38 Last weekend I came up with what I figured was a really good idea – start a wiki for chemical procedures in the lab so that everyone in the chemoblogosphere could participate. Simultaneously (and independently), J came up with an idea for a database about various chemical properties and techniques. His idea was much more broad, but it’s a great one. For some strange reason we both went to Mitch (My reasoning was simple: Mitch is by far more connected than I am to the chemoblogosphere). After dabbling and debating we finally agreed to part ways because we couldn’t agree on the format. I think books are stupid and no one reads them anymore and Mitch doesn’t think people are earnest enough to give a fuck to build a wiki on chemistry.
This lead to two things. Firstly, Mitch’s appropriation of my idea but no Wiki and no lab techniques, instead he wants you to help him make a book that categorizes named reactions. To show that there’s no hard feelings I said I would help advertise that, so here I am. It’s a lovely idea, I hope it’s successful.
Secondly, there still needs to be a wiki or SOMETHING on lab techniques – for instance, the different methods of packing columns, disposal of solvents and reagents, how to degrease NaH, maybe. Lots of different things we do in the lab that we just take for granted but learned from generations of chemists before us. While working in a large lab may lend itself to a person who can advise you on every possible reaction, most of us don’t work in large labs and it would provide for great teaching materials.
Would there be any interest if I went rogue and set up a wiki and had you, the loyal Chem Blog reader, as my army of photographers and journalists composing everything from how to pipette to how to dry pack a column?
These two projects aren’t competing, so it’s not like you need to “pick one” the idea is still collaborative and I’m hoping I can convince Mitch to let me use his server to run the wiki…
Also a big fucking BOO to Senator Feinstein for being such a goddamn tool.
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I’ll help. This is a much needed resource for chemists.
Would there be any interest if I went rouge and
rouge brightens nipples. rogues enjoy the result.
The standard stuff is everywhere. The good stuff is rare and valuable. Don’t put teflon tape on cut aluminum threads then screw together. An inch of narrow bore glass tubing and two tiny serum caps make handling syringes partly filled with organometallics in volatile solvents a cakewalk. If anybody says “trimethylaluminum” remember your doctor’s appointment. A vibromixer makes “freeze pump thaw” a silly thing. Don’t whip a vacuum ampoule of degassed liquid – the fluid slug hits bottom like a sledgehammer. Stuff like that.
What is this vibromixer you speak of? It sounds like either a vibrator or a method to save me hours and hours of freeze pump thawing. Either way, my curiosity is peaked.
I think he means a sonicator…
Vibro-mixer is a contact-activated vibrator commonly used in biology labs. Sonicators work fine also – in our medchem lab we stopped using freeze/thaw. Just 5-10 min of gentle sparge with Ar through the septa while the flask is sonicated works fine for all Pd(0) reactions.
It’s a little gizmo with a rubber cup atop that whizzes around off-center. Hook your ampoule up to the line through a flexible hose, stopcock off. Turn on the vibromixer, touch the ampoule’s base into the rubber cup. The fluid spins like all Hell as you hear “slosh”. Crack the stopcock a tad (bubbles!), then close it. Wait a moment for equilibrium, then repeat. Solvent vapor whooses the air out each time you crack the stopcock. Finally, give it stronger stopcock openings. Pretty soon “slosh” (air bubbles) goes to “tinkle” (cavitating vapor bubbles) and you are done. If you are willing to lose ~1% volatiles you can easily save 15 minutes/tube and a lot of cryogen.
Cut the bottom (less than a centimeter rim) off a styrofoam coffee cup. Take a cork borer and center a hole slightly smaller than the tubing on your ampoule. Slide it down to the base. Vibro-vacuum degas and leave attached. Add a drop of spit to the junction, wiggle a bit, add liquid nitrogen and more as necessary. Your volatiles now freeze out at the base of the tubing. No need to freeze the whole tube.
Take your glassblowning torch and with a somewhat bushy flame warm glass tubing above the collar. Add some more oxygen to focus the flame and *using its side*, warm the tubing at 120 or 90 degree intervals, same height, to make three or four *shallow* indentations. Carefully pull a little fresh vacuum again. Ease back on the oxygen and progressively warm the indented girdle all around past sodium light. The tubing collapses into a perfect bishop’s mitre seal with no pyrolytic carbon deposition. More oxygen to pull off above the seal. Break off the styrofoam collar.
Uncle Al blew and ran an ungodly number of long vacuum ampoules doing methacrylate, acrylamide, and N-vinyl-pyrrolidinone medical polymers. When you have 20 or 50 ternary compositions to plot in multiple theory of experimentation crapolas you run those puppies, hang them in the John Holmes Commemorative waterbath, then go to lunch. Tech time before and after is SOP. Warming initiated monomer after freezing is stupid – and dangerous.
Silanize the ampoule – Gelest Aquaphobe CM (Siliclad if you are an Enviro-pussy) or Rain-X – if you want a decent rod to side out after polymerization.
Uncle Al recommends lab notbook entry as “ampoules were prepared, loaded, degassed, and sealed.” When they fire your sorry ass after the problem is solved the next pudknocker in the hole can earn his salary by working out the fine details, again.
That sounds like a pretty good idea. I have to do freeze-pump-thaws on a regular basis, and it doesn’t take much to freeze out argon and then get a faceful of surprise when you thaw too quickly.
Good idea. Right now I find Organic Syntheses to be pretty good for the same purpose (not as a reference, but reading about various synthetic techniques in the context of the procedures published in Org Synth). You’ll want to check out any potential legal issues too and CYA (i.e. if someone follows a procedure and gets hurt) as well as being vigilant about defacement of the Wiki pages.
An interesting, possibly pre-Wiki-esque version of what you had in mind: http://chem.chem.rochester.edu/~nvd/ (the Not Voodoo site from the Univ. of Rochester)
Why a book on named reactions? I have 5 really good ones on my shelf. And besides… aren’t there already a dozen web sites where you can look them up?
The point is not to make a book.
I just wanted to design a simple experiment to see if there was a better way to motivate chemists to collaborate online besides a wiki. Name reactions are so simple I figured I would try with that.
Might you run the risk of people feeling it’s not worth the effort a few months into the project because it’s well worn territory? I know you’re gauging interest and looking for a win. I also read your post on your blog, and I had the same thoughts then. But something tells me your mind is pretty well set on the reactions.
I’m in. As long as there’s a section labelled “Cowboy”.
You should check out openwetware. It’s mostly biology oriented but it sounds similar to what you’re thinking of. There are protocols, lab websites, and even courses hosted there.
We have something similar to this for our lab. It’s a bunch of solid state chemistry techniques like carbon coating tubes,how to make proper ampoules, handling uranium and thorium, handling thallium, etc, etc. I could easily share.
This is a great idea and I am definitely up for updating the inorganic/materials technology catergory on this wiki since I am behind the curve on the synthetic end.
I’m in.
Definitely in. Not sure what I can contribute, though…
I hear you on Me3Al, Uncle Al. When someone mentions triethylaluminium-catalysed amidation I always send them to this site:
http://www.inetres.com/gp/mili...../M202.html
The God Fart: Big thin gauge bomb casing with a low-explosive bursting charge down its center, covered detcord along the outer surface dividing it into segments, filled with a tonne of AlMe3. Palletize; add parachutes, strobes, and screamers. Drop it from a cargo plane. At about 500-1000 feet, with everybody looking up in dark of night, pop it.
My first job out of college was working in a lab that made and used Me3Al on *large* scale. Very fun stuff indeed, especially neat.
someone wiki’s an article on how to recrystalize bisphosphines without them oxidizing (or maybe its just my bisphoshine??) and i’ll contribute lots
I think Kyle’s idea about lab techniques could be immensely useful, since we’re losing a lot of the old tradition and a tremendous amount of knowledge… the only concern would be to ensure the safety of what gets posted, despite the fact that it would surely be ‘use at your own risk’.
As for the named reactions book… not sure I understand where the difference lies between something like that and say, Beilstein / Gmelin Crossfire? If the point is collaboration I think an online compilation of lab techniques could be much more useful because it’s so much more difficult to find.
This is good, especially if it explains how to do things SAFELY. Safety in my lab is like a foreign word, no one gives a fuck about it.
If you and J want a compromise why don’t you print out sections on how to do reactions and then staple them to a LCD monitor? Its a great compromise, and its the tactic that democrats and republicans have been doing forever.
Couldn’t contribute anything to it myself having only just finished high school, but if it was made I would certainly spend quite a bit of time on it. Being unable to afford many books, – let alone take any kind of advanced course one the subject – abother online source of Chem. information would be great.
I’m in.
There’s already a wiki available for this at openwetware.org. Sure – it’s all about biology methods right now, but I’d recommend talking to those guys and start editing already.
Um, oh right, Matt already said that. +1 then.
MIT’s OCW has a section titled “Digital Lab Techniques Manual” at
http://ocw.mit.edu/ans7870/res...../index.htm
another +1 for the openwetware.org/chemistry/subdiscipline
I typically stand on the sidelines and just read these blogs, but I would certainly contribute (and use!) something like this.
The outline is already there…
Seems the Bionic Brothers will have to spring a miracle now…
Can Two Molecules Have the Same NMR Spectrum? Hexacyclinol Revisited
Giacomo Saielli† and Alessandro Bagno*,‡
Org. Lett. ASAP DOI: 10.1021/ol900164a
“An in-depth DFT computational investigation (B97-2/cc-pVTZ level) of the 1H and 13C NMR spectra of the recently disputed natural substance hexacyclinol, including J(1H,1H) couplings, is presented. Structures 1 and 2 have been compared with regard to the suggested possibility that two molecules have very similar NMR spectra as to be indistinguishable. Despite a remarkable similarity of functional groups present, the two
calculated spectra differ in many features related both to chemical shifts and connectivities”
I think this is a great idea. I learned a lot of things from my elders, but there’s a lot that I didn’t learn, thinking so-and-so knows that, I’ll ask him if I ever need to know. I never needed to know, now I lost track of so-and-so and I don’t know how to do it (e.g., making diazomethane). There are other things I did once or twice and forgot how to in the intervening years (e.g., tips for making and isolating labile TMS enol ethers). And there are some things I learned that might be way too cautiously paranoid or maybe even just mindless tradition (use ceramic spatulas with LAH because metal spatulas could cause dangerous decomposition).
Having a repository of all these kinds of things in a sort of peer-reviewed wiki, or other similar forum, would be tremendously useful. And I have to agree with the other commenters about this being a far more worthy undertaking than named reactions. There are lots of other very good repositories of named reactions, and I can’t see getting people too motivated to try to make yet another one. There isn’t a really good, comprehensive site for the oral tradition of practical lab technique, so this seems to be a more pressing need.
A technique wiki would be a lot more valuable than another named reaction book. There are already a lot books and pages about that kicking around and unless you can contribute something really significant I don’t see the point. A lab wiki would be most valuable as a place to find general descriptions accompanied by peer reviewed references and a discussion page where people can share their personal experience.
I think a wiki page sounds like a great idea. I am sure I would try to contribute to some techniques. It would be nice to greatly exceed the excellent information already available at places like
NotVoodoo or Al’s Notebook among others…
I like this idea, and wrote my own blurb on my favorite reaction.
You’re about 7 years too late for anyone to consider it useful. There are many alternatives on the web today. And are you going to personally vouch for the veracity of the wiki’s claims???
You won’t know when you’re being scammed.
What about talking to the Open Notebook Science chem prof from Drexel University (Jean-Claude Bradley)? http://usefulchem.wikispaces.com
Laura – it doesn’t seem like what’s being discussed here is making lab notebooks public but rather tried and true lab techniques. Adding to what several others have already mentioned it does seem that OpenWetWare is a perfect fit for this.
First off, we need a JoVE like website for organic synthesis. Second, Sigma should be hosting a wiki for each of its products.