moleculeoftheday | March 20, 2007Ethylene oxide is the simplest possible epoxide, or three-membered cyclic ether:
It is a superior disinfectant, but it's a gas, and quite toxic, so you'll probably never use it. Even in biology labs, an autoclave is used to disinfect (essentially a pressure cooker - water is heated 12C/21.6F degrees above its normal boiling point). EtO is ubiquitous in disinfecting medical supplies - especially things like bandages and gauses, where a wet autoclave is problematic. Some beasties can happily survive (and reproduce) at autoclave temperatures.
It also has a role in the production of ethylene…
moleculeoftheday | March 16, 2007Edit: Looks like I might be off on this.
If you're in Chicago, the river will be green this weekend. For that, you can thank fluorescein:
Fluorescein is strongly fluorescent - if it absorbs a photon, 97 times out of 100, it will be re-emitted as light (see yesterday's entry on fluorene for more information).
Fluorescein is a phenomenally useful fluorophore; it finds use in biology to fluorescently tag molecules, as well in medical imaging.
Happy St. Patrick's day!
moleculeoftheday | March 15, 2007Fluorene is a very simple aromatic hydrocarbon. It's often used in physical chemistry classes to teach an important lesson about fluorescence: rigidity matters:
Fluorene is essentially a rigidified biphenyl:
When a molecule absorbs a photon of light, it carries around an extra packet of energy; this is termed an "excited electronic state." Just what happens to that packet of energy depends on the molecule. Lots of molecules absorb light - your red dry-erase marker and pink highlighter both contain dyes that absorb green light. The difference between the dry-erase marker and the highlighter…
moleculeoftheday | March 14, 2007Lunesta shares its mechanism of action with the benzodiazepenes - Valium, Rohypnol, Xanax, etc. It doesn't actually belong to the benzodiazepene class of drugs, but they all work on the same system - GABA. Not coincidentally, the much-maligned GHB works by virtue of the fact that it is metabolized to GABA in vivo.
Lunesta belongs to a class of drugs that work similarly to benzodiazepenes but in such a way that they have a lower (but still nonzero) potential for abuse and dependency.
moleculeoftheday | March 13, 2007Seroquel antagonizes serotonin, dopamine, and histamine, but it doesn't look a whole lot like any of these:
The benzothiazepene (benzene fused to the seven-membered ring containing nitrogen and sulfur) ring system bears a little resemblance to the benzodiazepines, the class to which Valium belongs, but sulfur and nitrogen are completely different kettles of fish from almost every standpoint - not to mention the rest of the ligand, particularly the piperazine (six-membered ring containing two nitrogens) moiety.
Seroquel finds use as an antipsychotic, along with numerous off-label uses.
moleculeoftheday | March 9, 2007Like ethidium, proflavine is a nucleic-acid binding dye that intercalates, or inserts itself between base pairs.
Proflavine found some use as an antiseptic at one point (as far as I know, that day has passed). It is one of the earliest known intercalators. Unlike ethidium, its fluorescence actually goes down upon binding to DNA; this is the more common case for fluorescent DNA-binding drugs. See the spectrum of proflavine cation here.
moleculeoftheday | March 8, 2007I've been thinking about chromophores a lot lately; expect the entries to reflect this.
POPOP is a laser dye and has an exceptional amount of resolvable fine structure for a relatively large molecule. See the spectrum here, from the Oregon Medical Laser Center's excellent collection of spectra and emission quantum yields. Contrast, for example, the spectra of p-quaterphenyl, p-terphenyl, and even biphenyl.
Don't be disappointed, but tomorrow's another dye!
moleculeoftheday | March 7, 2007See also: yesterday's entry on folate.
Methotrexate is a mimic of folic acid. Shortly after we discovered what folate was, we started looking into what else we could do with it.
During the 1940's, George Hitchings and Gertrude Elion started work on a number of nucleic acid-related compounds that would prove astonishingly successful and later garner them a piece of a Nobel prize. One of these was methotrexate - the structure of folic acid is below for comparison.
As mentioned yesterday, folate plays a key role in nucleic acid synthesis - something rapidly-dividing cells need by the boatload…
moleculeoftheday | March 6, 2007Folate is a cofactor, or a small molecule that is involved in the function of an enzyme. It's involved in a number of enzymatic reactions; perhaps the most important relate to the biosynthesis of DNA.
It's amazing to think about the fact that we've only known about its existence for seventy-odd years, considering its crucial role in metabolism. No doubt this was (partly) due to the fact that the requirement for folate is vanishingly small; it's on the order of half a milligram a day! Because of folate's central role in DNA synthesis (along with various other reactions, many of which are…
moleculeoftheday | March 5, 2007For quantum mechanical reasons; triply bonded carbon tend strongly to be linear. Benzene-like compounds derive their special stability by virtue, in part, of being in a planar ring. Surprisingly, certain substituted benzenes can form "benzynes," which have an additional degree of unsaturation. Less surprisingly, they're very reactive species; these tend to be something observed by virtue of what products they produce. It's not something you get in a bottle.
moleculeoftheday | March 2, 2007Vinpotecine is a derivative from a compound found in the lesser periwinkle plant:
If you ever went to one of those "smart bars" in the late 90's, theres a good chance you tippled some vinpocetine. I'm not sure whether it's actually effective, but people have looked at it for everything from Alzheimer's, to a prophylactic drug in stroke patients, to something for people who just want to feel a little smarter ("nootropics").
moleculeoftheday | March 1, 2007Sorry if you're sick of this, but I'm having fun. You might remember my post on Havidol. (see also this follow-up). Justine Cooper (presumably) left a comment on the initial post, plus the prescribing information (PDF) has been updated. It's still not quite right - here, apparently, is your opportunity to make it right, and get a commemorative t-shirt in the process!
Previously, the entry for Havidol gave a name that didn't match the structure. The same was true of the molecular formula and molecular weight:
After making a couple posts to this effect, I got this follow-up:
We at HAVIDOL are…
moleculeoftheday | February 28, 2007I'm almost cheating, since this one is so closely related to cynarin. Chlorogenic acid is yet another compound found in artichokes, as well as coffee. In addition to modulating your ability to taste sweetness (though not in the levels or conditions found in coffee, it would seem), it has some specific metabolic effects.
Chlorogenic acid has the ability to alter some aspects of glucose metabolism. I don't work with it and I'm not sure where people are on what all it does biologically, but it has attracted enough attention to make its way into patent preparations for weight loss.
moleculeoftheday | February 27, 2007I am always completely confused when I meet someone who doesn't like artichokes. Not in the cheese-based dip, though that's not bad, either. I take my artichokes steamed, with a big bowl of drawn salted butter. The savory-sweet taste, the smooth texture, that puzzling satisfaction of only getting a little food out of your substantial efforts (sunflower seeds, anyone?), and the fact that it's probably the only food you eat by biting down and pulling the free end from your mouth all add to the experience.
My favorite thing about artichokes, though, is the fact that everything tastes oddly sweet…
moleculeoftheday | February 26, 2007Great entry from Khymos last week. Isohumulone is a compound found in beer imparting some of the (good) bitterness. Unfortunately, the magic of photochemistry can wreak havoc on it.
Isohumulone can be excited by the agency of riboflavin, an endogenous chromophore, causing it to cleave into a pair of radicals, one of which can react with free cysteine radicals in proteins, yielding a low molecular weight thiol, which can give beer that "skunky" taste. Dark bottles prevent this, but as the entry points out, clear-bottled beers are far from immune.
moleculeoftheday | February 23, 2007See also this followup.
Take another look at the Havidol post's comments. It looks like the chemistry's not only a little bit off - some other parts of the site look a little familiar.
And by the way, it's HCl, not HCI.
moleculeoftheday | February 23, 2007Ammonium carbonate is analogous to the other bicarbonate and carbonate salts you see - baking soda. In the presence of acid; or just sufficient heat, it will offgas ammonia and carbon dioxide, hopefully leaving pleasing bubbles in whatever you're making.
Whatever you're making better not have much moisture, though. Ammonia loves water, and any residual water will hold onto enough to give whatever food you're making a profound stench. This pretty much limits you to crackers; ammonium carbonate-leavened banana bread will not be pleasant.
The salt has been around for a long time but has been…
moleculeoftheday | February 22, 2007It's remarkable how different RNA and DNA are, considering they're just one atom different. RNA is much more prone to fall apart; you can put DNA in basic solution without any problem, but RNA will begin to hydrolyze. Life takes advantage of the ease with which RNA is degraded. It has a much more ephemeral role in the cell; your genome is encoded long-term via DNA, and RNA is typically generated only as needed en route to proteins.
Because of this, RNA is degraded quickly when it's not around for a good reason. This is accomplished by the ubiquitous, aptly named RNAses. They're all over your…
moleculeoftheday | February 21, 2007Denatonium, sold as Bitrex, is among the most bitter compounds in the world. Why in the world would industry seek out such a thing? To put in things we don't want you to eat, silly.
I think it was developed to denature nonbeverage alcohol (to avoid having to pay alcohol tax, booze not intended for your mouth is made toxic or disgusting; Bitrex does mostly the latter), but it finds its way into loads of stuff (including, puzzlingly, hygeine products - most of which probably taste pretty bad on their own, no?). My favorite use for it is anti-nail biting polish. It takes a certain dedication to…
moleculeoftheday | February 20, 2007See also the followups (one, two) to this post.
From the taking jokes too seriously department...
Havidol is a fake drug campaign by Justine Cooper that's on display in NY at the Daneyal Mahmood gallery (warning, slow loading, natively embedded video). It seems like a pretty well-done faux-drug site, and the gist seems to be mocking the idea that "lifestyle drugs" are becoming more and more ubiquitous.
I could go on about on the social aspects of this kind of drug and this kind of commentary, but that's not what I'm aiming for. (Besides, plenty of people are on that; even Reuters covered it…