Chirality

another Nature article that needs mentioning: this time, Green Chemistry

2011-01-05T19:30:00.000-08:00

While you're reading from Nature, don't miss this well-written article about Green Chemistry.

drug design, drug abuse

2011-01-05T19:12:00.000-08:00

Nature is publicly sharing a column by medicinal chemist David Nichols this week: you can find it here.

It is a personal and sad commentary on how scientists involved in synthetic chemistry, who work to increase understanding of diseases and develop new drugs to treat or cure them, may inadvertently end up supporting the development of new street drugs.

pointing fingers

2010-12-21T21:49:00.000-08:00

KTVZ reports tonight that the water tested by EWG was from a private water company, Avion Water, rather than the City of Bend. You can read the news report here.

I commend the local reporters for doing a good job with a scientific topic, but I hope they find a source who is not invested in the outcome of the testing. Avion Water, the City, and the ACC aren't going to be able to persuade me of much, because each could be reasonably expected to want this little problem to just go away. It's possible the EWG has some other complicating interest, too, beyond public health.

It's not time to panic, but we need to attend to this. Preliminary experiments indicate we might have a problem. That's all EWG has shown us. There is a serious shortage of data and a compelling case for more testing, now.

Time to go back to the lab! Water from all over town should be collected and tested, using EWG's more sensitive testing method, so that we can have an informed discussion.

NIMBY!

2010-12-20T19:03:00.000-08:00

The community of Bend is pretty darned proud of our wonderful tap water. It really is amazing quality stuff, tasteless, odorless and about as wet as any water you could find anywhere. Even more remarkable, to someone who doesn't come from this part of the world, is that such wonderful stuff could come tapped into our homes with very little processing.

There has been some local chatter about potential upgrades to our current water system, especially the part of the supply that comes from the Bridge Creek drainage. That portion of our local water is surface water, which means that there is some potential for it to be contaminated from the surface. With some pressure mounting, it looks like that system is going to have to undergo some upgrades in the near future.

And then comes this news: the Environmental Working Group has tested water in 35 municipal supplies and has found chromium-6 in 31 of them, including in Bend (which tests at 0.78 ppb). What does this mean for us? It's too early to know, but it certainly is a call for more and better testing, and additional information for us locals about the sources and consequences of having it in our water at the current level.

The presence of chromium-6 from natural sources is a possibility, but I do find it a little concerning that this notice doesn't come with immediate access to the sort of maps of those deposits that we might want. I wonder if anyone tracks this sort of thing? It seems like it would be an easy thing to do, and that testing for natural contaminants of concern (like chromium, or arsenic, or fluoride in high concentrations) would be standard procedure when establishing new wells or other water supplies.

The statements from the ACC are also not very helpful, and also add to my discomfort with the lack of information flowing to us.

How do we compare to the other cities tested? The graph about halfway down the page (titled "Chromium-6 levels in 25 cities’ tap water exceed safe limit proposed by California officials*"), in the original report, is pretty striking, and disturbing.

SoCMA, ACC, and more....about the potential for a Green Chemistry standard

2010-11-29T20:55:00.000-08:00

Advancing Green Chemistry shares with us an article detailing the current discussion--or is it a squabble?-- about establishing a standard for Green Chemistry. There are a lot of very powerful people interested in the outcome of this discussion, it appears! Important people are listening and participating. But there also appears to be some potential for gridlock as these groups try to find a standard that is good for everyone.

A variety of stakeholders care about the outcome of this discussion. The public is of course one group that may benefit from a clear and rigorous standard. It would make it easier for us to make greener choices without having to draw on a great deal of technical expertise (which few of us have). On the other hand, industry is likely to strongly resist any standard which is going to give some products a competitive advantage over others. AGC discusses this problem at some length. But it's good reading.

One of the great strengths of the Green Chemistry community is its inclusiveness. It bring all kinds of perspectives to the table. When people with differing viewpoints find themselves working on a problem together, the opportunity to innovate for real change is more likely. But the solutions that these various groups can agree to are rare, and difficult to discover.

It's good and difficult work, and we'll hope that the outcome brings us a step forward.

Advancing Green Chemistry keeps a close eye on the chemical industry (ACC is an acronym we all ought to know), and provide frequent updates on issues interesting to the Green Chemistry community through their Facebook page and Twitter feed.

fourteen.4 grams

2010-11-26T16:30:00.000-08:00

Based on some serious Google research and with the help of my Introductory Chem class, I have determined that the 15.0 lb turkey cooked at my house yesterday contained a grand total of 14.4 grams of tryptophan.

While the debate continues on the streets and at the water cooler about the biological effects of consuming a hefty portion of roast bird, there are a lot of other good reasons to get a nap on Thanksgiving afternoon.

Turkey is not exceptionally high in tryptophan compared to some other fairly common foods, which leaves me wondering how the tryptophan story ever got off the ground in the first place.

Happy Thanksgiving weekend.

spinning vinyl

2010-11-18T19:29:00.000-08:00

My collection of vinyl records still sits in my living room under a coffee table, though I haven't played them in years. I have a turntable and a component system that is old enough to play them but it's just too much work, and a lot of the music I have is not interesting to me anymore.

I expect I would encounter some trouble if I tried to play them anyhow, since many of them were made when records were stamped on thin vinyl, which would warp over time if not occasionally rotated. Letting them sit on one side for years could have caused some major problems.

I spent a lot of time as an adolescent listening to records, so just talking about them gets me feeling a little nostalgic.

LP (long play) records like this are called vinyl because they are made from polyvinyl chloride. Vinyl chloride is CH2CHCl, an alkene with a chlorine attached to the sp2-hybridized carbon, aka the vinyl position. Addition reactions can be used to produce polymers which often end up bearing the names of their raw materials, or suggestions of what those raw materials are: polyvinyl chloride (PVC), polyethylene (HDPE and LDPE), and polystyrene (PS) are all made from alkenes, through addition reactions that cause them to polymerize.

Organic students may recognize, if they think of it, that after forming a carbocation in an addition reaction one could imagine another molecule of the original alkene behaving as a nucleophile...the double bond itself is rich in electron density. This is the underlying principle of the addition polymerization reactions that allow us to make all these different plastics.

Wikipedia has relatively informative articles on LP records, and on vinyl chloride. PVC is not very environmentally friendly if you consider the problems that come along with handling the vinyl chloride monomer which it is made of, though some have argued it is very environmentally friendly precisely because it lasts so long--and often is used in applications to replace wood, or other plastics with shorter lifespans.

A few years ago a great (but admittedly biased) documentary about PVC was put out by Bullfrog Films. You can watch the trailer here, and it's in our College Library. It's worth your time and presents the serious problems associated with PVC with great humor. And you know what's funny and ironic? The videocasette that the film is on is probably made of.....you guessed it: PVC.

To celebrate the release of the latest Harry Potter movie....

2010-11-17T20:15:00.000-08:00

....Daniel Radcliffe sings the periodic table song.

Here's the song sung by the author, Tom Lehrer. Frankly, he does it better. But he's not Daniel Radcliffe!

My favorite song about elements is a little newer....TMBG does the Elements

more cosmetic chemistry

2010-11-11T18:31:00.000-08:00

The masks they refer to deep within this article are surely not respirators....but I can imagine little cute filter masks. I'm presuming of course, but if that's what they're talking about they're not going to do a bit of good protecting people from volatile solvent vapors.

Can you imagine going into a nail salon where the employees are wearing respirators? Yeah. That would be bad for business. Yeah.

H2CO

2010-11-11T17:59:00.001-08:00

Here's a good one. I caught this story a few weeks ago, when it was still a pretty unformed thing, but it appears that the situation is heating up.

Ah, formaldehyde, you disgusting stuff.....

what's the value of a penny?

2010-11-08T20:00:00.000-08:00

Rare earth elements include Scandium, Yttrium, and the collection of elements with atomic numbers from 57-71: also known as the lanthanides. While their names are probably pretty unfamiliar to many--Prasiodymium, Promethium, Samarium, etc--their use has been increasing and their interesting magnetic and chemicals are increasingly exploited in high technology applications.

There has been some news recently about the global supply of these elements. While we have deposits of them in the U.S., recent supplies have been coming out of China. Until really recently, that is, since there have been issues with supply and allegations of price controlling.

Now the New York Times reports on another potential source of these elements. Manganese nodules on the surface of the ocean apparently contain not only valuable copper in significant amounts, but also rare earths. If the combined value of the materials in these rocks makes the economics work out, maybe people will start mining the sea floor for them.

Somewhere deep in the article the author mentions that the concentration of copper in the ore mined in the San Jose copper and gold mine in Chile (you know the one) is only half that of these nodules, which contain a paltry 1% copper.

That leaves me wondering why someone doesn't just collect all the pennies I have accumulated over the years and extract the copper from them. They're surely more than 1% Cu and it would be easy to get hold of them.

good news in the land of AIDS

2010-11-04T17:42:00.001-07:00

Well, it's not news that I'm getting older, but at least I am doing so at the same rate as everyone else. I remember the world when telephones had cords, reheating food meant putting it on the stove, and nobody knew of AIDS. Around 1986 I was working at the University of Iowa Hospitals when I encountered my first AIDS patient. I was doing phlebotomy. He was a haemophiliac. He had contracted the disease from injections of Factor VIII, used to control his disease.

We had to monitor his level of Factor VIII and it was a huge deal to go into his room and get the blood. Lots of precautions. He was a very sick man, and died within weeks. I learned right away how horrifying the disease was.

Years later things are much different for AIDS patients. We have retrovirals that make their lives much better, and their lifetimes much longer. But it is still an awful thing, and it is still great to hear about advancements in AIDS research.

NPR tells of just such a story, which references some work published in Science. Yay.

I think I want some tonka beans

2010-11-03T21:00:00.000-07:00

A great story about food, drugs, and chemistry is available online over at the Atlantic.

A quick look at the structures of coumarin and the drug known commercially as coumadin, both available from Wikipedia, will reveal their obvious similarities and differences. I remember reading about the history of the drug and the story of sweet clover disease in cows in my text books many years ago. Until I read the Atlantic story here, I didn't realize that coumarin itself has no anticoagulant activity.

So now, after reading the article, I would really love to try some tonka beans. Like many people I love vanilla, and I also love the smell of fresh mown hay.

a very local tie to the KBR/Chromium story

2010-10-27T19:07:00.000-07:00

The Bend Bulletin had a front page article about a week ago about Oregon National Guard troops exposed to Chromium-6 during work in Iraq in 2003. The story has been in the news for quite a while (an Oregonian story from 2009 is still posted here), but I didn't realize we had a connection quite this local.

Turns out the story is an AP article and is available free from various sources on the web. Here is one.

Happy Earth Day

2010-04-22T21:22:00.000-07:00

If you do not know who Rachel Carson was, you should. If you do know who she was, this is a lovely dramatization and interview.

Part I loads up automaticallly. Parts 2 can be loaded from a link directly above the main frame.

Behold the power of hormones

2010-04-22T20:30:00.000-07:00

Just as we started a discussion of chemical messengers in class this week, npr provides us with a fascinating story about oxytocin. The trust hormone, eh? Seems like quite a stretch to link it to complex things like anti-government sentiment, but perhaps there is a kernel of truth in there somewhere. Much as I'd like to deny it, hormones are powerful things, and probably shouldn't be underestimated.

We really don't understand any of this stuff very well. We like to talk like we do, but come on. The cranium is one heck of a barrier: it's very tough to understand much of anything that goes on inside of there even with sophisticated imaging tools. We're still discovering hormones we never knew we had. We are kindergarteners when it comes to understanding how receptor systems work with these messenger molecules.

Our biochemistry is clearly affected by external stimuli of all sorts: bears jumping out at us behind corners, but also coming home to dog poo on the carpet or being surprised by a chance meeting with an old friend. Who is to say that little daily things like hugs, smiles, birdsongs, or the smell of rain do not cause biochemical changes that can change the way we function...just a little? While science requires evidence to back up any specific claims about this sort of thing, I like the idea.

Chasing Molecules

2010-04-07T20:21:00.000-07:00

Elizabeth Grossman has provided us all with a book that features some of the brightest minds and best ideas in Green Chemistry. It is called Chasing Molecules, and includes both heebie-jeebie inducing stories about toxics in our most local environments and also stories of hope. Chemists play both the role of hero and of villain in the stories she tells. It's refreshing to get a balanced message such as this.

Many of the Green Chemists she talks about are among my favorite people in the field: John Warner, Amy Cannon, Paul Anastas, Jim Hutchison, Richard Wool, Terry Collins, and others. I have met these people! What a hoot!

I have to confess I knew about the book but hadn't read it until I attended a meeting where Ms. Grossman herself was in attendance. I should have had her sign my copy. I hesitated. And I missed her. But her message is not lost on me. And I hope the book allows her to bring her message to a broad audience who will listen.

Thanks to all authors who have the patience and talent to write books that popularize science!

what's good for you may be bad for you, and etc.

2010-03-03T21:28:00.000-08:00

CBC News (Canadian Broadcast, that is) reports today on a lawsuit levied against a number of manufacturers of fish oil pills. It appears that levels of polychlorinated biphenyls (PCBs) are high enough to make for real risks for consumbers.

I'm not a toxicologist, but sometimes I would like to be one. I have found resources on the web that give me links to reports of toxicity from these compounds, but I'm not savvy enough to weigh the risks related to the exposure that is reported in the news article. How much is kind of scary, and how much is really scary? While the CBC gives me concentration data (hoorah!) I don't exactly know how to react to it.

Thanks to the Sightline Institute for pointing out the story via Sightline Daily.

Ready??

2010-02-28T18:45:00.001-08:00

It's time to fire things up at Mount Bachelor Observatory again, we're preparing for another season of sampling. Oh: you haven't heard of MBO? You can find out what's happening there by looking here and here.

Other groups will also be active, but the groups listed are those that have been around the longest, and that have had us most closely involved in their work.

After the gorgeous weekend we've had at the mountain, I'm feeling pretty excited for the upcoming work!

about autism and toxics

2010-02-25T20:29:00.000-08:00

Nicholas Kristof has written an op-ed about the potential links between autism and toxics for the NY Times. The article is impressive. It's cautious and honest. I think it's definitely worth a read no matter what you think of the precautionary principle.

base oxidation rundown

2010-02-24T21:36:00.000-08:00

Does the base of a ski oxidize after sliding on snow?

This question was put in front of me on the ski trail Sunday, and I've been thinking on it and doing a little investigating.

Ski bases appear to be made of polyethylene (polyethene, I suppose IUPAC would call it). There are no functional groups at all, just long, long chains of hydrocarbon. Polyethylene is completely saturated with hydrogen. It's nearly unoxidizable, unless you actually set it on fire.

A protective coating of wax on the base reduces the chance of air oxidation even further.

So I have to agree with some forum (I apologize for not having the url here) somewhere: when bases begin to show white (or grey on my black bases) it may be called oxidation in the ski lodge, but that isn't really the issue. Instead, the snow has physically damaged the base by putting lots of tiny little shreds into it, roughing the surface. It is of course real damage to the surface of the ski that will reduce glide, and it is to be avoided. You're overdue for a new coat of wax.

How rapidly this problem develops is going to be largely due to snow conditions when you're on the skis. Watch for it especially after fresh snow, when the snow crystals are still sharp, or when the snow is cold and icy.

excatly right now

2010-01-26T16:46:00.000-08:00

I am sitting on a couch that is coated with this goop. At least I am strongly suspicious of it, although not because anybody in my family has thyroid disease. I am suspicious because I remember many years ago (too many to name...you don't really want to know how old my couch is) I remember paying about 75 bucks extra for the couch and loveseat we bought to be treated to make them stain resistant. At the time, of course, it seemed like a decent idea. We wanted to protect our investment.

Now that it's time to buy a new couch I am much more inclined to lean the other direction and look for natural fibers and materials. It may be a bit of an overreaction but I am sure that I have spent a lot of time snuggled down under a blanket just like I am right now: 6 inches from the fabric surface, likely coated with PFOA.

It's a little icky to think about I must say.

how to spend a Sunday evening

2010-01-24T18:59:00.000-08:00

Try to get a handle on all the good stuff you can find at Science Blogs.

want to be a doc?

2010-01-17T08:40:00.000-08:00

This article from the NY Times has something to say about the likelihood you'll do well....and it is not about your GPA.

2010-01-13T21:11:00.000-08:00

So we all know the platypus is weird but that weirdness goes way beyond anything I ever imagined. This stuff wasn't in my biology book.

I am left speechless.

Platypus Genome Explains Animal's Peculiar Features; Holds Clues to Evolution of Mammals

pranking

2010-01-09T19:39:00.000-08:00

I don't remember where I heard this, but it was recently: the story is that someone created some serious fright with an old prank that involves some chemistry. Baking soda had been poured into ketchup bottles, and when the bottles were refilled and capped, the vinegar reacted with the soda and created pressure inside. The next person who opened the bottle was startled when the pressure blew the cap and contents out of the bottle.

The story is that this caused an actual bomb scare. I'm dubious, and I can't back up my story because I don't remember where I heard it and I can't find anything on Google.

There you go. I'm not suggesting anybody do this. But maybe I'm suggesting we should all be cautious when we're getting into the ketchup bottle at our favorite family restaurant.

shenanigans

2009-12-31T13:38:00.001-08:00

Somehow I need to reorient myself to the holiday of New Year's Eve, because I just am not much of a fan of it. I think it's a holiday tailor made for extroverts. As a card-carrying introvert the parties, crowds, and general noisiness causes me stress.

So for a slightly intellectual, introspective take on noisy New Year's party fun I'd like to introduce you, dear Reader, to Bassam Shakhashiri. "Dr. Fun" is so utterly fun and charming that he can make an auditorium full of chemical educators sit on the edge of their seats, waiting to see him demonstrate something they've not only seen 10 times before, but that they have probably done themselves 10 times before. THAT's how cool he is. He's a smiling sage.

I got to thinking of him as I thought forward to the fireworks that will come out tonight. You might want to look at his web page on fireworks. And if that's not your thing, help yourself to any of the other marvelous and accurate descriptions of chemicals of the week, or for that matter anything else at Science is Fun.

After all it's a new year tomorrow, and an opportunity to do something new.

restaurant recipe hack: successes and failures

2009-12-27T08:48:00.000-08:00

This entry would go into a category titled "trivia," if I had such categories for my posts. It also shows I've been away from the lab for a little too long.

One of my favorite menu items at a local pub is tortilla chips with artichoke-jalapeno dip. The dip is awesome but it goes over the top good because they bring the stuff out and it's all hot. I realized a while back that having warm chips was key to making this stuff special. And then I found some really good dip at the store, and decided I could easily heat everything at home.

So I hacked the recipe--or more like the presentation--by heating the chips for about 5 minutes in a 300 degree oven. It was perfect.

The next day I thought I'd repeat the experiment. But I didn't want to wait for the oven, I was hungry, and for a moment I stopped thinking and stuck the stuff in the microwave for 30 seconds.

Result? Bubbly hot dip. Cold chips.

And a reminder that microwaves work by heating water, which absorbs microwave radiation. There is virtually no water in tortilla chips. The oven is worth the wait.

read any good books lately?

2009-12-18T19:54:00.000-08:00

I'm looking ahead to next term, when some of my Organic students will once again need to write a term paper. Last term's topic was Green Chemistry and the Presidential Green Chemistry Challenge awards.

For the past few years I have had students read Carl Djerassi's autobiography, The Pill, Pygmy Chimps and Degas' Horse, but for a variety of reasons I may not assign it this year. The problem is finding another book that fits the bill: I need something that is ideally focused on organic or synthetic chemistry, I need something that is a narrative of sorts (not a text), and I want a book that brings up things that don't get brought up in class. These are reasons I have enjoyed assigning Djerassi's book. It's a great window into the life of a synthetic organic chemist.

I'm running up to the library tomorrow to pick up a copy of a book called the Carbon Age by Eric Roston, which sounds like it has some potential. But I'm looking for other possibilities. Have you read anything good? Is it about Chemistry? I'd be delighted to hear your suggestions--or warnings about books that wouldn't be suitable.

oh, chirality!

2009-11-19T21:14:00.000-08:00

You can scroll back to an entry from January 2009 to find the article I wrote on chirality. For those who are in my class this year, and who weren't last, this could be interesting.

For those of you who have been in the fan club for a while, go ahead and disregard this note.

let go of the side of the pool

2009-11-18T20:06:00.000-08:00

Thanks to my undergraduate advisor Cathy for noticing t his link at Scientific American. Don't fear your mistakes! Share them with others and use them to focus your mind and attention. There are indications that you will learn better (and I promise I won't judge you for making an error in front of me).

As the ever-wise Zelda says, you can't swim until you let go of the side of the pool.

Circium Pitcheri

2009-11-12T19:56:00.000-08:00

Many many many many years ago (it was the 90s) I spent about 1.5 years' worth of Thursday mornings in the lab at Chicago Botanic Garden, working with Kayri Havens genetically typing a number of rare plants including the Pitcher's Thistle. We usually talked about our samples using their Latin names. In this case it was Circium pitcheri.

What a great blast from the past to see them in the New York Times! As I was digging into the article I was thinking, "oh my gosh I think this is work done by people I know!" then "oh my gosh I think I know that project!" then "oh my gosh I think this is a plant I have worked on myself!"

Working with the scientists at ChiBot taught me that there is a lot more in museums, beyond displays for the public to look at. I gained a deep and persistent appreciation for plants, for their ability to adapt to specific environments and expand their territories.

I also learned that my lab skills allowed me to make contributions in areas far outside my specific field of expertise. After all, what business did I have in their lab? Was I a plant expert? Nope. But life is like this: sometimes we imagine we have less to offer than we really do have. Speaking up is the first step to being in on some great stuff.

Is the periodic table the same around the world?

2009-11-12T19:17:00.000-08:00

I was asked this question last week. I answered incorrectly. I stand corrected. I said yes, thinking only about how the element symbols and arrangement are universal. But the names are different in different languages, even though many are derived from latin so come out very similar in different languages. But to get a taste for the variety out there, check out these different variations, many of which are produced by the same people:

In Spanish

In French

In German

In Dutch (because I have a special place in my heart for the Dutch)

In Arabic

In Swahili

In Russian, the language of Mendeleev

It is somewhat surprising that the languages that use different alphabets would use our alphabet characters for their elemental symbols. Can you imagine learning element symbols with an alphabet different than your own? It sure would seem more cryptic.

While some element names are very different (check out Sulfur, for instance), others seem quite universal (the Noble Gases). I wonder why? Perhaps those elements that have been discovered and named more recently, since communication across the world has become easy, have internationally-agreed upon names. Hydrogen appears to have its name translated literally in German and Dutch....to wasserstof. Funny!

To top it off (if you're still reading) there is always the Periodic Table of Comic Books . I know it's not a language, but it's funny and creative so I'm including it here anyhow.

Deuterium

2009-11-08T16:03:00.000-08:00

I spent a lot of after-school time watching Hogan's Heroes as I was growing up. Sargeant Schultz was always good for a laugh, and I can remember his references to "heavy vasser" and a red bucket that was labelled so. Many years later I learned that heavy water was of some concern during the war, as the Germans appeared to be experimenting with it as a moderator for nuclear reactions. To the allies, this indicated an interest in developing nuclear weapons. Heavy water is water containing deuterium (D) the isotope of hydrogen that contains a neutron and hence that has an atomic mass of 2 rather than one. So heavy water weighs 20 amu/molecule, or 20 grams per mole: a modest 10% more than regular water.

Disrupting the development included a really dramatic destruction of a supply of heavy water, which was all produced during that time in Norway. The PBS series Nova has described both the sinking of a ferry carrying the stuff on "Hitler's Sunken Secret," as well as an attack on the plant that manufactured the stuff in the first place. The plant made use of a series of multiple distillations, if I recall correctly, to enrich samples of water, which naturally contains a small amount of D2O.

Gilbert Lewis (of Lewis structure fame) was the first person to isolate D2O, incidentally.

Heavy water is actually a little more dense than regular water, since deuterium weighs a little more than hydrogen. But the effect is fairly modest and wouldn't be noticeable if you were carrying a little flask of the stuff.

The drywall problem continues

2009-10-29T16:27:00.000-07:00

The Chinese drywall story is back in the news. National Public Radio has an update.

My dog has quite the lifestyle

2009-10-13T11:16:00.000-07:00

Molecule of the Day points out how easy it ought to be to put our dogs on diets. Feed them less, right? So why are there diet drugs for dogs? Maybe it's about our inability to control our interactions with food, even to ask our dogs to abstain. Or maybe it's about sharing our concerns about weight with the family members that so far have been blissfully unaware of this American obsession. Or maybe there are drugs out there that could have use in people but just haven't made it through FDA approval.

Whatever the reasons may be I have to laugh as I think about these as lifestyle drugs for dogs. My dog has quite the lifestyle. No work, free food and drink, lots of affirmation and attention, and no responsibilities to anybody.

That was fun.

2009-10-09T15:40:00.000-07:00

A helpless audience of GS199 students were subjected to 50 minutes of joy-filled rambling by me today, on the subject of Green Chemistry. Oooh I had fun! I hope that they did, too. It was an interesting experience, explaining this to a general audience. I appreciated their interest. It is a very fun story to tell, optimistic and varied and full of good characters.

Featured tales of Green Chemistry successes were the ibuprofen synthesis, TAML oxidant activators, and Non-fluorous, highly CO2-soluble materials.

Links are to the EPA summaries of the projects.

Now it's time to get out and enjoy the weekend.

What are they looking for?

2009-10-09T15:31:00.000-07:00

Tis the season that recommendation letter-writing is beginning to wind down, just as the school year is beginning to wind up. I think this week is the first time in about 3 months that I haven't had somebody's letter request sitting on my to-do list. I'll admit it: I am relieved.

It's not that it's a job I don't like, it's just that it is a job. Crafting a letter that is honest, professional, and that gets the message right can be a difficult thing to do.

As I look out over the sea of expectant faces in my new classes I know that this coming year will bring more requests. I'm already watching for the qualities of character I hope to be able to write about later. Those would include things like flexibility, honesty, drive, and the abilities to both listen carefully and act decisively.

Students out there who know or think they know that they'll be seeking admission to medical or other professional health programs, studentdoctor.net has an article that does a good job of explaining how to think about and manage your presentation of yourself in your personal essay. Much of what is here is also relevant to how you might want to be perceived for letters of recommendation. This might be valuable reading.

Why I adore Hans Rosling....

2009-08-27T08:26:00.000-07:00

It's not entirely explainable with words or simple graphs. It's best understood by actually watching him operate with his animated data. See his new TED talk here.

OSU pals make the Oregonian!

2009-06-19T13:40:00.000-07:00

...this work brought to you by my favorite peeps at OSU. These folks have previously brought us wonderful research on air quality at our very own Mt. Bachelor Observatory, with help from some great students at COCC.

glycosides in my garden

2009-05-23T15:36:00.000-07:00

Memorial Day always has felt like an odd holiday for me. Growing up the only real memorial thing that would happen is that my mom and dad would each take their mothers to the cemetery to put flowers on the headstones of their spouses. There wasn't much for direct links to the military, it seems. But Memorial Day was always a day to work on some project outdoors. As an adult I still find myself planning for and doing work around the house during the holiday weekend.

So today I went to the nursery and bought some plants and tree bark for my yard.

I knew I wanted to get some digitalis, because there was some growing here when I moved in and I find it gorgeous in a showy kind of way. But I also love it that digitialis is the source of commonly prescribed cardiac glycoside digoxin. I didn't realize until I did a little web searching today that the plant actually is not just a little poisonous--it contains enough of the glycoside to really mess you up bad even if small amounts are ingested.

I also picked up some kinnickkinnick, which is Arctostaphylos. I bought it because it will look good and do well where it needed to go, but it turns out to be darned interesting, too. Turns out it is a relative of the familiar manzanita, and like digitalis, it contains a glycoside compound that is biologically active. In this case the glycoside is named arbutin. It inhibits the formation of melanin and has been used in herbal treatments for urinary tract problems. But these extracts have been the subject of some concern since they may be carcinogenic.

a new blog to watch

2009-04-16T12:25:00.000-07:00

Emily Monosson has a blog that has been recommended to me, called the Neighborhood Toxicologist. I'm linking it from here, from the list of Stuff I Like that is in the right-hand corner of my page. I haven't had a chance to give it a close inspection but I have reason to believe it'll be good.

Meanwhile, in Ochem the current topic is Electrophilic Aromatic Substitution. In an email conversation with a student, I was drawn in to a discussion about polycyclic aromatic hydrocarbons, or PAHs. There is so much descriptive chemistry I would like to include in my courses, but there just isn't much time and it is often the kind of information that is accessible to my students anyway, if I just point out to them where to look.

So with that said, I once again can plug Wikipedia, which has an excellent article on PAHs.

biology meets chemistry meets physics meets engineering

2009-04-04T15:56:00.000-07:00

This is one of the best cross-disciplinary stories I have seen in a while. Who'da thunk this would work? What a creative idea! Biological systems are so cool, since over time they are often optimized to utilize available materials and make the best possible use of what is in the environment.

is your drywall off-gassing poisons?

2009-03-26T17:56:00.000-07:00

ABC News ran a story this evening about a woman in Florida who is claiming her house has made her sick, and that Chinese drywall may be to blame. The story included no details worth mentioning--it was a classic case of little information but lots of "two sides" reporting.

CNN does a much better job, reporting that the materials have been tested and shown to contain some strontium sulfide, which potentially could lead to the production of H2S, explaining both a sulfurous smell and problems with corrosion of pipes and wires in the house, which is quite new.

You can read more here.

mmmmmmeta

2009-03-24T10:22:00.000-07:00

Science News reports on a group that has devised an efficient way to substitute at the normally-resistant meta position on aromatic rings. Thanks to Sean for the link.

MSRA among the piggies

2009-03-12T20:29:00.000-07:00

Thanks to my college advisor for posting a link to this article about drug-resistant staph in pigs. And of course, thanks also to Nicholas Kristof for researching and writing it in the first place.

SciAm on Sustainability

2009-03-09T19:28:00.000-07:00

I was tipped off to this article today, and although I haven't read it I'd bet you a dollar it's good.
So I'm posting it without a pre-read. Meanwhile, out in the news, the conversation about changes in funding for research involving embryonic stem cells is heating up rapidly.

nuclear forensics

2009-03-09T08:45:00.000-07:00

National Geographic News has posted an article describing the emerging field of nuclear forensics. The article appears to suggest that the nuclear decay products of an unknown sample were used to determine its origin, which happens to be the first nuclear bomb test.

Oregonian reports on Chromium Exposure Among National Guard Troops

2009-03-08T09:19:00.001-07:00

The link is here.

EJ Corey and Retrosynthesis

2009-03-03T19:35:00.001-08:00

Check out this little gem of a synthesis, credited to EJ Corey, the esteemed developer of retrosynthesis: Trabectedin (from Wikipedia). Astounding.

My Synthesis professor in grad school used Corey's book as a foundation for our course and told us his (not Corey's) 9 days in jail for a BUI offense provided a stretch of uninterrupted time for reading. The book is called The Logic of Chemical Synthesis, and it's becoming a classic.

a tragic accident

2009-03-03T19:22:00.000-08:00

It is unfortunately too easy for any of us to forget the hazards associated with some of the stuff we work with. The LA Times reports that this recent fatal accident involved tert-butyllithium, an organometallic reagent that is used as a base, but that has similarities to the organolithium reagents used for generating carbon nucleophiles in organic synthesis reactions.

10 best?

2009-03-02T21:47:00.000-08:00

While poking around the web looking for full-text versions of Djerassi's original papers I discovered this list of the "10 best organic chemists of all time." I couldn't help but notice that many of you, Readers, will know the reasons for nomination if not the actual names.

I smile as I read these names and their contributions. They are an amazing bunch of minds. I can't comment about the drinking: I have no first hand experience with any of them.

I didn't find the Djereassi papers, by the way, but I think I have them in my office. Somewhere.

doublets of doublets: I'm beggining to see!

2009-02-26T19:22:00.000-08:00

Poking around in some books on nmr today I found someone who directly addresses the doublet of doublets phenomenon. You can't imagine how happy I was to see this.

I'm beginning to get it. As usual, Straumanis is right. The book explains that in most situations, nearest neighbor hydrogens are similar enough to one another that the splitting occurs in a way that follows the rules for splitting we have learned. In a few situations, though, when the neighbors are very different from one another (as expressed by something called their coupling constant), they split the signal sort of separately and generate a doublet of doublets.

The book provides an example that looks a lot like the fluorinated benze we were examining, except it has a nitro (NO2) group across from the F.

The fluorine is the reason for the different coupling constant in our molecule, but I am still sorting out the details of what role it plays. I also still don't have complete clarity about why these coupling constants could vary when the coupling has all been explained to me using the quantized spin states (as I tried to describe in my earlier post).

south Deschutes: voting on the nitrate fix

2009-02-26T09:57:00.000-08:00

There are strong opinions on both sides of the conversation regarding the ballot initiative called the groundwater ordinance referendum. For the uninitiated, a clear and brief description of the situation can be found here.

I'd like to think I'm a well informed voter, but there are a lot of things going on behind this ballot.

What is the real relationship between nitrates and health problems?
What is the relationship between nitrates in groundwater and environmental problems?
Is nitrate mitigation going to protect the health of groundwater in more general ways?
If nitrate pollution is a real threat to health or the environment, what regulation is appropriate?
Why is this vote in front of us, after extended study and an ordinance passed by the county board of commissioners? Is it appropriate to have the public decide on such a technical issue?
What alternative solutions exist?

Any post that tried to address all of these issues would be long and probably set off a firestorm. I only want to comment on the first item on my list of questions. Unfortunately, even with a Ph.D. in biochemistry, I am confused about how to answer this one.

Nitrate can look like a real problem, if you consider the following health effects, pilfered from the EPA consumer fact sheet on nitrates/nitrites:

Short-term: Excessive levels of nitrate in drinking water have caused serious illness and sometimes death. The serious illness in infants is due to the conversion of nitrate to nitrite by the body, which can interfere with the oxygen-carrying capacity of the childs blood. This can be an acute condition in which health deteriorates rapidly over a period of days. Symptoms include shortness of breath and blueness of the skin.

Long-term: Nitrates and nitrites have the potential to cause the following effects from a lifetime exposure at levels above the MCL: diuresis, increased starchy deposits and hemorrhaging of the spleen.

Then there is this quote, pulled from a web page of the department of health and human services:

A large proportion of hemoglobin in young infants is in the form of fetal hemoglobin. Fetal hemoglobin is more readily oxidized to methemoglobin (MHg) by nitrites than is adult hemoglobin. In addition, in infants, NADH-dependent methemoglobin reductase, the enzyme responsible for reduction of induced MHg back to normal hemoglobin, has only about half the activity it has in adults.

But last week I just happened across this, from American Scientist, a publication of Sigma Xi that I respect an awful lot.

Just answering the first concern about nitrates: are they a real health concern? is proving difficult. I could vote based on the precautionary principle, but I realize the economic impact to families living in that area would be huge.

The more I have to vote on these voter initiatives, the less I like the initiative system.

doublets of doublets

2009-02-25T23:51:00.000-08:00

I am still not able to resolve the doublet of doublets question that came up Tuesday. But since I promised, I am going to try to explain as well as I can what I'm thinking about it. If you are reading this, give yourself a break if you don't know how an nmr picks up signals. If you are reading this and do understand nmr, I would be delighted to have you help me improve my understanding.

Here's what I (think I) know:

Spin 1/2 nuclei, such as hydrogen, have spin that gives them magnetic moments.
The spin states in such nuclei are described as being either "up" or "down," and are quantized.
Inside the nmr, an applied magnetic field aligns spin states and then an applied radiofrequency signal can cause spin flips at particular frequencies. These spin flips cause absorbances which are converted to signals, generating the spectrum.
The chemical shift for a given set of equivalent hydrogens indicates what frequency is required to generate this absorbance, which varies depending on the environment that nucleus sits in.
Hydrogens that are nmr equivalent absorb at exactly the same frequency.

Still with me? Good. I am about to address splitting:

Absorbance peaks are split due to interactions that occur through bonds, but between nuclei of the hydrogen(s) generating a particular peak and those which are described as "nearest neighbors." We have learned how to identify nearest neighbors, so I won't go into that here.
The splitting occurs because the neighboring nuclei have a minor but real effect on chemical shift. Their spins can be in or out of phase with those that are generating the signal, adding to or subtracting from the chemical shift.
For every nucleus involved in these relationships, there is a particular number of possible spin-state alignments, which happens to equal the number of nearest neighbors plus one.
Therefore the peaks are split into that many (neighbor Hs plus 1) like we learned, and forms a set that varies in intensity like a Pascal's triangle.

Now, finally, for the confusion about the doublets of doublets:

Occasionally one hydrogen attached to a carbon is nmr inequivalent to another on the same carbon. For example, two hydrogens on an sp2-hybridized carbon could qualify, if the stuff on the other end of the alkene is distributed asymmetrically.

In this case it makes perfect sense to me that these hydrogens would each have a slightly different chemical shift, and that each one would be split by a nearest neighbor, generating an overlapping "doublet of doublets," rather than the triplet signal you would otherwise expect.

I can't understand the other example Straumanis gives, however, which involves hydrogens around an aromatic ring that has a single fluorine substituent. There are 3 groups of equivalent hydrogens on this structure: those at C1 adn C5, those at C2 and C4, and one at C3. He seems to argue that because the H at C1 exists in a different environment than the one at C4, that the signal from the H at C3 will split into a doublet of doublets.

If peak splitting is based purely on the spin-state interactions of the nuclei, what environment those nearest neighbor hydrogens are in doesn't seem to have anything at all to do with it.

Signals from hydrogens on aromatic rings do tend to get all overlappy and scrunched up, so he could be perfectly correct, but I can't sort out why. I think I need to send the question to him, or to a group of others I know are using the workbook.

who is absolutely hot?

2009-02-20T10:27:00.000-08:00

Nova, the classic PBS program that recently rebroadcast it's awesome Absolute Zero show, publishes an "occasional column" (what a great idea!) that has recently addressed the possibility that there is an corresponding Absolute Hot. Thanks, Krokodile, for the link.

...and even more on Thimerosal

2009-02-12T19:33:00.001-08:00

Derek has posted an awesome piece on the Thimerosal/Hg/autism story, here.

2009-02-11T20:24:00.001-08:00

I don't think this requires any
description at all.

Thanks to "Million Moments"
for sharing.

JACS is not quite so fun

2009-02-11T20:16:00.000-08:00

No similar news items from JACS, the Journal of the ACS. Oh, well. Then again, there is always Chemical and Engineering News, which has good online articles and links to other resources. ACS just is not enthusiastic about opening access to their journals to the public, except in small ways.

Somewhere in my online ramblings I tripped into this, which may be of interest to those who are interested in all the fuss about Thimerosal and autism.

ES&T: what's NOT available on line?

2009-02-11T19:54:00.000-08:00

The ACS journal Environmental Science and Technology (ES&T) appears to have lots of great content available free on the web. Oh, joy! Now if I could only find more time and more energy, I could get around to reading this stuff.

Here is an example article: this one is on the presence of pharmaceuticals in drinking water.

And here is another, on nitrate contamination in drinking water.

Could it be that other ACS publications have similar resources available on the web? I'm a little embarrassed to admit I don't know: I'm going looking right now.

chemistry in the news: good news!

2009-02-05T20:42:00.001-08:00

OPB reports on a chemical that appears to repel pine bark beetles, a real scourge in the pine forests on the east side of the Cascades. It is called verbenone, and is a terpene produced by lots of plants, including those of the genus Verbena.

our local National Teach-In is tomorrow!

2009-02-05T20:22:00.000-08:00

The National Teach-In on Global Warming Solutions is going on now. Tomorrow several institutions in Central Oregon will be involved. OSU-Cascades, Central OR CC and at least one area High School are gathering from 11 am till 2 pm to talk, teach, eat, and discuss.

Everyone is of course welcome. From 1:30 until 2 the actual dialog will occur, featuring a number of students and City Counselors from Bend.

Hope to see you there!

chloraseptic=death?

2009-02-05T20:07:00.000-08:00

This morning's news included a story suggesting that Nazi hunters at the Simon Wiesenthal Center have determined a certain war criminal, Aribert Heim, probably died and was buried in Egypt in the early '90s. He was apparently involved in "medical" experiments that sound awful--including deliberately injecting people with poison.

When I heard the story I immediately was taken back to a class yesterday, where the conversation led to the meaning of "phenol" and I casually mentioned that phenol, while rated as toxic by chemical supply houses, happens to be the ingredient in Chloraseptic throat spray. Ha ha ha, I chuckled, "How is it both medicine and poison?" and then I looked a bit deeper into this compound. It has a fascinating rap sheet.

Phenol is not only used as a topical antiseptic in Chloraseptic, it also:

is considered toxic and mutagenic, and carries a health warning of "3" (highest is 4) on the NFPA label
is the source of the odor best known as hospital smell
is a raw material in phenolic resins, which included the historically important polymer, Bakelite

In addition to all this, it was also used by the Nazis to kill people by injection.

So wasn't it a coincidence to learn all this yesterday, and then wake this morning to the story of the Nazi doctor who may have committed these horrific acts with, perhaps, this very compound.

Russell Marker percolates up

2009-01-28T20:59:00.001-08:00

A few days ago an entry from In the Pipeline included the phrase "Mexican yams and their biggest fan," with the last two words linked to somewhere. oooh! Intriguing! I thought maybe I'd know who this fan was. The link takes us to a Chemical and Engineering News article about Russell Marker. So of course the article discusses the history of Syntex and mentions our man of the hour: Dr. Djerassi.

Herr Doktor Djerassi

2009-01-27T19:57:00.000-08:00

If you know anything about him you won't be surprised to hear that Carl Djerassi has a personal/professional web site devoted to the promotion of his books, plays, art, and generally himself. He provides access to lots of interviews where he shares his opinions on all of these topics--oh, yeah, and also of science and the development of the oral contraceptive pill.

There is one interview in particular which is a nice audio file. It's nice, if you are reading his autobiography, to know what he sounds like. His demeanor in interviews also provides insight into who he is in a way that is not quite captured in the book. So if you're curious, follow this link and find the BBC audio file, and have a listen.

Stereochemistry and the Pharmaceutical Industry

2009-01-27T19:20:00.001-08:00

I heard part of an interview with Thomas Quasthoff on the radio last weekend. I'm not into opera, but his voice and presence is amazing. I became aware of Quasthoff several years ago when he gave an interview on TV....perhaps it was 60 minutes? I don't remember for sure anymore.

His biography is compelling, and illustrates the importance of stereochemistry in drug manufacture. In recent years there has been some argument about whether the FDA is too slow to approve drugs; too careful about approvals. Maybe, but maybe not. In the case of thalidomide I think everyone would agree there are many who were spared a difficult life because the FDA hesitated. Unfortunately in many other countries it was approved without sufficient testing.

hey, followers and students

2009-01-25T11:16:00.000-08:00

Let's wiki!
I have been looking over the Wet Paint wikis that are constructed by my ochem students, and I am really impressed. I haven't had so much fun with something that seems like grading for a long time.

I am missing contributions from a few students, though, and I know two of them are people who watch this blog. So if you fit that description, please check your wiki site to see if I have been invited to be a member, and if I have accepted.

If you have no evidence I have looked at your blog, please invite me to join.

what's new in green chem?

2009-01-22T20:17:00.000-08:00

I'm headed to Portland this weekend to reconnect with some professional buddies who are also into Green Chemistry. What's new in Green Chem and in Green Chem education? I can hardly wait to find out.

If there ever was a group of cool chemists, this is it.

Dear Mr President

2009-01-22T19:57:00.001-08:00

I know you're surrounded by well informed people with cultivated opinions. I know you are facing an unimaginably difficult task: leading this country through really difficult economic times, coping with foreign policy nightmares, and improving the function of our health care system.

As a chemistry educator many of my students are pursuing careers in health care. I teach people who want to be nurses, people who want to be physician assistants, doctors, and pharmacists. I teach in a place that is, at its roots, a rural community. We are geographically somewhat isolated, and people come from many more rural areas around here to get their health care.

Health care is increasingly becoming tough to find in those outlying communities, and our community is limited in its capacity to train nursing and other health care students because even our regional hospital is not all that large. At my college, the health programs are tremendously competitive, and the limit to producing new health care workers appears to be a lack of money to make it possible for the college and the supporting hospital to train very many people.

So I have people anxious to become nurses and doctors who love this part of the world and want to live and work in places like this. Yet the training for these people draws them into urban places, and debt after school often draws them into specialization or urban jobs so that they can not return.

If we are going to invest huge sums of money into reconstructing our economy, I would be delighted to see some of that money used to produce a system that can support the education of these people in a fashion that allows them to come back to small communities for their professional practice. This is what they want, and it is what our communities need, especially as the population of our country--most dramatically in these very same rural communities--becomes older and needs more care.

Pre-Med? Read on.

2009-01-13T16:22:00.000-08:00

This message is from Kate.

Hello Fellow Pre- Med Students~

I hope that by this time you have heard of the MCAT. If not then you definitely need to talk to someone. If so then you have probably heard of the MCAT prep course that all recommend you take. The University of Oregon offers one over in the valley during the summer.

I have spoken with Diane Pritchard at U of O Bend about getting a course over here for we Bend-kids. She said that it is very possible, we would need about 10 to 12 students to make it go. The trouble lies in the fact that Diane has tried to do this in the past and after getting a good initial response then had everyone bail on her. So needless to say she is not super interested in doing all the leg work if no one is going to follow through.

That is where I come in. I am a Pre-Med student who doesn't want to drive to Eugene twice a week this summer to get ready for the test. Check out this link for the most up-to-date info on the course http://www.uoregon.edu/~als/services/testprep/textdocs/mcatuoprep.pdf

If enough folks are in Diane would make this happen for us. Course costs $625 I think, and well worth it I hear.

My email is kwillis@cocc.edu and let me know of your interest.

Have a great day and happy learning~ Kate

Cahn-Ingold-Prelog Rules

2009-01-13T16:12:00.000-08:00

Ochem students: you may remember today's brief discussion of the rules for assigning priority to groups around a chiral center. I promised I'd get back to you about an issue that came up in relation to this. I was unsure of myself on an issue surrounding what I think we can call a more-complex example. Well, I am disappointed in the textbooks in my office. None of them provide an explanation that is adequate to deal with the structure we were looking at in class. But there is a straightforward (if not simple) way to solve the problem.

And, as usual, it was I who was misapplying the rules and not our esteemed author.

Guess where I found a good description, illustrated with examples, concise, accurate, etc.? My favorite web source: Wikipedia.

Chemistry and Cookery, the Column

2009-01-06T16:18:00.000-08:00

I discovered today that Harold McGee, author of On Food and Cooking, has a column available to read for free at the New York Times. Being an old fan I don't know how I missed this for so long, but I am quite happy to have found it! Links to the columns can be found most easily by starting at his website, Curious Cook.

oops.

2009-01-05T17:47:00.000-08:00

Cyanide ion (CN-) and sulfuric acid produce HCN, a highly toxic gas. When inhaled, HCN interferes with celllular respiration and can lead to what amounts to molecular-level suffocation.

I am grateful to the writer and editors at the Oregonian for giving specifics on this accident. So often I see vague references in the media to spills or accidents involving chemicals, without actually naming them. As in, "a tanker turned over and spilled a toxic chemical...." ammonia? chlorine? xylene? The consequences of such spills can vary dramatically.

Good eye for the person who noticed the foaming, too. The evolution of the gas seems to have tipped him off to the fact that something was amiss.

Anybody know what they do with cyanide in a chip factory?

what I got for Xmas

2009-01-02T15:02:00.000-08:00

My DNA is on its way to the lab.

SciFri

2009-01-02T14:56:00.001-08:00

Do you think radio lacks because it can not deliver video content? I must respectfully disagree.

Science Friday (from Talk of the Nation, hosted by npr) has a fantastic website that includes a library of videos that may even rival those of TED. At the moment I am particularly taken with the Hungry Scientist presenting carbonated fruit. But there is much more to explore. The Hungry Scientist blog also deserves checking out.

Suddenly winter break seems way too short.

watch your ash

2008-12-31T08:41:00.000-08:00

npr broadcast a story about the coal ash spill in Tennessee this morning. The spill occurred a while ago but questions are persisting about the degree of hazard associated with the stuff. Bloomberg also has a story about this incident, but makes a more disturbing claim that wells in the area have been reported to contain levels of "some metals" that exceed safe levels. Yet EPA considers coal ash, which is produced in huge quantities at coal-fired power plants, a special waste that is recyclable into building materials, etc., not really a regular hazardous waste.

Is coal ash hazardous? Does the dose make the poison in this case? I don't have the answers but this story doesn't seem to be going away. Given time maybe the news media will deliver us some more good information. In the mean time I may have to dig into the EPA's web to see what else I can learn.

ahhhhhh, skiing.

2008-12-23T15:32:00.000-08:00

It is finally ski season around here. I ventured out yesterday after applying a new coat of wax.

The wax I selected was the $12 version of red wax. This is the cheap stuff, often referred to as "hydrocarbon wax." The color of the wax indicates the temperature at which it is designed to provide optimal glide. There were other waxes at the store--yellow, blue, and purple, and there were more expensive waxes, too. Some were very expensive. How do they differ?

TOKO explains this on their web site. I do squirm a bit with their casual use of language and structures, but I appreciate their willingness to talk about these things in public! The waxes are color-coded for temperature mostly because the formulations need to vary based on how much liquid water is in the snow. Under warmer and/or wetter conditions, the wax will provide better glide if it is more hydrophobic. Warm temperature waxes are also softer. In cold and/or dry conditions there is less liquid water in the snow, so hydrophobicity becomes less important and the waxes are designed to be harder to stick well to the ski when the snow is cold, dry and abrasive.

Cheap waxes are mostly long-chain hydrocarbons. Wax can be made more hydrophobic by the addition of fluorine, which is expensive and therefore makes for faster but pricier waxes. Fluorinated waxes provide their benefits mostly under warmer or wetter conditions. The expensive cold-temperature waxes use graphite or molybdenum to reduce friction on the snow.

I love the pictures on TOKO's web page and I especially love the diagram that shows the measure of hydrophobicity by examination of the water droplet. But I have a hard time reading that fluorine is a molecule, and their explanation of what makes a good fluorine vs. a bad one looks pretty weird to me. More fluorine molecules in the wax? More high quality fluorine molecules? What? They're not sounding like chemists here, to me. It would be more appropriate to determine percent fluorine by weight, and make comparisons that way.

Maybe this is a bit of deliberate obfuscation to keep the public confused, in the same fashion as car companies advertising "miles per tank" instead of "miles per gallon."

gifts for the chemists in your life

2008-12-15T15:33:00.000-08:00

1. On Food and Cooking, by Harold McGee. A classic connecting science and cooking, but in that order. Other books in the sub-genre of Science of Cooking often read more like cookbooks. Fun ones, yes, but cookbooks. McGee's is a science book.

2. Scientific playthings, especially interesting materials. Some of my favorites are magic sand, insta-snow, and and Sculpey, which is bakeable polymer clay. I've also seen some very un-dense baked clay, but I don't know what kind it is. It's almost foamy. The piece I saw was sculpted into a beautiful brain and spinal cord, and the entire life-sized brain was one solid piece. I haven't had much luck baking larger pieces of Sculpey.

3. Do it at home: massive quantities of baking soda and vinegar are inexpensive and no further away than the grocery store. Boil a little red cabbage in a small amount of water to produce a pH indicator solution that you can use to test any of a number of household items: soda, vinegar, baking soda solution, clear soap solutions, etc.. Some groceries also sell dry ice, which is fun to play with provided you are careful. Dry ice in a sink of warm water with soap bubbles is super entertaining. It is possible, I have heard, to remove the superabsorbent polymer from a diaper. If you cut open the liner and get the stuff separated out I bet it could be fun to mess around with.

4. Kits that allow the average kitchen to feel more laboratory-like. New England Cheese Making Supply has intro kits that allow you to produce a nice Mozarella in less than an hour. Craft stores sell kits for soap-making. Edmund Scientifics sells root beer and hot sauce kits. If you have a local brew-supply store you can find not only beer-making kits, brewing supplies that can be used regularly if you think you'll get into that, and also soda-making supplies that often allow you to choose which kind of soda you want to make. Typical options include cola, creme soda, and sarsaparilla.

'tis the season.

What the heck is caffeol?

2008-12-12T21:05:00.001-08:00

A book that I own called Chemistry and Cookery, published in the 1930s, has a great section about coffee that is fun to read as a chemistry book and as a piece of history. It has a big section about coffee preparation methods, all written well before most people were drinking coffee brewed with an automatic drip coffeemaker, let alone having access to espresso.

The discussion includes frequent reference to an oil called caffeol, which the authors refer to as a volatile oil that is easily lost through extended heat, boiling, or long storage especially in an open container. What is this caffeol, I wondered, and why do I not hear it referred to by those who wish to advertise their beans as the best available?

I went to Wikipedia. I found a single mention of it as a volatile oil responsible for flavor and aroma in coffee, but with no structural information.

So I googled "caffeol." I found numerous references to it as a volatile oil responsible for flavor and aroma.....no structure.

So I googled "caffeol structure," and found a book excerpt (thank you google books!) from Coffee Flavor Chemistry by Ivan Flament and Yvonne Bessier-Thomas that actually gives caffeol a bit of attention.

What do they say? Lots. It takes several pages (starting at about page 61), and they're complicated and it's late and the story is long and meandering. But what grabs me as I look at the pages from the book is that there are two tables listing what must be about 20 compounds identified in coffee aroma. I also know nobody has managed to bottle an artificial version, so we have probably not worked out the composition of the entire mixture. Nothing smells quite like the real thing.

I am putting that book on my Christmas list.

those of you who are in to combustion, read on

2008-12-08T21:13:00.000-08:00

The Christian Science Monitor has an article about a guy who has developed a stove to burn rice husks efficiently, potentially improving the quality of life for people who burn biomass for cooking and also providing a readily available source of fuel for them.

If you read through the comments at the bottom of the article you can find a place to link to the plans for his stove as well as an email where you could ask questions.

Polarimetry | yrtemiraloP

2008-12-08T16:58:00.000-08:00

Don't panic if you don't get this the first time around. There is time to learn it more carefully, later. But.....

Some of my dear readers were introduced to polarimetry on Friday. A hallway conversation after the lab involved two isomers of the type that can be distinguished by their rotation of plane-polarized light. Both compounds are recognized by us for their tastes. They are the (+) or dextrorotatory isomer called R-carvone and (-) or levorotatory S-Carvone.

Both share the same connectivity and the same molecular formula and while both contain several double bonds, they are not geometric "cis-trans" isomers of one another.

The dextrorotatory isomer is a major substituent in caroway, and is also present in some quantity in dill and in the peel of mandarin oranges. Which I love, by the way. Which are in season, by the way. Get them now because they are seasonable! consider it a chemistry research project.

The levorotatory isomer is a major oil in spearmint. Yep, that's different than caraway or dill, in my book. I have heard however that some people are unable to distinguish between these two substances.

That's a curiosity to me, since the proteins that mediate our chemical senses...smell and taste....are almost always themselves able to clearly distinguish these types of isomers.

These substances are also great examples of terpenes, which I'd love to describe but will have to save for another post.

As always, there is more you can read at Wikipedia.

a couple of quick plugs

2008-12-02T20:51:00.001-08:00

...for the links I have listed in the upper-right hand corner of this page, under "Stuff I like."

In The Pipeline has been a fascinating read for me, both because it offers up some challenging chemistry and also because it provides great insight into the process of drug discovery. If you're interested, look at it. If you find the articles are difficult, scan through a few and I think you'll learn to appreciate it for that other reason. It's an insider's view of the pharmaceutical industry.

Molecule of the Day is just plain fun, and yields a little inspiration for paying attention to Ochem on any given day.

Sightline is both a news outlet and a link to a blog I like to read, called The Daily Score. The focus is energy and sustainability issues in the Northwest US and SW Canada.

TED is unexplainable. Just check it out and enjoy the streaming video. There's so much there that's good I don't even know where to start.

Science in the News is a daily News roundup that provides me with most of the Science-related stories that make the National News, and many local papers. It's my first source of Science-related news stories.

Go ahead, check them out. Links are right there in front of you, to the right of this post.

spinning vinyl

2008-12-02T20:22:00.000-08:00

I have an old turntable in my attic. And I still have my old LP records, including some real classics from the 80s, and at least one especially-expensive high-quality pressed album. It's Pink Floyd's Wish You Were Here. Oh, and I have an EP of Kraftwerk's Tour de France. Great stuff, though I haven't played them for years.

Vinyl records are pressed PVC, or polyvinyl chloride. PVC is a polymer made from a monomer called vinyl chloride, which has the formula CH2CHCl. The alkene polymerizes by an acid-catalyzed addition mechanism to produce long chains. The "vinyl" part of the name is straight from the chemist's lexicon: vinyl means the chlorine is directly connected to the sp2-hybridized carbon.

PVC is manufactured in huge quantities and is the subject of a certain amount of controversy--because of hazards associated with the toxic, carcinogenic monomer it is made from, and also because PVC plastics are often made soft ("plasticized") using phthalates, which sometimes leach from the finished materials and have their own toxicity hazards.

Those of you who are O-chemmers will get the chance to learn more about PVC at the start of Winter term.

Recreational Dimensional Analysis

2008-12-01T13:36:00.000-08:00

We did a little math in CH104 this morning.
By our calculation and with some data retrieved from good old Wikipedia, we determined that it would require consuming about 1500 6-oz. glasses of wine per day in order to dose yourself with enough resveratrol to mimic the experiments that showed a benefit in mice.

Which is not to say that lower dosages wouldn't make any difference, or that mice are a perfect model for human nutrition. But it was a fun time, at least for me, and brought home the value of doing a few calculations the chemists' way.

Chromium Six

2008-11-25T16:03:00.000-08:00

Have you watched Erin Brokovich? The movie is based on a true story of a real person and real litigation over water contaminated with Chromium (VI).

Chromium (VI) is chromium in a +6 oxidation state, as it is in CrO3 and K2Cr2O7, and other heavy-weight chromium oxidizing agents. It's both toxic and carcinogenic. There aren't a lot of other heavyweight oxidizers out there, so this stuff is used frequently. One alternative that gets some use is KMnO4, potassium permanganate.

Oxygen gas (O2) and ozone (O3) also are used to oxidize stuff, although O2 is pretty slow for laboratory chemistry. However it is cheap and readily available, and on longer timescales it reacts readily with a lot of stuff, including things we don't want it to react with.....like the surface of a cut avocado or apple, or the metal surface of a shovel left out in the elements over the winter.

Diabetic ketoacidosis and bicarbonate

2008-11-25T15:50:00.001-08:00

Diabetics have a lot to worry about. Living with the disease surely isn't easy, and poor control of serum glucose levels can cause a wide variety of ugly, debilitating problems like blindness and circulatory problems leading to gangrene and amputations.

The seriousness of the disease was made real to me years ago by an experience I had in a hospital, where a previously perfectly lucid and cheerful old guy was admitted incoherent and super-sick. The doc ordered a bunch of diagnostic tests, but it was an easy diagnosis once the chem screen results were back: the guy's blood sugar was something like 400. His blood pH was like 6.9.

In situations like this there are a number of ways a person can end up dead. But one thing that causes concern is lowered blood pH. What can be done? Well, in addition to giving insulin when needed, sometimes lowly old bicarbonate (HCO3-) is also used to add buffer capacity to the blood and stabilize pH. At least, this is what I have heard. I don't have a good citation for this info.

Audience--especially those of you who have clinical or veterinary experience (pets get diabetic, too!)--can you help?

The old guy lived for a while longer, by the way. His ability to make sense was rapidly regained once his blood sugar returned to normal.

seein' fluoroscein

2008-11-23T14:08:00.000-08:00

The other day it came up that the dye making Mountain Dew yellow might be one and the same as the stuff that is used to color antifreeze. Seemed possible to me. I just happened to be familiar with this particular compound, called fluorescein, since I used it in grad school as a fluorescent tag on some molecules I was interested in.

As usual I searched Wikipedia, and I found a nice article about fluorescein. And according to my completely unverifiable web research, Mountain Dew is dyed with yellow number 5, and fluorescein dyes include yellow numbers 7 and 8.

The list of uses Wikipedia has for fluorescein is pretty amazing, though. In addition to its use as a dye and as a flluorescent chemical marker, it is also used in forensics to detect latent blood stains, in hydrology (dump it in at point A and look for it at point B, where you think the water flows), and medically to detect problems in the eyes and vascular system.

As to its use as a colorant in auto radiator fluid, I found an article posted on MedLine that suggests this was at least true in 1990, when the article was published. The gist of the article is that when given a dose of fluorescein similar to that which one would get from ingesting a toxic amount of antifreeze, men passed enough fluorescein in their urine that it could be detected with something called a Wood's lamp, which must be a uv lamp.

That's pretty weird but I think it's also pretty cool!

more on cholinesterase inhibitors

2008-11-19T20:53:00.000-08:00

Organophosphate pesticides are in the news again this morning.

A quick Wikipedia search left me sighing and unsurpised to see that all the culprits in the Oregonian's article--diazinon, malathion, and chlorpyrifos--are organophosphates and acetylcholine esterase inhibitors. My, oh my, I thought we'd finished on that topic.

Incidentally, I remember as a little girl getting my first garden and soon after buying my first cardboard can of Sevin. I also remember television ads for Lorsban and Dursban. It's an Iowa thing, seeing ag chemicals advertised during the evening news.

Gulf War Syndrome in the news

2008-11-18T21:41:00.000-08:00

Many of you may not remember how much fuss there was about a strange affliction that veterans of the first Gulf War reported soon after they returned from the Middle East. But in the early 1990s it was big news: Gulf War Syndrome. The synmptoms were of the sort it would be easy to dismiss because they aren't "threshhold" types of things where a person knows something is wrong. Instead they are vague and could conceivably be assigned to all sorts of causes: stress, PTSD, depression, etc.. Now--about what, 18 years later?--we have a report that suggests the syndrome is real and that the cause could perhaps be one of two things: pesticide exposure or exposure to substances used to protect against nerve gases.

As is usually the case the news didn't get super-specific about the names of things. So I checked Wikipedia to see what's there and was delighted to see they've got a nice description of the report contents on the site. To see it just search Gulf War Syndrome.

The pesticides were probably used to protect our soldiers from communicable diseases or simple irritation associated with insects, including sand flies. They were likely organophosphates or carbamates. These substances are acetylcholine esterase inhibitors. Aceetylcholine is a neurotransmitter that is removed from the synapse by acetylcholine esterase. The inhibitors block the enzyme, causing a buildup of acetylcholine in the synapse and altered nerve function. Hence the insects get screwed up and croak. Hence, perhaps with lots of exposure, people get symptoms related to nerve function. Such a syndrome is described for farm workers who get accidental poisoning, although symptoms of massive exposure don't sound quite the same as those described for the Gulf War Syndrome.

The other possible source of the problem are agents used to protect against nerve gases that could have been used as chemical warfare. These agents include Soman (mentioned in the Wikipedia article) and also more familiar agents like Sarin and VX....which we have manufactured in the U.S. and which are now being destroyed at places like the Umatilla Chemical Depot in Umatilla. Just like the pesticides, these substances are all acetylcholine esterase inhibitors. They act via a very similar biochemical mechanism.

Interestingly, the protection against such agents that may be implicated in the Syndrome is again an acetylcholine esterase inhibitor. It is called pyridostigmine. I'm not sure how it works but my guess is that it competes for binding to the acetylcholine esterase but does so reversibly, so it can block the nerve agent without causing severe or long-term effects. .....or maybe it does. ....maybe in combination with exposure to other acetylcholine esterase inhibitors.

Check out the structures for pyridostigmine and for the pesticide sevin on Wikipedia. See the similarity?

It's a fascinating and sad story that continues to unfold.

Markovnikov: theme and variations

2008-11-18T21:33:00.001-08:00

I did some scouting around about how addition reactions involving a cyclic intermediate can lead to Markovnikov products (products that you would predict would form from Markovnikov's rule, based on a carbocation intermediate). The explanation as I understand it goes like this:

Fact: cyclic alkenes that undergo addition of halogens like Br2 end up with the halogen atoms trans in the product. Similarly halohydrin formation results in trans configurations.

Fact: a carbocation mechanism does not agree with the statement above, so it does not explain the reaction.

Fact: cyclic intermediates such as the bromonium ion can be appealed to, and provide an adequate explanation for the trans stereochemistry. So we use this mechanism.

Fact: these reactions yield Markovnikov products.

It's these last two facts that seem contradictory, unless you take a more nuanced view of the cyclic intermediates. Imagine that these intermediates are not exactly symmetrical. If they are shifted a bit so that there is some carbocation character in the cyclic intermediate, then we could explain both the trans orientation of the added groups and also the Markovnikov product formation. Which is the best explanation there is.

the white zombie

2008-11-13T20:59:00.000-08:00

Want an electric car? You don't have to compromise when it comes to acceleration:

http://www.youtube.com/watch?v=zp_jwE0KdOk&feature=related

That would be 103 mph. Check out Oregon Field Guide's rebroadcast on Sunday evening (6:30) if you want to see more.

an inconvenient admission

2008-11-13T20:19:00.000-08:00

I've talked with classes about climate change for years but I have never watched An Inconvenient Truth. By the time the movie came out I was pretty sure that much of the science that would be discussed would be stuff I'd already heard about. Plus, anybody who knows me very well knows I'm famously impatient with movies.

Today's Al Gore-style slideshow presentation by Bill Bradbury was full of new images for me. I don't know how closely the slideshow follows the movie, but the images were moving, sometimes beautiful and of course sometimes shocking. I was pleasantly surprised at the injection of local information and our presenter's enthusiasm and interest in his audience. Nicely done, Mr. Bradbury.

But--having heard the criticisms of the movie--I was on the lookout for overgeneralizations or convenient (yet terrible) coincidences, and I have to say I thought I recognized a few instances of that. It's a dificult challenge and serious responsibility to bring these messages to people, and I hope that two things happen: 1. The integrity of the presentations will go from good to great by continual scrutiny of what gets said and shown, to be sure that no exaggeration is allowed to creep in, and 2. The message will change as the audiences hearing it become more informed and more accepting of the science, from a persuasive "this is actually happening and you should be concerned" speech into a "here's how we can make change."

de colores

2008-11-11T17:30:00.000-08:00

The fall colors are just about gone for the year, and leaves are falling fast. I love fall. This time of year the larches in Shevlin Park have gone from green to yellow and are in the midst of dropping their needles. Big sections of the park are covered with a carpet of yellow. As always, I enjoy the scene as a regular person, thinking stuff like "gee, that's pretty!" and "wow, cool, needles falling off a conifer!" but I also can get geeky and enjoy the scene from a chemist's viewpoint. "Gee, anthocyanins!" and "what's the name of that protein that makes the leaves actually drop?!" and "why do some trees have so many reds when others in the same habitat are so yellow?"

It's delightful to think that the bright colors so noticable at the peak of fall are actually hiding behind the greens of the chlorophylls all summer long. While we don't eat tree leaves (do we?) we do hunt down highly-colored fruits and vegetables that contain pigments like lycopene and beta carotene because they are health-promoting. What do all these colored substances have in common? They're typically highly-conjugated alkenes. Lots of double bonds, large molecules, lots of resonance structures, loosely-held electrons, ready to be promoted to higher energy levels with just a minimum-energy photon: one that falls into the range of the visible. This is chemically why they are colored. For those of you who understand: small HOMO LUMO gaps.

These same double bonds make those fruits and vegetables we love susceptible to darkening from oxidation if they're left out in the air for too long. I have heard it suggested that tree leaves may contain some of these compounds to protect them from the damage of high-intensity light in the visible and uv range. That they absorb the energy of the visible light and in so doing keep other more critical molecules from being damaged. How curious.

Maestro Chem Educator Bassam Shakhashiri has a great page on fall colors here:
http://scifun.chem.wisc.edu/chemweek/fallcolr/fallcolr.html

Here's a link to a journal article about anthocyanins, which are red and purple, as protective compounds:
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=125091

And about that supposed protein I thought was involved in leaf dropping: the compound I thought responsible is abscisin.....actually abscisic acid. It's not a protein (as is suggested vaguely by the original name). And turns out Wikipedia says it's not even thought to be involved in leaf drop anymore, even though that's how it got its name.

Bill Bradbury to visit Thursday

2008-11-07T16:18:00.001-08:00

News! Secretary of State Bill Bradbury is coming to class next Thursday! However we need to start earlier than our usual meeting time (his schedule is busier than ours, and it is of course our pleasure to host him at his convenience). He will start at 12:00, and be done by/around 1:30. If you can possibly be here on time, be here. If you come late, we'll invite you in (and he'll know the situation so you don't need to feel sheepish).

We can do our quiz later.

Tell your friends. Since Tuesday is Veteran's Day there is no way for me to deliver this message by voice to the entire class. If any of you have questions about this send me an email or leave a comment here.

cis/trans isomerism: a tasty tidbit

2008-11-06T15:38:00.000-08:00

Do geometric stereoisomers matter? You bet. Here's one reason why:

All the things we hear about trans fats in our diets relate to the presence of trans-alkenes in the fats we eat. Nearly all (but not all) naturally occurring fats are cis. The majority of the trans fats we eat come from fats that have been manipulated by hydrogenation: an addition of hydrogen across the double bonds. If a particular alkene group does not get fully hydrogenated during this process, it can switch from the cis to trans orientation. New industrial processes are allowing us to hydrogenate fats in ways that avoid this problem.

The amount of unsaturation in dietary fats has traditionally been determined by finding the "iodine number" or "iodine value." This number is calculated by reacting iodine with the fats, until a purple color shows up. The presence of the iodine color indicates there are no more groups on the fat that will react with it. The reaction that normally consumes the iodine is an addition reaction (of X2, in this case I2) across the double bond.

Those of you lucky enough to be in Organic this fall will discuss this particular reaction type in class next Thursday. I can hardly wait!

studentdoctor.org

2008-11-04T16:26:00.000-08:00

Interested in Medical or Dental School or Pharmacy? A former student pointed me to studentdoctor.org a while back. You may want to investigate the conversations that are out there.

Exams are graded and scores posted!

2008-11-01T16:35:00.001-07:00

Enjoying crystallization, even on weekends

2008-11-01T11:23:00.000-07:00

Crystals have been on my mind a lot the last week or two.

I was asked a fun question this week about the formation of snowflakes. This morning I see that the Cascades are socked in, hidden behind heavy clouds, and I'm beginning to think about snow again, as I look forward to ski season. Last Friday and the week before the Organic class was doing recrystallization in lab. I've got their reports on my desk, ready to grade. My introductory class has been learning about ions and ionic compounds, and the resulting crystals. Crystals are everywhere!

The question I was asked is about snowflake types, and whether there is a connection between snowflake type and the temperature where the snowflake forms.

I'm no expert on this stuff, and I doubt the situation is simple. I have browsed Barnes and Noble enough to know that there are field guides to weather, and that they include some neat stuff about snow, but I don't own one of these books and I haven't ever taken the time to dig very far into it. Experience tells me that cold and dry air leads to tiny and sparkly-perfect but tiny crystals (champagne powder), while wetter and warmer conditions can lead to big flakes.

I would guess that both temperature and humidity would have a dramatic effect on snow type. Other things like shearing from winds might also matter.

As I think about this now I'm trying to link the formation of snow crystals to what we see in the lab, in solutions --which may be importantly different!-- but to make big crystals in the lab we cool the solution slowly and don't disturb the flask while they form. This results in a situation where there is more opportunity for crystal growth and the nucleation events (which is when the crystals start forming) are more rare, so there are fewer, bigger crystals. If the solution is cooled rapidly, you get lots of nucleation and little chance for crystals to grow.

Wikipedia has a good and pretty technical page on snow, here.

Regular, Premium, Superpremium: is it worth the extra cost?

2008-10-26T20:36:00.000-07:00

Making a decision about whether to spend the extra money on premium or superpremium gasoline involves a number of factors, some of which aren't very easily related to the composition of the gas. If you're the kind of person who spends Sunday afternoons massaging wax into the hood, your decision might not be related to chemistry.

Regular and premium gases are all mixtures, and they do differ in composition. One possible difference between the regular gas and the more expensive versions involves the type and quantities of additives such as detergents in the gas.

Another difference is reflected in the Octane rating. These are the numbers (87, 92, 95) that you may see on the price displays, or on the pumps themselves. As a student of organic chemistry you now know that octane is an 8-carbon alkane. The octane rating is not about octane content, though. Octane rating is about the combustion characteristics of the gasoline. The number comes from:

Isooctane (which IUPAC would call 2-methylheptane) is given the "ideal" rating of 100.
n-Octane (no branches) is given a value of zero.

A gas with an octane rating of 87 burns with the same characteristics as a blend of 87% isooctane, and 13% n-octane.

Note that these two compounds are related to one another as constitutional isomers. Yet they are importantly different in their behavior in the engine. While these alkanes would be hard to tell apart if your burned them in the lab, in the highly optimized systems of our cars the differences between them become significant.

In case you're curious, I buy the cheap gas. In the owner's maual for my 2003 Civic I am advised that gasolines with greater than an 85 Octane rating are adequate for my car, and that using gasolines with Octane ratings greater than 87 will not provide a performance advantage or result in a longer life for my car.