Author Archive
What is that thing? The new GHS symbol for carcinogens
by Chemjobber on Apr 07 2012 (9298 Views)
The Globally Harmonized System of Classification and Labeling of Chemicals (GHS) is the new international standard for shipping and labeling chemicals so that their hazards are communicated in a logical fashion. Since we're now in a globalized commerce system, where (for example) Aldrich sells chemicals all over the world , GHS creates a single standard for how different hazards (physical, health, environmental) will be communicated to shippers and receivers.
So if you look at the new symbols, they're all pretty boring. I feel like the skull on the "toxic" label is just a little bit different and the dead fish for the "environmental hazard" is a little graphic, but gets the point across well.
But here's my question -- what's this label on the right supposed to communicate? Any guesses?
That is the new GHS symbol for carcinogenicity. While I understand that you can't write "HEY, DUMMY! THIS WILL GIVE YOU CANCER" in fifteen different languages, I feel that this thing that looks like the T-1000 after being hit with a shotgun will just lead to confusion in all parts of the world.
I shouldn't criticize and not offer a better solution, but I'm not positive that there is one. It's such a difficult concept to attempt to communicate. The broken double helix motif of the cancer hazard sign is aesthetically pleasing and logical, but it requires an understanding of basic molecular biology that Starman this symbol doesn't require.
Is earwax an organocatalyst?
by Chemjobber on Jun 05 2011 (8567 Views)The June 6th edition of Chemical and Engineering News has a funny little item in the Newscripts section (written this week by Steve Ritter) on a gentleman who believes his earwax could be a reagent:
Dylan's earwax TLC
Later on, as a zoology undergraduate student at the University of Wisconsin, Madison, [Charles V.] Johnson took a daring chance in a chemistry lab: He substituted earwax applied to a boiling chip for a palladium catalyst in an organic synthesis experiment. It worked well to make all-trans-stilbene, although his professor didn’t seem impressed.
That’s the thing that has bothered me most,” Johnson says. “My instructors didn’t think there was anything to it.”
After graduating, Johnson worked as a chemical technician at Sigma-Aldrich; he is now retired. He has toyed with a few other attempts to use earwax as a catalyst over the years.
For example, Johnson was at his dentist’s office last year and was inspired to try an experiment making a filling. He took methacrylate-based material commonly used in dentistry, added a touch of earwax, and it seemed to work well to polymerize the methacrylate. “It hardened right up,” he says.
Johnson has contemplated what the active catalyst might be in earwax, but he hasn’t been able to do an analysis to find out. Most likely it’s a protein or amino acid, he believes, or possibly a lipid. Organocatalysts typically are biomolecules such as the amino acid proline or a synthetic catalyst such as an imidazolidinone.
I suppose that I should note that I find Mr. Johnson's theory very odd and I'd like to see more data. Wikipedia indicates that keratin is indeed one of the constituents of earwax, so it is plausible that the keratin (or one of its constituent amino acids) is responsible for the putative catalytic activity.
All of this allows me to recall the work of Dylan Stiles and his sadly defunct blog "Tenderbutton." His classic (and celebrated) TLC of his earwax was one of the initial triumphs of the chemblogosphere. If one of the steroidal constituents of earwax turned out to be Mr. Johnson's catalyst, I foresee an excellent collaboration between Johnson and Stiles that could possibly lead to the world's first earwax-based oxidative industrial process.
Ice is not just ice
by Chemjobber on Feb 13 2011 (11120 Views)
Dozois' "ice rock" on the left, typical ice on the right (Photo credit: Katie Robbins, for The Atlantic)
Gourmet ice? Yeah, it's not really my thing either (I'm not much of a drinker, and when I do, it's mostly microbrew.) But I found the story of entrepreneur Michel Dozois on the The Atlantic's website to be pretty interesting and something that I find just tiny little bit terrifying as a chemist:
Although he was using recipes he'd made many times before, in this new setting, suddenly none were quite right. "My cocktails sucked. I'm pissed," he recalls. "The ingredients were almost the same. The recipes, I know, I had them. They were great. That's the moment where you're like dude, what am I doing wrong? And you're flipping out."
It wasn't until he took a sip from one of the rejected cocktail glasses, by then just a pool of melted ice, that he realized the source of the foul taste. "l looked down at that and I realized, it's f--king sh--ty ice. That's what that is. The ice is f--king up all of my cocktails. Every one of them."
Now there's something I haven't been thinking about as a chemist, which is the contents of the ice that I'm throwing into reactions for cooling, dilution or precipitation. Dozois has begun selling gourmet ice to high-end bars in L.A. with different shapes. Some of Dozois' ice (like the pictured "ice rock" above, left) allows for cooler drinks without as much dilution. His preparation is quite involved:
Dozois says the key lies in three principles—filtration, aging, and shape. The water is filtered twice, using reverse osmosis, through which he says the company loses about eight ounces of water for every one ounce preserved. Once purified, the water is then frozen, where it is aged for at least 48 hours, increasing its density and making it colder and stronger. Though other ice connoisseurs don't age their frozen cubes, Dozois considers this step so integral to his product that he took the name Névé, the word for compacted snow that ultimately becomes glacial ice.
The ice is then cut into one of four different products. "Every cocktail calls for different dilution, different ice, different needs," Dozois explains. In addition to the Old Fashioned cubes, Névé also makes sells a longer, narrower Tom Collins cube made for high ball glasses, and a sexy orb-shaped version, modeled after Japanese ice spheres. Of all the products, Dozois has a special fondness for the "shaking ice," a small cornerless cube, which because of ageing and its unique design can withstand a vigorous joggle in a cocktail shaker without breaking.
While this doesn't deal with reaction chemistry directly, I am reminded of the different uses of ice for precipitating compounds from solution. Certainly, you wouldn't want one big block of ice (less surface area); you'd probably want a smaller, more pellet-like ice for the best precipitating results (and possibly, the best cooling of reactions.) Interesting how the same principles guide mixologists and chemists to different choices.
Pipettes and bulbs: always surprises for the experimentalist
by Chemjobber on Jan 28 2011 (12780 Views)
A pipette bulb is a good friend to a chemist; a 5-inch or a 9-inch glass pipette is only a good backscratcher without a 'rabbit rubber', as my undergraduate stockroom would label them. (Really, I'm not kidding.) There's always a couple in my lab coat pocket.
Anyhow, I've always insisted that there is no need to force the bulb onto the pipette; pinching the pipette bulb at the very edge of the collar and gently placing the pipette snugly into the collar is all you need. In the picture to the right, you'll see an example of that having been done to the left-hand pipette. I have also maintained that you'll get significantly less suction power if you insist (as many students do) on forcing the pipette into the pipette bulb.* The pipette on the right has close to 1 cm of its end rammed into the bulb.
Yet, I am chagrined to note that there is not a significant difference in the amount of KMnO4 solution drawn into the pipettes. How disappointing -- what will I find to disdain now?
A parting shot for a pet peeve: folks who roll the collar (if possible) down onto the pipette, as if, uh, um, er, uh, utilizing a prophylactic. That's really unnecessary. Just sayin'.
*Obviously, if you were to place the entire end of the pipette into the bulb, then you would not be able to force enough air out to generate a vacuum.
Separating the lanthanides: physical versus chemical methods?
by Chemjobber on Dec 11 2010 (13100 Views)
Photo credit: Reuters**
There has been much talk about rare earth metals recently. In short, the People's Republic of China has become the dominant source of rare earth* elements in the world; the PRC government has used that fact to their strategic advantage. I don't really wish to get into the political debate; suffice it to say that I think there's more smoke than fire here and that predictions of war are probably overblown.
There are quite a number of articles on the subject, but only one talked about the chemistry. I was struck by a quote in an article on ForeignPolicy.com by Tim Worstall, a trader in scandium and other rare earths (now there's a job I didn't know about):
Another possibility is that we find a new and different way to separate rare earths, as we find new and different sources for the ores. The main difficulty is that chemistry is all about the electrons in the outer ring around an atom, and the lanthanides all have the same number of electrons in that outer ring. Thus we can't use chemistry to separate them. It's very like the uranium business: Separating the stuff that explodes from the stuff that doesn't is the difficult and expensive part of building an atomic bomb precisely because we cannot use chemistry to do it -- we have to use physics.
It's quite apparent that Mr. Worstall is referring to the unusual electronic configuration of the lanthanides, where the 4f orbitals are 'hidden' behind the 4d and 5d orbitals. This electronic configuration is also responsible for the lanthanide contraction, in which the atomic radii of the lanthanides are smaller than predictable by periodic trends.
However, I'm not quite sure what Mr. Worstall means when he draws a distinction between chemical and physical separation of the elements. Both this article (from Oxford) and the Wikipedia article on the lanthanides suggest that countercurrent exchange methods are used on industrial scale; it appears that separation is performed by means of ionic radii and size. While this certainly doesn't rely on the reaction chemistry of the lanthanides (because it appears they all act similar), I have a difficult time calling these techniques physics-based.
Readers, can you shed any more light on the issue? Do you agree with Mr. Worstall's distinction between chemical and physical means of purifying elements?
*It should be noted that the rare earths are, as they say, neither rare or nor earths.
**Photo from this International Business Times article.
A guide for reporters on the 2010 Nobel Prize in Chemistry
by Chemjobber on Oct 06 2010 (24924 Views)(cross-posted with Chemjobber)
Somewhere in the good ol' US of A, USA (DON'T HAVE TO CREDIT CHEMJOBBER):
3 chemistry professors, Richard Heck (formerly of the University of Delaware), Ei-ichi Negishi (Japanese descent, of Purdue University) and Akira Suzuki (Japanese descent, of Hokkaido University) were awarded the 2010 Nobel Prize in Chemistry "for palladium-catalyzed cross couplings in organic synthesis" by the Royal Swedish Academy of Sciences. These are techniques for bonding (or connecting) smaller carbon-based molecules together to make larger carbon-based molecules.
Creating carbon-carbon bonds can be difficult and can sometimes involve using dangerous, impractical or environmentally unfriendly reaction chemistry; the techniques pioneered by Suzuki, Heck, and Negishi make these reactions simple enough for novice chemists to perform and practical enough that they can be run on multi-ton scale. Since their introduction in the late 1970's, palladium-catalyzed chemical reactions have touched every part of the field of chemistry, including life-saving drugs, plastics and organic LEDs. The modern pharmaceutical industry would not be able to produce many of their products without palladium-catalyzed reactions.
The prize has been long-awaited by many chemists. "It's about damn time", said Chemjobber, a very junior synthetic organic chemist. "I don't know what it took to get those Swedes to finally get their thumb out." It is believed that part of the reason is the rules of the Nobel Prize: there can be no more than 3 awardees at one time, and they all must be living. Many chemists contributed to the field of palladium-catalyzed reactions. Professors Sonogashira, Tsuji, and Kumada could have all been part of this award, and the chemistry Nobel committee is notoriously controversy-shy.
Professor Heck has retired and currently lives with his wife in the Philippines. Professor Negishi is still teaching and research at Purdue University in West Lafayette, Indiana. Professor Suzuki is still teaching and researching at Hokkaido University in Sapporo, Japan.
(CJ here: Man, this is harder than you would think.)
How many ways can you say something without plagiarizing?
by Chemjobber on Sep 17 2010 (27925 Views)In a recent post by Derek Lowe on a Chinese journal's finding that 31% of its submitted papers contained plagiarized material, an editor for a scientific journal noted in the comments that he randomly selected a Tetrahedron Letters paper from a developing country and Googled the first sentence. That sentence ("Multicomponent reactions (MCRs) are important for generating high levels of diversity...") shows up in very similar form in three different papers, all from institutions in Iran and China. In two of the papers, the second sentence of the paper is exactly the same, all 22 words.
Also, compare the two first sentences, the first by Shaterian et al.[1] and the second by Adib et al.[2] The highlighted words are the same.
"Multi-component reactions (MCRs) are important for the achievement of high levels of brevity and diversity. They allow more than two simple and flexible building blocks to be combined in practical, time-saving one-pot operations, giving rise to complex structures by simultaneous formation of two or more bonds, according to the domino principle."
"Multicomponent reactions (MCRs) are important for generating high levels of diversity, as they allow more than two building blocks to be combined in practical, time-saving one-pot operations, giving rise to complex structures by simultaneous formation of two or more bonds."
Nicolaou et al.[3]: "The azaspiracids are a group of notorious marine neurotoxins whose accumulation in mussels causes serious human poisoning known as azaspiracid poisoning syndrome (AZP) upon their consumption."Geisler, Nguyen and Forsyth[4]: "The azaspiracids are remarkable natural products that combine a unique, complex structure with an acute and perhaps chronic human health hazard."Evans et al.[5]: "(-)-Azaspiracid-1 is a structurally complex marine neurotoxin that is implicated in seafood poisoning."
Is this sort of cutting-and-pasting 'real' plagiarism? -- it's just the quotation of a particularly useful string of words, one might assert, not the stealing of ideas. I don't think this is a very good way of thinking about things, but I can't quite reason why. In addition, I doubt that any of the authors of the MCR papers were native speakers of English. Clearly, that plays some role in their choice to cut and paste; again, not an excuse, but another contributing factor. I'm trying to see if I can come up with extenuating circumstances, but I just can't.
My adviser in graduate school held out "the same five words in a row" as a general rule of thumb for how to spot and/or avoid plagiarism -- what about the same five ideas in a row? What do you think, reader? How do you avoid cutting and pasting? And what should we do (if we should) to stop this sort of thing? Do we need TurnYourJournalSubmissionIn.Com?
(Visible) scars of chemistry
by Chemjobber on Aug 01 2010 (49201 Views)
Mitch's post showing the video of "the mark of the chemist" reminds me of one of the most visible remembrances I have of graduate school: the scar on one of my middle fingers (see left.)
On a lovely Saturday in the lab (my music playing, no one else around), I dropped a Dewar flask from a shelf onto the lab bench. Along with the pop that announced its destruction, I saw that my finger was bleeding. My adviser brushed off my protestations that I was fine with "[CJ], you're bleeding all over the floor." He was right and off I went to the campus health center.
It's been at least 6 years since I've had the scar. It's healed, but left the interesting black mark that you see and a lump that I suspect may be embedded glass. But when I think about chemistry and potential dangers that I could face, all I have to do is look down at my hands.
UPDATE: The Curious Chemistry Grad Student shows off a couple nice burns.
Cargo cult science in the Gulf, news at 11
by Chemjobber on Jul 20 2010 (20509 Views)
Credit: WKRG/Mediaite
The Gulf oil tragedy has already shown the ignorance of some reporters about chemistry. However, a Mobile TV station and their chemist has taken it to new heights when they blamed the oil spill for (likely) bad glassware.
WKRG is a local TV news station in Mobile, Alabama; they sent intrepid reporter Jessica Taloney to collect samples of local beach water. (See video of story below.) They asked a local lab to analyze the samples for oil and grease; the lab owner and analytical chemist, Bob Naman, suggested that the level of oil and grease should be pretty close to 5 ppm.
Of course, all the samples showed the presence of oil and grease, with amounts up to 200 ppm. While these results are not particularly surprising, the result of one sample was not obtainable because the chemist claimed that the sample exploded during the extraction. Rather than blame the broken separatory funnel on a star crack or a lack of venting, the chemist said that "We think that it most likely happened due to the presence of methanol, or methane gas, or the presence of the dispersant Corexit."
No. This is just wrong. Having actually shaken separatory funnels full of mixtures of water and flammable solvents (including methanol!) on a daily or weekly basis for about 10 years now, I have yet to see any of them explode. Surfactants like Corexit are not known for being particularly explosive, especially at room temperature.
I think it is far more likely to be coincidental; in addition, wouldn't a true explosion have left much less of the funnel? Heaven help us. (When the reporter obtained another sample from the same area 4 days later, the oil and grease concentrations were at the 1 ppm level. Not explosive enough? (That's a joke, non-chemists.))
T
The most bracing (and sad) chemical sentence you will read today
by Chemjobber on Jun 28 2010 (14471 Views)“I will roar argon into chlorine, xenon into fluorine, all the noble gases into reactive ones... My lament will terrify even the stars.” - Jessica Stern, Denial: A Memoir of Terror
From Dwight Gardner's review in the New York Times. Dr. Stern is an expert on terrorism; she believes her interest in terror stems from a brutal and violent incident from her childhood.
Puzzling polymorphs
by Chemjobber on Jun 07 2010 (15895 Views)
Polymorphism is a common and sorta crazy issue in pharmaceutical process chemistry. Basically put, a drug molecule in the solid state can have multiple crystal forms. Different impurity profiles and different crystallization techniques (solvents, heating/cooling rates) can produce different polymorphs, which can have wildly different physical properties and bioavailabilities. A famous story of troublesome polymorphism is Abbott's ritonavir, where in the middle of manufacturing for sale (not during the R&D phase!), a new, much less soluble polymorph started showing up in batches. Moreover, once the new polymorph showed up, it was very difficult to generate the previous polymorph. Even crazier, a team of scientists went to another plant in Italy where the process was still working as desired, and soon after the team left, the new polymorph appeared. It took a crash program to understand which conditions were generating the new crystal form to get it under control.
A recent article by Pradash et al. in Organic Process Research and Development illustrates the problems of polymorphism similarly: once the authors determined that there was another crystal form ('Form A') than the original ('Form B'), they undertook a screening process (looking at varieties of solvent and crystallization techniques) to find other polymorphs. Interestingly, once they discovered a new polymorph ('Form C'), they found that it was impossible to generate Form B in their laboratories. They selected Form C for its physical properties and moved it into the pilot plant; lo, they then found Form D. This new crystal form began predominating and "those seeded crystallization processes that consistently produced Forms A and C started to produce predominately Form D in the laboratory." (Click on image to see pictures of the polymorphs and the structure itself.)
When I read these accounts, I am filled with admiration for pharmaceutical process chemists, the interesting science that they get to do and the vast reserves of patience and sangfroid they must have. Chemistry (and manufacturing chemistry, especially!) is based on reproducibility and consistency; when issues arise, I suspect that there is a great deal of checking and double-checking to make sure that "this is really happening to us." Also, I can't help but wonder if those process chemists, when these issues are discovered, wonder if the laws of the physical universe are being temporarily suspended and some Loki-like diety is having its way with them.
How's your laundry's chemical hygiene?
by Chemjobber on May 16 2010 (34048 Views)
Credit: University of Ottawa EH&S
A recent report from the President's Cancer Panel on the environmental causes of cancer* had a rather interesting recommendation relevant to chemists. As to what you could do to lower your risk and your family's, here's what it said (page 111):
"Family exposure to numerous occupational chemicals can be reduced by removing shoes before entering the home and washing work clothes separately from the other family laundry."
So what do you think of that? As chemists, we are presumably more exposed than the typical person, although I suspect that there are industrial workers (coal miners?) who are even more exposed than us.
I know that I have typically avoided bringing my shoes into the home (but, then again, I've always taken off my shoes before I enter my home). Recently, I have begun washing my work clothes separately from my family's. Due to my work circumstances, I'm guessing that I carry home more compound that the average chemist. Then again, it's the same washing machine. Short of running an ethanol rinse between washes (can you imagine the cost?), I don't know if there's a good answer for that one.
I'm terribly interested to know what other people's habits are about their clothing and chemical hygiene? Do you let your kids hug you when you walk in the door from work? Do you let your dog chew on your work shoes? Inquiring minds want to know...
*Folks (e.g. Derek Lowe) have been pretty critical of the report. I've noticed that it's pretty long on assertion myself. Nonetheless, it's an interesting topic.
Photo from the University of Ottawa's lab EH&S site.
