Always look on the fluorescent side of life

This week’s chemdoodle is on the colourful side, and not just literally.

Rhodamine B on canvas

Last weekend I spent for a change in Amsterdam instead of the lab. No, and I didn’t just use my time there to engage in biochemical test on myself but also went to the Van Gogh museum. Big recommendation from my side, even if you’re not a big fan of paintings. The museum really went out of its way to bring a scientific side to the art, showing how important XPS and pigment analysis are for conserving the paintings. It was in their shop that I purchased the beautiful tiny canvas and stand I drew this week’s chemdoodle on. It definitely had to be something colourful, very colourful…heck, why not fluorescent? That’s why it’s Rhodamine B this week, a classic pink dye, which is just one of the many dyes with a xanthene core structure.

Apart from being extensively used in biochemical fluorescence applications, Rhodamine B can be used for staining acid-fast bacteria (where it binds to fatty acids in the cell walls), as a medium for tunable lasers or even to trace rabies vaccination in wild racoons.

xanthene and rhodamine B
Rhodamine B with its xanthene core structure. This week drawn with Chemdoodle!

Fluorescent dyes and tags are an intrinsic part of biochemical research and I think they deserved a hell of a lot more attention. Also, fluorescence is generally awesome and soooo pretty to look at (As an organic chemist who generally gets all the boring white colourless solids, I still get overly excited about colourful things). Fluorescent dyes not only come in all kinds of colours, they also have such enticing names such as Pacific Blue, Alexa Fluor or Texas Red (no Texas carbons unfortunately).

Spectrum of fluorescent dyes
Fluorescent dyes in all their beauty!
Winning image from the Science and Engineering Visualisation Challenge.
Molecules exposed to light get bombarded by photons all the time. The energy of theses photons lifts electrons into higher excited states – fluorescence, the process of emitting photons, is one of the ways molecules deal with the excess energy and getting their electrons back into ground state.
excited electron and unimpressed photon
Fluorescence is slow. And by ‘slow’ I mean around 0.00000001 seconds…pretty sluggish when you compare it with the femto to pico-second scale of other electronic processes like internal transitions or vibrational relaxations.

jablonski diagram fluorescence
Jablonski diagram of the fluorescence process. Black background makes everything better. For more jablonsking check here.
Let’s say a molecule receives an energetic input from a photon of a certain wavelength, which excites an electron (green arrow). This electron then squiggles its way through the higher excited stages down to the first excited stage (squiggly purple arrow), as getting rid of energy is so much faster that way. At the first excited state, the slow fluorescence (blue arrow) can compete with the other processes that get the electron back to the ground state; that’s why the emitted photon is less energetic (has a longer wavelength) than the absorbed photon. Often times the absorbed photons are of ultraviolet wavelengths whereas the emitted ones are in the range of visible light.
matlaline blue fluorescence
Wood extracts from South American tree species. Blue fluorescence is caused by Matlaline. (R = glucose)
Fluorescence occurs naturally, in minerals, plants and animals. I bet people were as fascinated in the 16th century by a flask containing the fluorescent solution of extracts from certain South American trees as I was by the fluorescent minerals in the Swedish mineral museum I went to when I was little.
Fluorescent minerals
Fluorescent minerals. So pretty, even my 6-year-old self thought so.

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