moleculeoftheday | September 11, 2006A diverse series of compounds, known as the phenethylamines, are created from the amino acid tyrosine (bold, at bottom, below). In vivo, things like adrenaline and dopamine are generated. Small amounts of tyramine are also generated. These are particularly concentrated in fermented foods like cheese, beer, wine, and pickles. Normally, the body can process these with facility; an enzyme called "monoamine oxidase" exists to do just this. If a food with a large amount of tyramine is ingested, though (mistletoe, apparently, fits this bill), or the MAO pathway is compromised (certain, older…
moleculeoftheday | September 8, 2006And I don't have the patience or energy to get it to right now. Come back Monday for something fun, hopefully I'll have it sorted by then.
moleculeoftheday | September 7, 2006There are two kinds of fatty acids: saturated and unsaturated. Saturated fatty acids have no carbon-carbon double bonds (-CH=CH-), they have only (-CH2-CH2-) single bonds. Notice that carbons only involved in single bonds have one more hydrogen than those involved in a double bond. They are "saturated" with hydrogens.
Double bonds come in two forms: cis and trans. A cis double bond has both large substituents (the carbons in the fatty acid chain) on the same side of the double bond. A trans double bond has large substituents on either side of the double bond. Below is a picture of three 18-…
moleculeoftheday | September 6, 2006
Longtime readers will recall this Palahniuk-inspired image from my articles on the old site about the twelve-carbon detergents Sodium Lauryl/Dodecyl Sulfate and sodium laurate/dodecanoate.
Today, I point you to Adam Engelhart's excellent (and thoroughly overdocumented) home preparation of countless soaps. The roundup:
Lavender oil - in an almond oil base, I think. "Oils" from something that smells nice either come in tiny expensive vials (in which case they're a steam distillation of all the volatile greasy things in there, the "essential oil"), or in large, slightly less expensive bottles (…
moleculeoftheday | September 5, 2006The dimethoxytrityl, or DMT, ligand, is one of my favorite protecting groups in organic chemistry. Oftentimes, you need to "mask" part of a molecule to keep it from reacting during a step in a synthesis. DMT does this without breaking a sweat and gives you pretty colors to look at to boot.
Those phenyl rings form a pinwheel type arrangement (in 3-D, that is, they're twisted out of the plane of your screen).
When bound to a molecule, DMT doesn't have much of a color. When it's removed with acid, though, you actually get a (rare, usually unstable and only transient) solution of dimethoxytrityl…
moleculeoftheday | August 31, 2006Now with cyanide, it's Laetrile:
Which hydrolyzes to:
Please check out the laetrile entry on the old site. Various proponents of this bizzare cancer treatment (which liberates cyanide, of all things, upon hydrolysis) pop up occasionally. If anyone knows of any peer-reviewed studies on Laetrile, I'd love to see them (other than the cancer study noted below and on the old site, thanks!).
What's fascinating is that it's a structure we know liberates cyanide, and people still go crazy for it. It's not like it's some herb with hundreds or thousands of different molecules in there (although many…
moleculeoftheday | August 31, 2006Teflon, while it seems like a material in a weird class of its own, is actually just the fluorinated analogue of polyethylene - milk jugs and Saran wrap.
Fluorination, however, does funny things to molecules. Difluorine, or F2 is an absurdly reactive molecule. It has a lot of energy to give up in oxidizing a substrate. The flip side of this is that fluorinated molecules tend to be in a deep thermodynamic well (and therefore very inert). For this reason, PTFE is used in cookware coatings and electrical insulation.
The other thing about fluorination is that it confers certain odd colligative…
moleculeoftheday | August 30, 2006Ferrocene is another one of those weird molecules we just stumbled on. Upon reacting the anion of cyclopentadiene with an iron (II) salt, an "unusually stable" compound resulted. In inorganic chemistry, that often means stuff like stable to water or air, since much of this stuff falls apart gleefully.
The image doesn't quite do it justice; ferrocene is actually a "sandwich" of an iron (II) ion and two Cp rings, as you see here. A whole array of "metallocenes" was discovered later, but ferrocene is a classic. Many undergrad chem labs have you synthesize this (or the related, more sensitive…
moleculeoftheday | August 29, 2006I may get one up later, but there's a good chance you'll just have to wait til tomorrow for the next installment of MOTD-y goodness.
moleculeoftheday | August 27, 2006These are rare enough that I'm surprised every time I see one. It's a very simple molecule, that apparently makes its way into certain fruit flavorings: ethyl thiolactate.
As you probably have guessed by the numerous references to it, I love the flavor and fragrance field. I don't think I could stand to work in something that's so hit-and-miss, but smell is up there on my favorite-sense list. When a functional group that's normally so notoriously stinky is present in an apparently pleasant molecule, it's always a bit of a shock.
If you've been reading for awhile, you'll remember my entry on…
moleculeoftheday | August 25, 2006Eriochrome Black T is one of those chemicals I mostly remember for its name. It's the kind of CSI-ey name that just rolls off the tongue. It has the unusual property of "complexometric" indication.
It's normally blue, but on binding to calcium or magnesium (the divalent cations largely responsible for water hardness), it turns red. I have fond memories of playing with this in my analytical chemistry lab in undergrad. The usual pat explanation is that it's a water hardness indicator (see the movies on that page!). I'm sure it was, at one time, but I have a hard time imagining Joe EPA setting…
moleculeoftheday | August 24, 2006You thought I'd make it a whole week without skipping a day, I bet. You were incorrect.
moleculeoftheday | August 23, 2006I love this one. It's not exactly a molecule. If you've heard of it, you're nodding and smirking, if you haven't, you'll be surprised. Back in the 1960's, people set out trying to make new meat substitutes. Apparently, it was suspected that there would be a worldwide shortage of protein by the 80's. I like to think it's because we were a lot keener to do weird things just because back then. One bizzare product of this search was Quorn. Amazing how much the image on that page looks like chicken stir-fry, eh? It is quite hypnotic to click through the Quorn website, looking at the crypto-chicken…
moleculeoftheday | August 22, 2006It's hard to overemphasize the effect WW2 had on science. I'm not just talking about atomic bombs or the ensuing cold war. A huge part of WW2 was shortages of just about everything. Textiles were especially susceptible, because their civilian and military uses are ubiquitous, and, at the time, we pretty much had wool, silk, and cotton (pretty much all you get as far as natural fibers go, save some exotic stuff like processed bamboo and modified celluloses). Obviously, planting things and waiting is kind of hard during the (relatively) short timeline of global war. This shot the young polymer…
moleculeoftheday | August 20, 2006Sorry for the short post today, grading and other during-the-academic-year commitments are about to take effect. If you have access, there is a wonderful article in Chemical Reviews ASAP this week:
"The Nose as a Stereochemist. Enantiomers and Odor," by Ronald Bentley. Since it's an ASAP article, there's no page numbers yet, but the url is http://pubs.acs.org/cgi-bin/asap.cgi/chreay/asap/html/cr050049t.html. The DOI is 10.1021/cr050049t S0009-2665(05)00049-X.
For some neat references on chiral odorants, see these MOTD classics:
Grapefruit mercaptan
Carvone
See you tomorrow.
moleculeoftheday | August 19, 2006Phenomenally late to the game, I've added a Donors Choose link to the blog. The idea here is that you pick a small microgrant to fund/help fund for a public K-12 classroom somewhere in the States. Requested funding ranges from hundreds to thousands of dollars. I love microfunding efforts like this, since many of them are in the low range, so you have a shot at contributing a significant chunk of something that will make a demonstrable difference in a classroom. I've set a (arbitrary, any spare change helps, etc.) goal of $10,000 (total, no one grant I have listed is nearly this much) for my "…
moleculeoftheday | August 18, 2006There really isn't much to this one - Lead (II) Oxide has the forumula Pb (II) O, or PbO.
I started this entry intending to discuss how it was used in generating so-called "lead crystal." All Swarovski, Baccarat, etc., "crystal" is is regular silicon glass with up to about 20% lead oxide added. Lead oxide has a high refractive index (the amount by which the speed of light is retarded in the material compared to a vacuum; that is, a material of refractive index 2 would slow light to half the speed of that of light in a vacuum - refractive index 1).
Why would we want a high-refractive index…
moleculeoftheday | August 17, 2006Diacetyl is a unique molecule because it's a simple enough structure that you could expect some biochemical pathways to find their way there via glycolysis or fermentation (sure enough, yeast does. more in a minute), and it has the ineffable aroma of butter
Predictably, certain flavor chemists have made liberal use of it (in the cloying artificial butter flavor that is ubiquitous in microwave and movie popcorn).
As mentioned before, yeast can produce some diacetyl in the process of malolactic fermentation. Many winemakers have taken advantage of this, especially producers of the buttery-oaky…
moleculeoftheday | August 16, 2006If you take a look at wine bottles today, you'll note that the sealing devices are all over the place. Traditionally, cork was used, and that's still the dominant seal, but you'll also see synthetic foam-type corks, as well as screw-caps. Cork was originally used in wine because it was a relatively cheap airtight seal. It was the best available at the time. It worked pretty well, too; wines with the capacity to age will last many years if stored sideways (ensuring the cork doesn't shrink, allowing air in). However, there is a sinister side to corks.
Some corks are contaminated with chemicals…
moleculeoftheday | August 15, 2006Whew. This one's a little embarassing. One of my favorite things about organic chemistry is just how much it's like Lego. Molecules that seem like indecipherable structures to the uninitiated start looking more and more like a bunch of building blocks. It's been said that organic chemistry is the chemistry of functional groups, and it's quite true. Chemists have to worry about the whole molecule, but any one operation is likely to work on one or two bits or pieces of the molecule at a time. This kind of thinking can be a bit dangerous, since sometimes a building block you dream up -…