moleculeoftheday | March 27, 2008Certain compounds occur as "hydrates"; that is, with one or more molecules of water. Sometimes there is just water trapped in the crystal structure at a specific stoichiometry (i.e., creatine), sometimes the water is actually covalently incorporated into the molecule, as in formaldehyde hydrate.
Sodium acetate trihydrate is the first case - just crystals of sodium acetate + 3 molecules of water. If you heat this up, it "melts," but it's arguably not "molten," you're just dissolving the NaOAc in the water and making a ~10M solution - well above the saturation limit, but it'll stay in solution…
moleculeoftheday | March 24, 2008Happy Dyngus day.
Formaldehyde is both a toxic and useful compound. Unfortunately, it's a gas, so it's tough to move around. Typically, you get it as a solution in water - with some methanol to keep it from polymerizing into "paraformaldehyde," which is the other major way to get it. Both are a pain - one has water, which is poison for a lot of reactions, and one acts like brick dust - it won't dissolve in anything.
Trioxane is the third way - it's well-behaved and soluble. Hooray trioxane!
moleculeoftheday | March 20, 2008As I've discussed in the past, certain dyes can detect radiation, stain DNA, sense solvent polarity, or (in olden times!) color the Chicago River green. This one can make a laser!
With sufficiently fluorescent dyes, you can actually take a laser and use it to "pump" a jet of a dye that absorbs the laser wavelength, and get a longer (lower energy) wavelength out. This often makes a mess - rooms with dye lasers seem to make it about five minutes before someone spills one of these day-glo lasing mediums on the floor.
MoTD science club: here's a polycarbonate bottle cast with a pink dye with an…
moleculeoftheday | March 17, 2008I posted Sunday and last year about the putative use of fluoresciein in the Chicago river on St. Patrick's day. As some readers pointed out, they apparently aren't using it anymore.
I don't even have a guess what they're using, then. The reason the solid dye is orange is because it absorbs blue-green light, and the reason the river looks green is because it fluoresces, emitting green-green light.
Whatever they're dumping in the river has about that absorption spectrum and about that emission spectrum, and it's got to have a very high emission quantum yield (that is, it has to convert…
moleculeoftheday | March 16, 2008Edit: Looks like I might be off on this.
CNN has a clip in the rotation right now about the yearly tradition of dying the Chicago river green for St. Patrick's day. They're saying it's a "secret orange dye." Well, let me put it through the decomplicator for you.
As you might remember from last year, it's fluorescein. That is all. Happy St. Patrick's day.
moleculeoftheday | March 14, 2008Like alizarin, indigo is a dye that we used to have to rely on a plant to make. Now we're able to synthesize it:
Indigo used to be prepared from natural sources, like plants. Modern synthetic techniques have made it cheap and plentiful. While this might seem like not such a big deal, can you imagine a world without colorful...well, much? Everyone wearing Amish white and dishwater grey?
Nowadays, we tend to use dyes that have nothing to do with plants, like Yellow 5, Red 40, and Blue 1 (the separation of which you can see here). Dyestuff technology has advanced with synthesis and physical…
moleculeoftheday | March 14, 2008Wow, sorry. I pretty much missed a whole week there. A consolation Friday entry coming up, but first, if you enjoyed Breaking Bad, you might enjoy Trampled Underfoot, the autobiographical blog of Todd Hall, a chef in the Southwestern US. His career oscillated for years between some dizzying successes and crippling substance abuse problems.
He was a rising star in Phoenix for awhile, even won a James Beard award, and was repeatedly profiled in the local indie rag. He ended up in jail in California for awhile for bad checks, and out of this came perhaps the funniest story about him.
He offered…
moleculeoftheday | March 13, 2008Flavylium is an unusual heterocycle - it has a trivalent oxygen atom. These tend to be quite reactive - trialkyloxoniums, some of the most potent alkylating agents, contain them.
As in the case of tropylium, aromaticity saves the day again. What should be a very unstable compound ends up being fine even in water.
You might know flavylium from such pigments as cyanidin and delphinidin.
moleculeoftheday | March 7, 2008As I mentioned in the previous entries on HF, mercury fulminate, and phosphine, I really like Breaking Bad.
As an astute commenter noted yesterday, they sometimes make some mistakes:
Like pentavalent carbon (green dots).
But they usually do a pretty good job and even sneak in some real chemistry:
See Walter fill orbitals!
During Walter's chemo last week, you saw some red stuff flowing into his IV. This was likely doxorubicin:
Doxorubicin is a DNA-binding molecule, like proflavine, ethidium, or paraquat.
Proflavine and ethidium are intercalators - they slip between the bases in DNA. Paraquat…
moleculeoftheday | March 6, 2008Well, it finally happened. I made it almost two years, but I repeated a molecule for what I think is the first time.
Hooray! Any pressure to be original is off! Here's the first of many best-of posts to come!
One thing I've done from time to time is crude experimentation on a recent household molecule, with accompanying photos. Here's a compilation of the ones I can remember putting up. If you have an idea or remember one I missed, leave it in the comments!
Thrill to:
CSI:MOTD: in which I use cyanoacrylate to expose latent fingerprints on stuff I've handled!
Paper chromatography: in which I…
moleculeoftheday | March 6, 2008The series of Breaking Bad chemicals continues (spoilers inside). Previously: phosphine, mercury fulminate. Today: hydrogen fluoride.
HF is just that, H-F, or a hydrogen bound to a fluorine. All the other acids in this group - HCl, HBr, HI - are gases. What we call "hydrochloric acid" is HCl in water, "hydrofluoric acid" is HF in water, etc. What's interesting, though, is that HCl, HBr, and HI are all strong acids - if you dissolve some in water, it will completely dissociate into H+ and Cl- (for example). HF doesn't do that, and that makes it unique.
While hydrochloric acid is strong stuff,…
moleculeoftheday | March 5, 2008As a commenter surmised in my entry on phosphine, I really like Breaking Bad. The main character is a chemist, and the writers have done a good job of working a lot of chemical tidbits into the mix (even ones not about methamphetamine, which drives much of the plot).
Now through Friday: molecules from Breaking Bad that aren't methamphetamine (or even related to it) (spoilers inside).
With pressure or friction, it will explosively decompose into nitrogen, carbon monoxide, and mercury metal.
Mercury fulminate made an appearance in last Sunday's episode. He takes a giant sack of the stuff into…
moleculeoftheday | March 3, 2008Butyric acid has been covered obliquely before - it's part of the nice-smelling amyl butyrate (which is eau de Juicy Fruit, pretty much). On its own, though, it's a foul vomit-smelling liquid (the Wikipedia article, however, notes that some intrepid chemist tasted it and reported it had a sweetish ethereal taste).
You may have gotten from the headline, though, that this particular organic compound has made the news lately because anti-whaling vigilantes threw over a gallon onto the deck of the Nisshin Maru, a Japanese whaling vessel. I can only imagine what it'd be like if I dropped a 4L…
moleculeoftheday | February 29, 2008Lots of chatter in the news today about finding ricin in a Vegas hotel room.
Image of PDB ID 2AAI from Wikipedia
Ricin works by inhibiting protein synthesis at the ribosomal level. This is a well-known method of killing something, and one on which many antibiotics work.
You'll note this looks different than most of my structures, and that's because ricin is a giant molecule in comparison - about 100 times larger than most of what you see here. It's a protein.
Proteins tend to be fragile things. Small molecules are a lot like jellybeans to proteins' gingerbread houses. Knock a jellybean off…
moleculeoftheday | February 27, 2008Dutasteride is of the same class of drug as Propecia and Proscar - the so-called 5-alpha-reductase inhbitors. These inhibit the enzyme of this name from converting testosterone into dihydrotestosterone.
Interestingly, the class is useful for both prostate hyperplasia (proscar) and hair loss (propecia) - these two are the same molecule. Avodart, which has been approved for prostate hyperplasia, was in trials for hair loss awhile back, but these were since dropped.
moleculeoftheday | February 25, 2008Longtime readers will know I like big dye molecules.
Once you get to the size of a phthalocyanine - a little over 1 nm across in any dimension (one of those bonds is about 0.15nm) - weird stuff happens. This explains, in part, G-quadruplexes and liquid crystals,
A friend of mine that made phthalocyanines saw something neat once - you can see them making swirly patterns if you leave a vial containing a solution of them on the bench for awhile, shake it up, it goes away, and it comes back later.
Once you make a molecule about this big (even a little smaller), things get a little weird.
Please…
moleculeoftheday | February 22, 2008All of life links up biomolecules effortlessly, from the august readers of this blog, to the humble bacteria that colonize the half-eaten food on their desks. It makes it frustrating for scientists who are trying to synthesize them. We have methods, but they're inefficient. (It gets even worse for DNA.).
It gets even worse when you try and work on a biomolecule you already have in water. Most of our chemical tricks rely on us avoiding water like the plague - a lot of what we use will react with it. It doesn't help matters that a biological reaction might have 10 million times more water…
moleculeoftheday | February 20, 2008Yesterday, I discussed a laxative drug that works by drawing water into the intestines (and introduced you to a helpful chart to aid description of particularly ineffable bowel movements).
Here is a drug that works on the same principle, but indirectly - it induces your intestines to secrete ions, which, in turn, cause water to transfer to your intestines and induce bowel movements.
The drug is a prostaglandin - you may know these from drugs that inhibit the formation of certain prostaglandins, such as ibuprofen. As you can see, the class of hormones has a broad range of physiological…
moleculeoftheday | February 19, 2008Whether it is constipation or diarrhea, irregularities in bowel movements on some level all relate to the balance of fluid in the intestines. Fiber doesn't just add bulk to feces, it holds onto water. If you go all Linus Pauling and take way too much vitamin C, you'll get diarrhea - the prodigous amount of dry water-loving solute you are ingesting will draw water into the intestines.
Many laxatives, such as sodium picosulfate, work the same way. Water follows ions, and this doubly-charged molecule draws water into the intestines, with the result of inducing a bowel movement.
If you are…