moleculeoftheday | November 6, 2006Fundamental to learning how energy is moved around in biology is understanding ATP equivalents. You've probably heard about how ATP is "the energy currency of life" - and rightly so; every mole of ATP hydrolyzed is equivalent to about 10 kcals. Bioenergetics isn't really a direct food-to-ATP transaction, though. One crucial part of the indirect dance that is bioenergetics is called oxidative phosphorylation. Here, some molecules (NADH and FADH2) that constitute the business end of a lot of the enzymes responsible for oxidation reactions get regenerated (becoming NAD+ and FAD).
Still…
moleculeoftheday | November 3, 2006Potassium iodide isn't much of a structure:
It's a source of iodide. Thyroid hormones contain iodine; the source of this is dietary iodide.
The human dietary requirement for iodine is vanishingly small; on the order of 100 micrograms per day. Trace iodine is present in seawater and many soils, so most people get some from seafood, fruits, or vegetables. In the absence of iodine, thyroid hormone levels are low. This induces a cascade of hormone releases; the last of which is the release of thyroid stimulating hormone. This enhances production of thyroid hormones. In excess, this induces…
moleculeoftheday | November 1, 2006Iodine week continues with IPBC, or 3-iodo-2-propynyl-N-butylcarbamate, a fungicide:
IPBC has been around for ages, but you see it more and more in cosmetic products. That "iodopropynyl" part, where the iodine is bound to the triply-bonded carbon, is a very reactive functional group. IPBC has been implicated as a cause of dermatitis (but fairly rarely).
Certain compounds can induce an immune reaction after repeated exposure. These are called sensitizers. At the levels you find them in consumer products, the worst you're likely to get is a rash (although not always). In the lab, we're usually…
moleculeoftheday | October 31, 2006Methyl iodide is another simple organoiodide:
Probably the most common lab use is tacking a methyl group onto something; MeI is a great substrate for the SN2 reaction.
Despite its ubiquity, methyl iodide isn't nearly the best alkylating agent. It's cheap and simple, so it sees a lot of use, but there are many things that are better, such as dimethyl sulfate (used a lot industrially, from what I've read), methyl triflate (PDF) (toxic and great), trimethyloxonium salts (my favorite), and the so-called "magic methyl," methyl fluorosulfonate, which has a pretty good vapor pressure (being…
moleculeoftheday | October 30, 2006Another theme week: Iodine.
Iodoform is, as the name suggests, the iodine analogue to chloroform.
Iodoform, as the Wikipedia entry mentions, isn't the best antiseptic in the world, but they're mistaken in saying it's not used anymore: iodoform impregnated gauze is still found in hospitals.
Another notable application of iodoform, also antiquated, is the iodoform reaction. This is one of a number of "wet tests" that were once used to characterize compounds. Before spectroscopic techniques became as robust as they are now, they had a place in the lab. Now, two groups of people bother reading…
moleculeoftheday | October 27, 2006L-methamphetamine is a fine example of how molecules that vary only in their chirality can have very different biological effects. Chiral molecules have non-superimposable mirror images. L-methamphetamine, at left, below, is found in Vicks Vapor Inhalers. (Notice how they obfuscate the name a little bit by calling it "levmetamfetamine"). This is the mirror image of D-methamphetamine - the street drug. As you'll see, the two compounds are very different medically despite having only a subtle structural difference.
If you're having trouble working out the difference, the dashed bond is "going…
moleculeoftheday | October 26, 2006Kavain is a member of a class of compounds known as the kavalactones. (A lactone is a cyclic ester; click here for examples).
Kavain is a species found in the kava plant, which is used by the aboriginal residents of some Pacific islands and has psychoactive activity. It's attracted use as a dietary supplement lately. It's also attracted some attention for possible toxicity, particularly to the liver.
moleculeoftheday | October 25, 2006Arecoline is a compound that occurs in the seed of the betel palm. It's taken by chewing the nut.
Arecoline, like nicotine, binds to certain receptors for acetylcholine. I've grouped them together so you can note the structural similarities.
Remember all that talk about protonated amines yesterday? Here's another place where it matters.
You'll note that I've drawn arecoline and nicotine with positive charges. As I mention in this old entry about nicotine, this is the physiologically relevant form (at your cells' pH, this is what you find).
The trouble with this, though, is that charged…
moleculeoftheday | October 24, 2006It's weird drugs for the rest of the week!
Salvia probably means one of two things, if anything, to most people: a houseplant (for which purpose it is ubiquitous) or a recreational drug that you can still get your hands on legally (for which purpose it is ubiquitous). It is funny to flip back and forth between pages where people are trying to figure out exactly the best way to get this stuff in your body and pages where people are trying to figure out which plant will go best with those azaleas and think that everyone's talking about the same thing. Plants are funny that way, I guess.
Of…
moleculeoftheday | October 20, 2006This might not apply to a lot of the readers, but I think a decent subset might find it important. As you know, it's not so easy to search for chemical information. With most search engines, you're limited to the tags associated with the document or (more often) the text within the document. Usually, chemical graphics exist as graphic files (as discrete raster image files, or as the aforementioned images embedded in PDFs, neither of which are yet amenable to searching).
IUPAC has settled on InChI as an almost-Open unique identifier for compunds. By tagging your pages with InChIs, you can make…
moleculeoftheday | October 20, 2006Pyridines and thiols are two of the stinkiest kinds of compounds you can come across in chemistry. You'd think if you put them together in a molecule, you'd have something nasty. Oddly, you don't:
Bafflingly, thiopyridine is apparently odorless. You'll notice I've drawn two structures here - this is a phenomenon called tautomerism, a special case of isomerism. This might play a role in the special non-stinkiness. Think of thiopyridine as a mixture of these two structures.
For more discussions on organo-stank, see this entry at Derek Lowe's blog. If you've never been, take a look; it's one of…
moleculeoftheday | October 19, 2006For a better idea of how the bond angles look, here is an energy-minimized structure of windowpane (4.4.4.4). Notice how it's (nearly) planar. That central carbon atom (middle gray dot, blues are hydrogens) is the one to watch.
Here is 5.5.5.6 windowpane:
And here is an unstrained compound, tetramethylmethane (2,2-dimethylpropane):
The changes are subtle but result in enormous energy changes. The molecules go in increasing order of stability (Decreasing energy). This is one of the things it's a little weird to start thinking about in chemistry. Molecules are rarely completely rigid;…
moleculeoftheday | October 18, 2006Like cubane, windowpane (also named "[4.4.4.4]fenestrane" for the Latin for window) is another of those compounds people like because it looks like something anthropomorphic, with clean right angles (in contrast to the bulk of molecules, which assume their bond angles with little regard for what looks nice on paper). This introduces a great deal of strain, since quantum mechanics would rather we avoid bond angles very far from ~110 degrees in these sorts of compounds. See this entry on cubane from the old site for more information on why right and 180 degree angles are so tricky here.
In fact…
moleculeoftheday | October 17, 2006PET is an ubiquitous plastic. You've heard it referred to as "dacron", "mylar," or just "polyester."
It it produced by (among other methods) the condensation of terephthalic acid and ethylene glycol:
PET is all over, from soft drink bottles to fabrics. Perhaps the neatest use is as mylar; an oriented form of PET. Back in the fifties we stumbled across it and we haven't looked back. There aren't many applications for a plastic mylar hasn't found its way into.
Awhile ago, my friend sent me a link to the Prelinger Archives, an amazing public-domain repository of gee-whiz video from the past…
moleculeoftheday | October 16, 2006Here is another molecule that's gone out of favor in recent decades: carbon tetrachloride:
Chlorinated solvents are great solvents. Something about the polarizability, medium polarity, (relative) lack of reactivity, just makes them the only thing that will work in a lot of applications. The three simplest chlorinated solvents are dichloromethane, chloroform, and carbon tetrachloride. Those are CH2Cl2, CHCl3, and CCl4. Those are in order of increasing degree of halogenation, and, coincidentally, increasing degree of toxicity. Methylene chloride/dichloromethane is regarded as a necessary evil…
moleculeoftheday | October 12, 2006Ethidium is a dye that's used in molecular biology to allow DNA to be visualized. Regular DNA isn't colored; it absorbs ultraviolet but not visible light, so you need to use tricks like making the DNA radioactive (which makes it pretty easy to spot), or using dyes that selectively bind to DNA. Ethidium does this by slipping in between the base pairs of DNA, or "intercalating."
One ubiquitous method of visualizing DNA is called gel electrophoresis. You have no doubt seen this on some CSI-type show. The basic idea is this: you put DNA inside a water-based gel. DNA is negatively charged, so to…
moleculeoftheday | October 11, 2006Sorry, but you're hearing about another odorant today:
2E,6Z-nonadienal is an aldehyde responsible for a good chunk of the ineffable aroma of fresh cucumber. Being an aldehyde, it's a bit of a fragile molecule, and doesn't last long in the pickling process, as this blurb explains.
moleculeoftheday | October 10, 2006Isoamyl acetate is a nice, fruity smelling ester - like a lot of the low-molecular weight esters. For this reason, it's used in the flavor and fragrance industry. You won't find it in perfume, though, for two reasons. The first is that esters aren't so hot for perfumery in general. They tend to hydrolyze down to their constituent acid and alcohol (in this case, isoamyl alcohol and acetic acid). The isoamyl alcohol will just smell like solvent; not too unpleasant, but it won't be attractive by any means. The acetic acid will give you a rich vinegary bouquet. For these reasons, esters are…