moleculeoftheday | January 16, 2007General anaesthesia has come so far, and yet not. Back in the day, we used to use lipophilic compounds like diethyl ether and alkyl halides like chloroform, and now we use...well, lipophilic alkyl halides like desflurane. Fortunately, desflurane doesn't cause so many toxic effects, due largely to the wonderful relative inertness of the C-F bond.
moleculeoftheday | January 15, 2007I don't think I'll ever be able to pick out which mushrooms aren't poisonous. Poisons vary pretty widely across species; a lot of them are small peptide type molecules. One of the few simple small molecule mushroom poisons is orellanine:
It bears a striking similarity to the bipyridyl ligand previously covered, Methyl Viologen (Paraquat).
moleculeoftheday | January 12, 2007Salts are mixtures of charged species, or ions. They have an avid tendency to remain solid due to the strong interactions between their charged components. About a hundred years ago, people started noticing certain compounds that were ionic would nonetheless melt below or around room temperature. This is a unique class of liquid - extremely polar, and capable of dissolving lots of odd stuff. They also tend not to evaporate very easily, the ionic interactions between components of the salt being so strong. For these reasons, a lot of people have suggested they could be used in "green chemistry…
moleculeoftheday | January 11, 2007Despite the name, penicillamine isn't an antibiotic; it's actually a metabolite of penicillin-class drugs. It is given as the pure chemical too.
It is an immunosuppressant, among other things. My favorite medical use of it is its role in chelating copper as a treatment for Wilson's disease, a rare disease caused by an inborn error in metabolism that causes copper to accumulate. Remove the copper, you treat the disease.
moleculeoftheday | January 10, 2007Albendazole is a member of the benzimidazoles - the 6+5 membered ring system at the heart of the molecule. The benzimidazole class of drugs is used to treat many parasitic worm infections. They work by impairing microtubule function.
The benzimidazoles are gratifyingly simple-looking drugs. Contrast Taxol, a much woolier-looking drug that operates on microtubules (in another way, which we'll cover another day; furthermore, that one works on cancer, not worms).
moleculeoftheday | January 9, 2007Last week it was revealed that for just about the entire 1970's, former SCOTUS chief justice Rehnquist was taking Placidyl. This is too long by any measure - it's been unavailable in the States for almost a decade (due to better alternative supplanting it), and even when it was available, it was thought to be less-than-prudent to prescribe it for more than a week. Further, he was taking about triple the recommended dose. He went through some ugly withdrawal symptoms, in one case insisting that the CIA was plotting against him.
It is hard to overstate the importance of the benzodiazepines in…
moleculeoftheday | January 5, 2007Chemotherapy, in the cancer-treatment sense, isn't very selective. Fortunately, cancer cells divide so much faster than regular cells, this imparts a measure of selectivity. All chemotherapeutic agents are poisons of one sort or another, but we continue to get better. Mechlorethamine is just an "alkylating agent," which means it will react promiscuously, forming covalent adducts with any nucleophilic species it encounters. Oftentimes, this means DNA, which means cell division will be impaired (for all cells). If this sounds a bit like carpet-bombing a knife fight, you begin to see the problem…
moleculeoftheday | January 4, 2007One of my best friends in undergrad, upon learning about the use of acetal protecting groups for carbonyls, exclaimed, "they're like ketone condoms!" Indeed. Protecting groups are ubiquitous in organic synthesis, and another one you see all the time is Boc, which is used to protect amines:
Boc2O, or "boc anhydride," is one of my favorites. Using it on your amine will yield a "boc protected amine." Upon acid deprotection, it yields the parent amine, carbon dioxide, and t-butylene. The latter two are both gases, which gives about as easy a cleanup as you could hope for (that's the problem with…
moleculeoftheday | January 3, 2007My dentist has an incredible knack for administering anesthetic without much pain. I'm not sure what combination of factors are at play, but getting work done there is essentially painless. My main problem for years was the fact that my mouth was numb for a good part of a day after leaving. I went today, and it had been a few years since I had anything done. For years, my dentist (and probably yours) used lidocaine, which works fine but has an elimination half-life of about 90 minutes. This time, the anaesthetic had changed.
In 1969 (20 years after lidocaine was discovered, and a mere 65…
moleculeoftheday | January 2, 2007Azelaic acid is a pretty simple small molecule:
It is used topically in dermatology.
moleculeoftheday | December 21, 2006I picked this molecule for one main reason: I was flipping through a physiology book and read this statistic: your body goes through on the order of one liter of bile per day! Did you have any idea? That is up there on my goofy big numbers in your body list, the champion of which is still this: your body contains a few tens of grams of ATP. The vast majority of your energy is supplied through the agency of this ounce or two of ATP. However, it's recycled thousands of times per day, and you go through the equivalent of a hundred pounds of ATP in one day, just to live!
Back to bile. Life faces…
moleculeoftheday | December 20, 2006Oxalic acid is a bifunctional carboxylic acid. Your body will make it as the result of metabolism of ethylene glycol if you ever drink antifreeze, resulting in the catastrophic precipitation of calcium oxalate in your kidneys. Some foods have (fairly low) levels of oxalate. A small portion of vitamin C/ascorbate is metabolized to oxalate, which is a very real concern if you're following Linus Pauling's lead and taking grams of the stuff per day.
moleculeoftheday | December 19, 2006There are a number of "strong" acids that are essentially completely dissociated in water - hydrochloric and sulfuric acid are two of the most common. Unfortunately, these are often volatile (as in HCl), insoluble, or otherwise ill-behaved in organic solvents. The organic sulfonic acids are quite strong - the functional group is essentially sulfuric acid with one of its valences occupied by a carbon functional group instead of another -OH. para-toluenesulfonic acid, or tosylic acid is probably the most common sulfonic acid used in the lab. Much stronger than carboxylic acids (the other…
moleculeoftheday | December 18, 2006The fluoride ion is important to synthetic chemistry, often because it can be used to cleave silyl ethers (the silicon analogue of a carbon ether). Fluoride is notorious for holding onto water (like any tiny ion - lithium is about as bad), so even an "anhydrous" solution of TBAF in (say) THF will often contain ca 5% water. The less water you have, the more "naked" fluoride anion you have, which is much, much more reactive than aquated fluoride.
moleculeoftheday | December 14, 2006You may have heard of a guy named Kurt Vonnegut. What you might not know is that his lesser-known little brother Bernie was the guy who came up with the idea of using AgI for cloud seeding.
From little bro Kurt's Timequake:
Question: What is the white stuff in bird poop?
Answer: That is bird poop, too.
So much for science, and how helpful it can be in these times of
environmental calamities. Chernobyl is still hotter than a Hiroshima baby
carriage. Our underarm deodorants have eaten holes in the ozone layer.
And just get a load of this: My big brother Bernie, who can't draw
for sour apples,…
moleculeoftheday | December 13, 2006Tris is one of the most common buffers out there and absolutely ubiquitous in molecular biology. The idea behind a buffer is that you have a compound that takes on a proton (hydrogen) at a certain pH, usually somewhere near neutrality, you have about half with and half without a proton, and you have a solution held near that pH. Tris buffers a shade above pH 8, which is a little basic, but not so bad. It's pretty transparent to UV light, water soluble, and cheap. The last is probably the big thing; we have a paint-bucket sized container of tris in the lab. It's probably the only compound I…
moleculeoftheday | December 12, 2006Methyl viologen is a groove-binding DNA ligand; that is, unlike an intercalator, which slips between bases, it slips into the grooves of the DNA helix.
You've probably heard of it as paraquat.
It is an herbicide, but it's not that specific; the stuff can hurt you, too. The mechanism of action here has less to do with it being a ligand for DNA, and more to do with its redox chemistry. Herbicides, including paraquat, have comprised a part of US anti-drug strategy for awhile. We've been spraying certain drug-related plants (mostly marijuana and opium) for decades, and we're still up to it. Note…
moleculeoftheday | December 11, 2006The catnip plant belongs to the genus Nepeta. The molecule responsible for its odd effects on cats is called nepetalactone:
Apparently catnip can repel insects in a garden, and some people have looked into whether nepetalactone works as an insect repellent.