyright iStockphoto/wierdeau
coral reef in Red Sea, copyright iStockphoto/wierdeau

The effects, however, are not always what one might expect. In looking at fish earbones, called otoliths, researchers reported in Science that higher carbon dioxide levels actually made these structures larger rather than smaller. (Cornelia Dean of the New York Times wrote about it on Andy Revkin’s Dot Earth blog).

Otoliths are the tree rings of fish life-cycles. What does this mean for the fish? Not necessarily good– changes in ear bones could mangle their navigations skills.

Of course all of this science sits around the edge of the passage of the American Clean Energy and Security Act (ACES) by the House of Representatives this week. There will be plenty of opportunities to talk more about carbon dioxide. . . . stay tuned.

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Molecule of the Week: Zinc gluconate

The Molecule of the Week is the active ingredient in Zicam, the nasal gel cold remedy that the FDA warned consumers to stop using this week. What’s the problem? Some users have reported losing their sense of smell after using the gel. On Tuesday, the FDA stepped in and issued a warning letter to Matrixx Initiatives about Zicam:

According to the labeling accompanying the Zicam Cold Remedy intranasal products, each of these products “reduces” the “duration of the common cold” and the “severity of cold symptoms,” including specifically “sore throat • stuffy nose •sneezing • coughing • congestion.” These claims make these products drugs, as defined by section 201(g)(1) of the Federal Food, Drug, and Cosmetic Act (the Act), 21 U.S.C. § 321(g)(1), because they are intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease or to affect the structure or function of the body of man or other animals.

The FDA has urged consumers to stop using zinc gluconate products that involve application inside the nose. Zinc lozenges are not part of the warning. It’s a healthy reminder: just because a remedy is “homeopathic” doesn’t mean that it’s also safe. Chemical activity comes with the molecule itself– it doesn’t matter whether it was made by a living organism or synthesized in a lab.

Zinc gluconate structure from Wikimedia Commons
Zinc gluconate structure from Wikimedia Commons

The molecule itself is interesting– like two sugar-like wings around a central zinc ion. The gluconate “wings” are oxidized forms of the sugar glucose, in case that name looked familiar. Zinc ions bind to electron-rich atoms (like those oxygens) on many types of biological molecules.

I’ll be interested in the follow-up investigation into Zicam and further scientific evidence. I’m not willing to put my sense of smell on the line until researchers know more.

Reuters Health: US tells Zicam maker to stop selling some products

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Molecule of the Week: Hydrogen

Though hydrogen is the smallest atom and is perched at the top left of the periodic table, hydrogen in nature exists as two atoms hooked together.

Hydrogen hit the news this weekend as a leak led NASA to scrub the Space Shuttle Endeavor launch:

Hydrogen is as clean as chemical fuels get: burning it produces water, a useful waste product. But just like a possible leak of other fuels including gasoline, hydrogen is a potential safety concern.

Hydrogen and helium (its sister element on the right side of the periodic table) form the basis of new stars. These chemicals rotate and condense, ultimately integrating their nuclei to form larger elements through nuclear fusion and releasing energy.

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