Tuesday, November 25, 2008

Chromium Six

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

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.

Sunday, November 23, 2008

seein' fluoroscein

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!

Wednesday, November 19, 2008

more on cholinesterase inhibitors

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.

Tuesday, November 18, 2008

Gulf War Syndrome in the news

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

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.

Thursday, November 13, 2008

the white zombie

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


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

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."

Tuesday, November 11, 2008

de colores

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:

Here's a link to a journal article about anthocyanins, which are red and purple, as protective compounds:

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.

Friday, November 7, 2008

Bill Bradbury to visit Thursday

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.

Thursday, November 6, 2008

cis/trans isomerism: a tasty tidbit

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!

Tuesday, November 4, 2008


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.

Saturday, November 1, 2008

Exams are graded and scores posted!

Enjoying crystallization, even on weekends

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.