It's war on my dad's farm: humans versus Mephitis mephitis, night time maneuvers complete with chemical weapons. Currently the skunks hold the high ground.
Last night my brother's dog threatened a skunk, with predictable results. The collateral damage included my shoes and feet. The Reverend's Wife produced a bottle of something guaranteed to elminate the smell and we decontaminated me and the dog on the lawn. I was more cooperative about being hosed down. The odor was overpowering, and even after twice deskunking me, my kids swore I still smelled of skunk.
Skunk musk is a mixture of low molecular weight thiols, sulfur containing compounds that have the basic structure ☐-S-H (where the box represents a functional group, such as methyl or butyl), and related compounds called thioacetates. Most thiols have a characteristic, and awful, odor. (Thioacetates don't smell quite so badly.) The simplest thiol is methane thiol, also known as methyl mercaptan, which is used to spike methane (natural gas) so that leaks can be detected. (Methane is actually odorless.) Humans can detect thiols at very low concentrations, less than 1 ppm, which explains why my kids could still pick up the odor.
Skunk odor can be neutralized by converting the thiols to less odiferous molecules. One way this can be accomplished is by reacting the thiols with hydrogen peroxide, which oxidizes the thiol to a sulfonic acid ( ☐-SO3H), which has virtually no odor. Bleach (a strong oxidizing agent) will work as well. A similar technology is used to remove thiols from industrial waste water, where the thiols are converted to disulfides ( ☐-S-S- ☐), which are oils that separate easily from the water.
Mercaptan comes from the Latin mercurium captans, something that seizes or captures mercury. Sulfur reacts very effectively with mercury, and one way to clean up a mercury spill is to sprinkle sulfur on the mercury. Thiol is Greek for sulfur.
If you need a recipe to remove skunk odor, try Humbolt's list. I can personally vouch for the effectiveness of the pet/human version. Note that tomato juice is not particularly effective.
1-para-methen-8-thiol is an uncharacteristically and pleasantly scented thiol more commonly known as grapefruit mercaptan.
More demystified chemical perils of summer...
Field of Science
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Change of address1 year ago in Variety of Life
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Change of address1 year ago in Catalogue of Organisms
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Earth Day: Pogo and our responsibility1 year ago in Doc Madhattan
Urrrrrr - it itches!
The spring was cold and so the itch to get outdoors once the warm weather arrived was hard to resist. As moms will tell you, scratching just makes the itching worse, and scratching even metaphorical itches can raise welts. Ask anyone who has heeded the siren call of summer and ended up with hives, or worse yet, encountered a patch of poison ivy.
My niece and I took a tour last week of the Mutter Museum in Philadelphia which has a great collection of wax models of dermatological pathology, used for teaching students in the days before slides and PowerPoint, including hives or urticaria. The name comes from the Latin for nettle, and the resulting skin wheals certainly bear some resemblance to nettle stings (as my youngest can attest after a close encounter with that plant). Histamine leaking from mast cells in the skin is responsible for hives' principal misery - itching.
True misery is reserved for those who have contacted Toxicodendron radicans - poison ivy - or a relative. These plants produce urushiol, which binds tightly to proteins in the skin. Molecules like this are called haptens, which comes from the Greek "to fasten". Antibodies don't recognize the small molecule until it fastens onto its target. Then the body reacts, in this case triggering the characteristic linear rash, and keeps reacting until the invader detaches from its binding site.
Despite the similarity in names between urticaria and urushiol, they come from different roots. Urushiol was first isolated from the Japanese lacquer tree - the urushi - by a Japanese chemist, Miyama.
Other haptens can react with the same sites as urushiol, including substances found in mango skin and fresh cashew nuts, with similar unfortunate consequences.
Urushiol isn't just a weekend gardener's nuisance, but can cause serious problems for fire fighters in working brush fires in areas such as the California hills, where poison sumac, another urushiol producing plant, thrives. The chemistry gives some clues to helping prevent and treat urushiol reactions. Application of an organic derivative of an absorbent mineral (bentonite) can soak up and trap any oil before it reaches the skin and binds- this is the principal behind the commercial product Ivy Block. Alternatively, something that binds strongly to the urushiol target but is not itself a hapten could act as a preventative. D-Limonene, found in citrus skins, has been floated as a possibility, but I couldn't find any evidence that it works!
Once the stuff has bound, you just have to wait it out. It takes a couple of weeks for the bulk of the urushiol-protein complexes to break down. In the meantime, steroids can reduce the inflammatory reaction and histamine blockers, H1 (like Benadryl) or H2 (Tagamet or Zantac) can provide some relief from the itch.
My niece and I took a tour last week of the Mutter Museum in Philadelphia which has a great collection of wax models of dermatological pathology, used for teaching students in the days before slides and PowerPoint, including hives or urticaria. The name comes from the Latin for nettle, and the resulting skin wheals certainly bear some resemblance to nettle stings (as my youngest can attest after a close encounter with that plant). Histamine leaking from mast cells in the skin is responsible for hives' principal misery - itching.
True misery is reserved for those who have contacted Toxicodendron radicans - poison ivy - or a relative. These plants produce urushiol, which binds tightly to proteins in the skin. Molecules like this are called haptens, which comes from the Greek "to fasten". Antibodies don't recognize the small molecule until it fastens onto its target. Then the body reacts, in this case triggering the characteristic linear rash, and keeps reacting until the invader detaches from its binding site.
Despite the similarity in names between urticaria and urushiol, they come from different roots. Urushiol was first isolated from the Japanese lacquer tree - the urushi - by a Japanese chemist, Miyama.
Other haptens can react with the same sites as urushiol, including substances found in mango skin and fresh cashew nuts, with similar unfortunate consequences.
Urushiol isn't just a weekend gardener's nuisance, but can cause serious problems for fire fighters in working brush fires in areas such as the California hills, where poison sumac, another urushiol producing plant, thrives. The chemistry gives some clues to helping prevent and treat urushiol reactions. Application of an organic derivative of an absorbent mineral (bentonite) can soak up and trap any oil before it reaches the skin and binds- this is the principal behind the commercial product Ivy Block. Alternatively, something that binds strongly to the urushiol target but is not itself a hapten could act as a preventative. D-Limonene, found in citrus skins, has been floated as a possibility, but I couldn't find any evidence that it works!
Once the stuff has bound, you just have to wait it out. It takes a couple of weeks for the bulk of the urushiol-protein complexes to break down. In the meantime, steroids can reduce the inflammatory reaction and histamine blockers, H1 (like Benadryl) or H2 (Tagamet or Zantac) can provide some relief from the itch.
Indolent Molecules
I heard a colleague talk today at the MidAtlantic Regional Meeting of the ACS about his work with fluoroquinones. These molecules (which despite their name contain no fluorine) fluoresce, that is they "glow" when exposed to light. The process can be short circuited by binding another molecule, a quencher, to fluoroquinone. The research discussed the quenching behavior of tryptophan. Tryptophan is an amino acid, one of the building blocks of proteins. 
Structurally, it's an indole; an aromatic six-membered ring fused to a five-membered ring containing a nitrogen forms the core.
Tryptophan is thought to induce sleep - and is often blamed for post-Thanksgiving meal naps. Melatonin, which also play a role in sleep regulation, is also an indole.
The indoles of chemistry get their name from the Latin for indigo, the dye from which the basic indole structure was first isolated. The indolence which some indoles induce has a different etymological root, dolorens - grief or pain.
Structurally, it's an indole; an aromatic six-membered ring fused to a five-membered ring containing a nitrogen forms the core.
Tryptophan is thought to induce sleep - and is often blamed for post-Thanksgiving meal naps. Melatonin, which also play a role in sleep regulation, is also an indole.
The indoles of chemistry get their name from the Latin for indigo, the dye from which the basic indole structure was first isolated. The indolence which some indoles induce has a different etymological root, dolorens - grief or pain.
Agonists and Allergies
My mast cells are leaking histamine and I am miserable. Histamine is a small molecule that binds to receptors in a wide variety of tissues including, alas, the respiratory system. It happens to increase vascular permeability - in other words, it's causing fluids to leak through my capillilary walls and into my nose. Sigh.I'm fighting back by taking a histamine antagonist, diphenhydramine to be precise. Antagonists bind to a receptor and block its response, in this case inhibiting the H1 histamine receptors in the respiratory tract (H2 receptors cluster in the gastrointestinal tract - and so H2 antagonist, like Zantac, are used to treat heartburn). Agonists are molecules that bind to a receptor and cause a response. Why would you want to take something that binds to a histamine receptor and provoke a response? Turns out there are a couple of drugs that are histamine agonists, including one for Meniere's disease and another that may have theraputic potential for diabetes.
What does the term amine have to do with camel dung? Read about it here.
The Carbon Footprint of that Computer
Someone asked me over lunch yesterday if I was worried about global warming. "Worried enough to ride my bike to work through the hills of Bryn Mawr!" was my response. The conversation eventually turned to how much energy computers used - should you turn them off to save energy (and thereby reduce the amount of CO2 being dumped into the atmosphere)? Their IT support had said to leave the machines on, on the grounds that the amount of energy used to restart them outweighs any savings from turning them off at night. I thought this was not true, and some back of the envelope calculations suggest shutting down from the night (even putting the machine to sleep is not sufficient) is 10 times more energy efficient than leaving it on.
Powering up my machine takes 3 minutes at full tilt. At 120 watts, this uses up about 22 kJ of energy. If I left it in sleep mode all night (at 3.5 watts), it uses 228 kJ. I save about 200 kJ of energy, if I shut it off for the night, rather than just put it to sleep. It comes to about 44 pounds of carbon dioxide a year. It's a drop in the bucket compared to the per capita amount of carbon dioxide produced in the US (19.8 metric tons in 2003) - about 0.1%.
If you want to check your own carbon footprint, the EPA has a calculator.
Powering up my machine takes 3 minutes at full tilt. At 120 watts, this uses up about 22 kJ of energy. If I left it in sleep mode all night (at 3.5 watts), it uses 228 kJ. I save about 200 kJ of energy, if I shut it off for the night, rather than just put it to sleep. It comes to about 44 pounds of carbon dioxide a year. It's a drop in the bucket compared to the per capita amount of carbon dioxide produced in the US (19.8 metric tons in 2003) - about 0.1%.
If you want to check your own carbon footprint, the EPA has a calculator.
Acetylcholine and Cranky Suburbanites
I went to work today sporting a pair of molecular earrings: serotonin and norepinephrine to be precise. Two non-chemist colleagues spotted them and wondered about the significance of the molecules (and where to get them!). "Serotonin for serenity, norepinephrine for energy." "Ah, you're in balance then!" When I walked past ten minutes later they were browsing the molecular earring site and trying to figure out how to pronounce "acetyl" (as in acetylcholine). The site says that acetylcholine can promote creativity, learning, dreaming and memory. In passing, I noted that many pesticides are acetylcholinesterase inhibitors, they block the breakdown of acetycholine, which can have nasty effects on the body. Which led one colleague to wonder if that was why "suburban cul-de-sacs were such cranky places!"
Acetylcholine is a neurotransmitter, a small molecule that plays a role in transmitting signals along neurons. Originally found to stimulate the vagus nerve (responsible for controlling heart rate, among other things), it was christened vagustoff by Otto Loewi who eventually won the Nobel prize for its discovery. Curare blocks the receptor sites for acetylcholine, thus preventing muscle contraction (and causing respiratory arrest). You can have too much of a good thing, the venom of black widows causes synapses to be flooded with acetylcholine.
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vagus is from the Latin for wandering, which is what that nerve does...
Acetylcholine is a neurotransmitter, a small molecule that plays a role in transmitting signals along neurons. Originally found to stimulate the vagus nerve (responsible for controlling heart rate, among other things), it was christened vagustoff by Otto Loewi who eventually won the Nobel prize for its discovery. Curare blocks the receptor sites for acetylcholine, thus preventing muscle contraction (and causing respiratory arrest). You can have too much of a good thing, the venom of black widows causes synapses to be flooded with acetylcholine.
______
vagus is from the Latin for wandering, which is what that nerve does...
Weird Words of Science 12: A need for speed
The nectar busily gathered by the bees outside my window has a high sucrose content. The bees add the enzyme invertase to the nectar to catalyze the inversion of the sucrose to glucose and fructose that are the major sugars in honey. Humans can speed up the same reaction by heating the syrup or by adding a touch of acid.
Both enzyme and catalysis are lofty words lifted by scientists in the 19th century to serve more prosaic ends.
Enzyme's first meaning in the bread used for the Eucharist in the Greek Orthodox tradition. It means "leavened". It's not such a stretch to borrow the word to describe stuff that encouraged cellular reactions to proceed, what had been called the ferment.
Catalysis was originally used to describe the collapse of a nation, its origins can be traced to the mid 17th century. It comes from the Greek "to loosen". In the 19th century, Berzelius suborned the term to describe the process by which chemical reactions are facilitated. Catalysts participate in a reaction, but are in the end are restored to their original form, like molecular Phoenixes. Why did Berzelius settle on this term? Did he hope to imply that the constraints which bound the reaction to a slow pace are loosened by a catalyst?
Both enzyme and catalysis are lofty words lifted by scientists in the 19th century to serve more prosaic ends.
Enzyme's first meaning in the bread used for the Eucharist in the Greek Orthodox tradition. It means "leavened". It's not such a stretch to borrow the word to describe stuff that encouraged cellular reactions to proceed, what had been called the ferment.
Catalysis was originally used to describe the collapse of a nation, its origins can be traced to the mid 17th century. It comes from the Greek "to loosen". In the 19th century, Berzelius suborned the term to describe the process by which chemical reactions are facilitated. Catalysts participate in a reaction, but are in the end are restored to their original form, like molecular Phoenixes. Why did Berzelius settle on this term? Did he hope to imply that the constraints which bound the reaction to a slow pace are loosened by a catalyst?
Turning Sugar Inside Out
This week's worksheet in general chemistry asks my students to analyze the chemical kinetics (the speed) of this reaction:
C12H22O11 (sucrose or table sugar) + H2O (water) -> C6H12O6 (glucose) + C6H12O6 (fructose).
It's called the inversion of sucrose, and the resulting mix of glucose and fructose is tagged invert sugar. The name suggests that table sugar has been turned inside out or perhaps upside down, but in fact it's simply been split into two simpler sugars. The inversion is not of the sugar itself, but of the way it bends polarized light. If you pass a beam of polarized light through a solution of regular table sugar, the light will "rotate" or bend to the left. The mixture of glucose and fructose "inverts" the rotation, and bends the beam to the right.
Invert sugar is less like to crystalize than regular sugar, making it ideal for sweetening candy or jams. The reaction in the absence of a catalyst is slow at room temperature, but can be completed . The simplest way to catalyze the reaction is with an acid, often citric acid or ascorbic acid (Vitamin C), and many jam recipes call for one or the other.
So why do these compounds "bend" polarized light? Like many biological molecules, they are chiral or handed. The right handed or D form bends the polarized light toward the right, the left handed form (denoted L) left.
Another name for the D form of glucose is dextrose, named for the direction in which it bends polarized light.
C12H22O11 (sucrose or table sugar) + H2O (water) -> C6H12O6 (glucose) + C6H12O6 (fructose).
It's called the inversion of sucrose, and the resulting mix of glucose and fructose is tagged invert sugar. The name suggests that table sugar has been turned inside out or perhaps upside down, but in fact it's simply been split into two simpler sugars. The inversion is not of the sugar itself, but of the way it bends polarized light. If you pass a beam of polarized light through a solution of regular table sugar, the light will "rotate" or bend to the left. The mixture of glucose and fructose "inverts" the rotation, and bends the beam to the right.
Invert sugar is less like to crystalize than regular sugar, making it ideal for sweetening candy or jams. The reaction in the absence of a catalyst is slow at room temperature, but can be completed . The simplest way to catalyze the reaction is with an acid, often citric acid or ascorbic acid (Vitamin C), and many jam recipes call for one or the other.
So why do these compounds "bend" polarized light? Like many biological molecules, they are chiral or handed. The right handed or D form bends the polarized light toward the right, the left handed form (denoted L) left.
Another name for the D form of glucose is dextrose, named for the direction in which it bends polarized light.
Dandelion Wine
At a party Saturday night someone mentioned a rumor about extracting illegal drugs from dandelions. This was news to me, I hadn't thought that dandelions had all that much to offer pharmacologically. Google didn't produce any hits, nor did my students know anything (though they did tell me that on MythBusters they'd made nitrous oxide from ingredients you could obtain at home). There is some evidence from rat models that dandelion extracts can interfere with antibiotic absorption (particulary those in the same class as ciprofloxacin), and it has potential for control of blood sugar, but I can't find anything in PubMed more interesting than that.
How did the leopard get it spots?
Biomorphogenesis, the process by which biological forms arise during development, is a fascinating area that crosses many fields, including computer science, mathematics, biology and chemistry. How do the stripes develop on a zebra? Alan Turing, one of the first computer scientists and the man who developed the computational engine that cracked the Enigma code in World War II, took on this problem in the early 1950s. In 1952 he published, "The Chemical Basis of Morphogenesis" [Phil. Trans. R. Soc. London B 1952, 237, 37-72]. He posits in this paper that oscillating chemical reactions, such as the Belousov-Zhabotinsky reaction, could lead to temporal-spatial differences in pigmentation. You can see why this might be the case in this animation of the reaction.
The BZ reaction is complex, the proposed mechanism consists of almost 20 steps - much more complex than those we are discussing in general chemistry this week! You can watch the BZ reaction in this video clip - the color changes look like magic.
The BZ reaction is complex, the proposed mechanism consists of almost 20 steps - much more complex than those we are discussing in general chemistry this week! You can watch the BZ reaction in this video clip - the color changes look like magic.
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