watch your ash

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.

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

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?

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

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

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

...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

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

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

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.

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!

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.

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.

the white zombie

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

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

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

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

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

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!

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.

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

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.