3/05/2007

now accepting mojo donations

I like to take pictures in the lab. (This should be painfully obvious to anyone who has been following this blog.) Fortunately, I have a nice variety of subjects, because most of what my labmates and I make is unusually vivid. On any given day, I could walk in and find a solution for every color of the rainbow. It wouldn't be hard to mistake a random something-or-other on the rotavap for Kool-Aid.[1] It's a safe bet that most organic chemists don't see these things on a regular basis. Those who do are awfully quiet as far as blogging goes, so I'm guessing that very few people appreciate just how troublesome highly fluorescent compounds are for the camera. Granted, not everything poses this problem. If they don't absorb camera-flash, it's a non-issue.[2] This is true for most garden-variety boring white-to-yellow organics. There's also not a problem if the flash-induced glow is close to the solution colour, which is the case for the perylene diimides I've worked with.


Right now, the solution pictured above is the one that's giving me problems. I could show you the nearly-opaque red stuff I see when I turn the flash on, or I could show you the dark blue solution I see when I turn off the flash and hold it so that the light shines through it. It's almost iridescent in appearance--most of the time, it's not all blue or all red but a blend of the two. You can see this below, but the camera definitely doesn't do it justice. The camera also doesn't show just how much I've abused the TLC pencil in the picture. A bit of it remains stuck on the bench.

After the dichloromethane shower, it doesn't click anymore.
Photography is still a side interest of mine, though, and thus not deserving of too much complaint. The most irritating thing about the above solution is that I'm trying to grow crystals from it. I didn't know this wasn't easy. It sounded easy.[3] But I'm after sizable, high-quality single crystals suitable for x-ray diffraction. It appears that growing these is more voodoo than science.

Please share your crystal mojo. I need it.

[1] In the lab, as in any self-respecting suicide cult, those who are there of their own free will are necessarily insane. Don't drink the Kool-Aid!

[2] This has me seriously wondering about the spectrum of light emitted by camera. Most things that fluoresce under long-wave TLC lamp seem to fluoresce under camera-flash...

[3] I'm good at being wrong.

11 comments:

milkshake said...

Dry nanotubes can catch on fire when flashed with camera from up close (simple effect of low albedo and slow heat dissipation). It is most dramatic in pure O2; in air the flame will go out and you will just hear a funny cracking sound).

For growing crystals, benzene is magic (at least, the crystalographers swear by it)

Also, do you happen to have somebody in your department who is good at X-rays of inorganic complexes? (I have two simple air-stable Pd catalyst complexes and they crystallize rather nicely and I would like to solve the crystal structure, to get a nice paper out of it) Please let me know I would realy appreciate the help, by their co-authorship.

Mitch said...

An open beaker may not be the best crystallization method.

Mitch

Ψ*Ψ said...

Snarky, aren't we? The shots were taken right before I put the stuff on the rotavap.

Mitch said...

I'm always snarky. ;)

What is snarky?

Mitch

Matt Jenks said...

Seed crystals are the way to go.

What? No seed crystals? Then try taking it up in benzene and then growing the crystals in an nmr tube.

Lakshmi said...

I should not even be writing platitudes here, but could not find your email id at first glance, and am too lazy to search ! I love your blog. Reminds me of my years in the smelly but lovely lab as a graduate (centuries ago). Can almost smell the benzene and feel the phenol on my skin when I read it. Keep up the good work.
BTW, I was HORRIBLE at growing crystals (and was an organometallic chemist, go figure !)...so won't even dare to advise.

Mike said...

Do it like protein crystallographers - hagging drop method. In two weeks you should have nice crystals ;-) (I suppose that wasn't a big help)

Chemgeek said...

What's the "hagging drop method?"

I used to grow porphyrin crystals by layering an EtOAc solution with pentane in a 100 mL reaction tube. The tube was only about 2-3 cm wide, so the solvent interface was pretty small. After about 2 weeks I got x-rayable crystals...usually.

evgeny said...

Well, there is the crystal growing guide (and another link). I tried some of their techniques and they worked (mostly vapor diffusion and solvent diffusion). Also, I read the counterion thingy and tried a metathesis to get a similar sized counterion to my compound and it crystallized much more easily.

http://www.xray.ncsu.edu/GrowXtal.html

http://www.cryst.chem.uu.nl/growing.html

I don't agree with them saying that crystal growing is an art. Most of the time for me, it was using their suggestions, which was not really artistic on my part. But yes, the most important rule that they mention, is patience. It took me a long time to learn that one. Also, my crystallographer is sometimes happy with crystals that aren't swimming in solvent (unlike what they say in the first link). This is good, seeing as some of my stuff reacts with common solvents like benzene or cyclohexane after sitting in it for enough time.

Mike said...

@chemgeek: You place a drop of your protein-solution (including precipitant) onto a cover-slip and hang it up-side down over a reservoir (i.e. short beaker) filled with the same solution as the protein is dissolved in. Vapour diffusion then slowly does the job. I'm not sure whether this works for non-water soluble stuff, as there may be more concerns about the volatility of the solvent. Also, protein-crystals still contain a high amount of water after crystallisation.

Chemgeek said...

Cool. Thanks Mike.