moleculeoftheday | August 13, 2008Trying to think of a molecule tonight, my friend suggested "pick an ugly one no one wants anymore...a clearance rack molecule." I immediately went to chlorinated solvents. They're in the backwater now, right? Carbon tetrachloride sure has a bad rep. I figured most of the organochlorides, except for the ubiquitous lab solvents, would, too. I was wrong.
Perchloroethylene, or "perc," is a dry cleaning solvent. A few years back, I was surprised to learn that the non-chemistry nerds in my family knew of it, and I came to learn that grandpa owned a dry-cleaning shop back in the day, where he, in…
moleculeoftheday | August 11, 2008Pyrene is a simple, four-fused benzene PAH:
What makes it neat is how it interacts with light. In particular, it's got some unusually sharp UV bands that are sensitive to solvent polarity. Additionally, the excited state dimer exhibits some especially unique photochemistry of its own, providing a way to sense whether you've got two stacked pyrenes together.
moleculeoftheday | August 7, 2008I love reading lists of fragrance chemicals. The assignment of pleasant, qualitative fragrance descriptions to chemicals with hard-nosed, rigorous functional group names always makes me giggle a little. Acetophenone, for instance, smells of orange blossoms. Today, I came across one that has both in the name: dewy propionate:
The Good Scents Company reports dewy propionate smells of dew, which I think is nonsense. Because odor is subjective, and because a surprising amount of overlap exists between unrelated things, odorants are usually reported with a few characteristics (or more). Flowery,…
moleculeoftheday | August 5, 2008If you have been reading SB long enough to remember the DonorsChoose promotion, you might be interested in this. It's videos of scientists talking about their first experiments and why they like science, and if you vote on the one you like best, DC gets a buck. Check it out here.
moleculeoftheday | August 4, 2008Erythorbic acid is a common food additive:
It is a particularly good antioxidant, much like Vitamin C, and can be used to suppress the formation of carcinogenic nitrosamines in hot dogs and other cured meats.
moleculeoftheday | July 29, 2008As I mentioned yesterday, derivatives of arylethylamines - phenethylamine in particular - are drug targets in depression, but a sophisticated mechanistic understanding remains elusive. When you have some idea what molecule you'd like less of, a favorite trick is to find something (an "inhibitor") that binds to some enzyme in the pathway to your molecule and mucks up the works.
Of this sort of drug, the first class is "reversible" inhibitors, which just hang out like hands in mittens. They nestle in an active site and keep other molecules from binding. As the drug is metabolized and its…
moleculeoftheday | July 27, 2008An aromatic ring, two carbons, and a nitrogen will get you a lot of places.From hallucinogens to decongestants to speed, the arylethylamine moiety works because it tickles neurotransmitter receptors. The effects of the assorted monoamine neurotransmitters are as varied as those of the drugs that mimic it - hypertensive, euphoriant, the works. This is part of how we try to explain to ourselves how antidepressants that block the breakdown of these neurotransmitters (MAO inhibitors) or their reuptake (SSRIs) might be working. What might happen if you took something that depleted some of those…
moleculeoftheday | July 24, 2008Choline is an ubiquitous vitamin. Interestingly, it makes a number of "deep-melting eutectics" with other dirt-common chemicals like Urea.
When complexed in lecithin, it makes a nice edible detergent. Mayonnaise wouldn't be possible without it!
moleculeoftheday | July 22, 2008A lot of reactions with nucleophiles' rates are determined by how good a leaving group you have. For leaving group reasons and others, DMAP is a great organocatalyst:
I am a sucker for non-pharmaceutical chemicals with their own domains, so please enjoy dmapcatalyst.com.
moleculeoftheday | July 18, 2008As was mentioned in the comments to my entry on a refrigerant Monday, what we use has changed quite a bit over the years. If you don't know how a fridge or AC works (they're the exact same thing), here's what happens: know how evaporation something makes things cooler (e.g., sweat?). Condensing something makes things hotter by the same principle. Refrigeration involves evaporating something and using the cold for what you want, then moving the vapor somewhere and compressing it (turning it into hot liquid) and dumping that heat somewhere else. Then you evaporate it again and get some more of…
moleculeoftheday | July 14, 2008I really, really love refrigeration. I will go so far as to say that it's the most important invention of the modern era. More than internal combustion, nuclear bombs and power, or electrification, refrigeration defines the US. If you're like most Americans, you preside over at least THREE refrigeration units - one in the house, one in the kitchen, one in the car. The Central Valley in CA, DC, Las Vegas, Phoenix, Dallas, Houston, Atlanta - a huge swath of the country would look very different without AC. Not to mention your grocery store.
Awhile back, we began getting concerned about the…
moleculeoftheday | July 2, 2008Dimethyl fumarate is a fungicide and sensitizer:
It appears it's made its way into some Chinese-manufactured leather sofas, and caused ill effects consistent with a sensitizer (basically an allergen) in some people.
Product-safety stories: they feel almost idyllic - they hearken back to last year, when all you worried about was contaminated imports and not global financial collapse.
moleculeoftheday | June 30, 2008In the news this week: aminopyralid:
Aminopyralid is an herbicide that may have made its way into some manure destined for home gardens and may have resulted in inferior produce. Interestingly, they think it's in manure not because of topical contamination, but via animals that ate contaminated silage:
It appears that the contamination came from grass treated 12 months ago. Experts say the grass was probably made into silage, then fed to cattle during the winter months. The herbicide remained present in the silage, passed through the animal and into manure that was later sold. Horses fed on…
moleculeoftheday | June 25, 2008Acetaldehyde is an intermediate metabolite of alcohol:
It's the first stop for ethanol on the way to benign acetate. Aldehydes tend to be short-lived and toxic species because of their reactivity, and acetaldehyde is no different. On the way to your hangover, though, alcohol goes from ethanol to acetaldehyde (via alcohol dehydrogenase) to acetate (via aldehyde dehydrogenase). Many east Asians, interestingly, lack an adequate supply of aldehyde dehydrogenase, and they experience a sort of accelerated hangover on consumption of even moderate amounts of alcohol.
moleculeoftheday | June 24, 2008Ornithine is an amino acid that occurs naturally in the body, but mostly as an intermediate in your body's nitrogen disposal cycle.
It rarely occurs in proteins, and we weren't sure why until some people tried to make some ornithine-containing polypeptides. Turns out it's not very well behaved, since a six membered ring will form, given any opportunity. It self-cleaves.
moleculeoftheday | June 18, 2008Chemistry spans orders of magnitude in terms of polarity. Many of the organic guys who read this work on stuff that never would dissolve in water (which becomes something of a pain when you try and make that something into a drug for aqueous things like people). And the biologists work on stuff that would just maybe dissolve in DMSO, but not even methanol, otherwise. Polarity defines chemistry. I know techniques that will help me isolate gobs of biomolecules out of water, and gobs of organic molecules out of ether. It's that intermediate, medium solubility stuff that's a pain!
Propidium is a…
moleculeoftheday | June 16, 2008That was probably the longest break ever. I'm trying to do better, but writing up multiple papers and grant applications, along with a pretty intense summer travel schedule just haven't augured well for the blogging. Onward and upward: tetrazole.
Tetrazole is one of those molecules I didn't believe existed off paper the first time I saw it. Lots of electronegative atoms in a row (usually nitrogens and oxygens) typically indicates something unstable, if not explosive, but aromaticity does its work here, and tetrazole works well. So well, in fact, that it works in that mild-as-mothers-milk…
moleculeoftheday | June 1, 2008Even in the case of floating severed feet, apparently!
Ebbesmeyer said it may not be a coincidence they were found in the same area. He said left shoes and right shoes often tend to wash up at different times at different places because they float differently.
He added that there are beaches that collect mostly rights and others that collect mostly lefts because the winds or currents sort out left and right foot wear.
moleculeoftheday | May 31, 2008I've been thinking more about energy sources since oil was at $50/barrel . Since we reached the staggering heights of the last few months, I've been puzzling even more over what people will move to next.
Key to understanding this stuff is how much energy it takes to get your source in a useful form. A paper from the 1980's is illustrative: oil cost more than 10 times less energy to get from discovery to usable energy in the 40's than in the 70's. A lot of technologies barely broke even. If anyone has a newer version of this work, I'm interested.
For better or worse, I think you're going to…
moleculeoftheday | May 29, 2008Gasoline and diesel engines operate using very different philosophies. In a gas engine, a spark ignites a compressed fuel-air mixture; in a diesel, air is compressed and gets very hot, and fuel is injected, resulting in ignition.
In the case of gasoline, the activation energy to start the fire is supplied by a high-energy spark. With diesel, the heat of compression must be sufficient to start the fire. For this reason, gas has an "octane number" (a measure of how difficult it is to ignite) and diesel has a "cetane number" (a measure of how easy it is to ignite). Low-octane gas can burn…