Dyes
moleculeoftheday | August 11, 2008Pyrene is a simple, four-fused benzene PAH:
What makes it neat is how it interacts with light. In particular, it's got some unusually sharp UV bands that are sensitive to solvent polarity. Additionally, the excited state dimer exhibits some especially unique photochemistry of its own, providing a way to sense whether you've got two stacked pyrenes together.
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 | January 30, 2008This one always shocks people the first time they hear it. Have you ever seen "carmine" on an ingredients label of some food in the red-purple color family? Yeah, you're eating bugs.
Carminic acid is extracted from the shells of certain insects.
And you're not necessarily safe if it doesn't say "carmine" - it can hide behind that glib reassurance, "natural ingredients" - which the food manufacturer is using in the first place because we started fretting over artificial coloring!
moleculeoftheday | September 21, 2007Benzophenone is something you probably encounter most often in sunscreen:
It looks like it should be a profoundly fluorescent molecule to the semi-initiated, but for quantum-mechanical reasons, it is instead a phosphorescent molecule and won't emit much at all at room temperature.. If you cool it down to liquid nitrogen temperatures you can see emission from the "triplet state."
You can also make a great solution-phase drying reagent from it - benzophenone ketyl. It's one of the neater things in an organic lab - a boiling purple solution giving you clear, pure, dry solvent.
moleculeoftheday | September 11, 2007Tiron is a metal ligand and can be used in colorimetric metal assays.
Transition metal complexes tend to have the happy property of having their frontier orbitals separated by energy characteristic of photons of visible light - that is, they end up having pretty colors. I've never actually used it, but Merck claims complexes with different metals that span essentially the whole visible spectrum - iron gives blue, copper greenish-yellow, titanium orange, and molybdenum yellow.
For another example of a colorimetrically useful metal ligand, see my entry on that wonderfully named staple of…
moleculeoftheday | June 22, 2007Henna tattoos are a pretty harmless way for hippies to entertain and adorn themselves. A relatively benign dye, Lawsone, stains the skin (or hair) a ruddy brown. Like a semi-temporary tattoo. However, you're limited to pretty much just that color. Some manufacturers have added p-phenylenediamine to their stuff, to create so-called "black henna."
p-phenylenediamine is a contact sensitizer (i.e., you can develop an allergy). This wouldn't be such a big deal if it weren't so ubiquitous - hair dyes, inks, and the like all have it too. Black's a tough effect to achieve.
Chemical sensitivity (the…
moleculeoftheday | May 9, 2007I just love this. Ever wonder how a rewritable CD works?
AgInSbTe is just an alloy of the four metals. When you heat it with rapid bursts of intense laser light, you get amorphous AgInSbTe (not very reflective). When you heat it with long pulses of low-intensity laser light, you get crystalline AgInSbTe (reflective). Get the intensity, beam size, and pulse length just so, and you can make discrete areas that reflect laser light (of a much lower intensity) to a much different extent. There's your ones and zeroes, there's your CD.
When you're done with it and want to rewrite, just blank…
moleculeoftheday | April 27, 2007The word chromatography, reveals its origins - in the beginning of the 20th century, Mikhail Tsvet - color compounds. The modern stable of robust, tunable separation techniques (i.e., chromatography) is probably one of the most important things chemistry has given us - and it's only a hundred years old. Today, chromatography is used mostly to separate compounds without any visible color at all!
It's hard, however, to understate the importance of dyes in the development of modern chemistry. We take colored fabrics completely for granted today, but dyes used to be a luxury. Dyes, too, also…
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 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 | February 14, 2007Reichardt's dye is pleasing in structure and function:
It is related to yesterday's molecule, betaine. It is technically a "betaine," but in a much broader sense, since it is an ammonium zwitterion (has a positive and negative charge). It posesses the property of solvatochromism - that is, it actually changes color depending how polar a solvent you use.
You can get it to turn essentially any color in the visible, just by varying the solvent you use. It has found a lot of use in characterizing how polar certain microenvironments are (such as cell membranes and similar micelle-type structures…
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 | 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 8, 2006Methylene blue is a well-known dye. It is useful as a biological stain, binds to DNA, and can turn your urine blue.. Incredibly, I'm opting to talk about how it's used in time-sensitive DVDs.
Awhile back, a DVD format called Flexplay was introduced. The idea here is that since DVDs are so relatively cheap to produce, there's no real reason to have the customer return them (except to avoid diluting the value of purchased DVDs). One ill-fated format, DIVX, came about a few years back, but it was unwieldy and essentially a pay-per-view system - special players had to be hooked up to a phone line…