More Bad Ideas

October 8, 2009

While I’m on the topic of covert nocturnal uses of things found in laboratories, I should probably mention one which is not quite so covert. It is, in point of fact, overt. Very overt. I’m talking about liquid nitrogen (LN2) bombs.

One of the classical definitions of bomb is a vessel which contains great internal pressures. This is in contrast to a more modern definition of bomb which is a vessel which fails to contain great internal pressures (usually created by some sort of chemical combustion) which has as a positive result a satisfying boom, but the undesired byproducts include flying debris, third degree burns, broken bones, lacerations, property damage, death, criminal charges, wailing, and a gnashing of whatever teeth remain after taking a flying hubcap the to face.

The flying fragments occur because it is entropically favorable for the particles of explodium to evolve from the cramped and musty confines of the solid or liquid states and become Nature’s free lovechildren that are gasses. The fiery death occurs because it is enthalpicly favorable for this to occur as well. It is possible to maximize the boom, but minimize the fiery death if the vessel is pressurized with an inert material through some sort of spontaneous process which does not release heat.

With that in mind, I refer you to the classical work on all subjects scientific: Real Genius. Think of a sealed container as Dr. Hathaway’s house, liquid nitrogen as an enormous Jiffy Pop, and the ambient heat which radiates off of everything as a 5 megawatt laser. The laser hits the popcorn which as it expands begins to fill the house. At some point the popped corn has filled the house yet more corn continues to pop and the house becomes a bomb. However, since there is no combustion in this process, there is no enthalpic gain so when the explosion goes boom it flings delicious buttery popcorn everywhere, but not fire.

Liquid nitrogen is encountered in many laboratory settings where things must be made very cold very fast, or kept very cold because with a boiling point of -196 C at 1 atm it has gone well past stick-your-face-to-a-flagpole cold and into a region where molecules are afraid to stir for fear that a serial killer will find them hiding under the bed. Generally it is considered a poor idea to keep leftover liquid nitrogen around the lab because of its tendency to condense oxygen from the atmosphere (see the previous section on exploding fiery death). The traditional method of disposing of excess liquid nitrogen is to throw it on the floor, which also doubles as a spiffy method for collecting all the dust you were too lazy to sweep up into little pills which skitter around the floor like frightened rabbits.

But I hear you asking “Wouldn’t it be nice to have a way of getting rid of excess nitrogen which would disrupt the hum-drum grind of daily lab affairs and possibly make someone poop their pants a little at the same time?”. That way, my friends, is cryocrackers. If you are slightly less sane, that way is cryocrackers and LN2 bombs.

Construction of a cryocracker is quite simple1:
1. Pour excess liquid nitrogen into an open container, such as a styrofoam cooler.
2. Obtain a polypropylene snap-top microfuge tube
3. Bend the top so that it is roughly perpendicular to the opening (this makes it easier to close when frozen)
4. Using forceps (if you’re a pussy) or your properly toughened chemist’s hands (if you’re a real man), hold the body of the tube under the liquid until the bubbles stop (exactly the way you’ve dreamed of doing to that person who keeps stealing your glassware and not washing it)
5. Pour out the majority of the nitrogen, leaving approximately 25 to 50 uL
6. Snap the top closed and IMMEDIATELY throw it away from you. Preferably under the chair of the lab mate who you’ve suspected of stealing your glassware and not washing it

tubes2If properly constructed, cryocrackers provide a unique opportunity to study the glass transition point of polymers. At room temperature, polypropylene tends to be a tough amorphous solid, capable of withstanding a fair degree of mechanical stress. However, at low temperatures it becomes a brittle, glassy, amorphous solid which is less able to bear such stress. The more nitrogen you use, the sooner the boom happens and anywhere within immediately and a few minutes of closing the cryocracker, the internal pressure will be too much for the now glassy polymer to bear, causing it to rupture and produce a satisfying *POP* noise. See the image for a fuzzy cellphone picture of a normal microfuge tube, and the new and improved version next to it2. An LN2 bomb follows the same principals, but is executed on a grander scale.

Construction of an LN2 bomb is even simpler than that of a cryocracker:3
1. Obtain a 20 oz. polyethylene terephthalate beverage bottle with a screw-on cap. Not a glass bottle. If you use a glass bottle to do this you are a terrible person who will get everything they deserve.
2. Go outside
3. Fill approximately 1/5 full with excess liquid nitrogen
4. Screw the top on firmly and IMMEDIATELY clear the area. Its probably also a good idea to use ear protection

When this one goes off it is loud. I mean “holy crap the cops are going to come” loud. Being the East coast elitist liberal that I am I have never fired a .44 magnum, but those I know that have both fired one and heard a liquid nitrogen bomb go off say that the LN2 bomb is much, much louder. And that is just with a 20 oz. soda bottle. I still have not worked up the stones to try this with a 2 L soda bottle.

You must, of course, only use this knowledge for good

1 My legal advisors, the law offices of Useyourbrain and Duh (I think they’re Dutch) tell me that I need to add a legal disclaimer at this point. You should not perform any of the actions mentioned herein. They involve cryogenic liquids which cause frostbite, and result in sharp flying fragments which may damage your eyes, cause other injuries, or break valuable equipment. Placing a cryocracker under a coworker’s chair will probably result in some sort of disciplinary action, or the precipitation of a full on myocardial infarction for which you will be legally responsible. Do not construct explosive devices and do not detonate explosive devices.

2 And imagine the sharp fragments of plastic flying through someone’s cornea or smashing your most expensive piece of glassware, or lacerating the flesh of the person who has the authority to fire your ass

3 For the love of god and all that is holy do not do this. You will be hauled off and charged under the Patriot Act.

Dye by Night

June 28, 2009

The Order Of Science Scouts: “Inappropriate Nocturnal Use of Lab Equipment in the Name of Alternative Science Experimentation / Communication” badge

Due to the clandestine nature of the activity, meticulous notes were not recorded by the principal investigator. Therefore, details are lacking and experimental procedures are  incomplete. This work is mainly reported because its the middle of Summer and I can’t sleep.


The girl I’d had my eye on when I was an undergrad worked in a laser lab. Due to malfunctioning  equipment, a large quantity of floor wax in the lab and a portion of the hallway outside had become contaminated with rhodamine.


Work was not undertaken until everyone in the department had gone home for the night in order to prevent goggle eyed stares from passers by demanding to know just what it was I thought I was doing.

A single edged razor and the better part of an hour were used to strip approximately 5 g of electric-pink floor wax from the hallway tiles*. It was surmised that since the custodians had long eschewed the department on the grounds that chemicals routinely leap from sealed bottles and kill people, this vandalism to the floor would not be particularly bemoaned.

The pink waxy solid was dissolved and filtered to remove traces of lint, staples, and gravel. An acid-base extraction was used to separate the rhodamine from the matrix, and the solution was concentrated in vacuo. Another hour was spent playing with chromatography conditions and purifying the product which came off the column in a fluorescent band like some sort of sophomore organic lab demo, yielding several mg of crystals which were sealed in a vial and presented to her for her birthday.

Results and Conclusions

It didn’t work out though, and for the best. She ended up dating someone who even though I tried my best to be jealous of at first, I have to admit was a great guy.

I graduated and got accepted to a program where I met a girl who I am deliriously happy with. However, when I reflect upon all the ill advised nocturnal misappropriations of scientific equipment I am guilty of perpetrating, this one stands out as not the most dangerous, but probably the silliest. Eventhough, they do say we regret most that which we do not try.

*It should be noted that in many older buildings, 9-inch floor tiles may contain asbestos. Keep this in mind before tearing them up with razor blades in order to impress a girl

Chromophores and You

June 3, 2009

Chances are if you work in a lab that does any sort of biochem related activities, at some point you’ll have to stick something to a protein. The two most popular points of attachment are primary amines and thiols because they’re fairly nucleophilic under conditions which won’t completely destroy your protein.


Primary amines are most often conveniently encountered in the form of lysine residues, or N-termini. In fact, most proteins are lousy with the damn things which is a problem if you want site specificity. The N-terminus tends to be more nucleophilic than other sites, but you’ll generally end up drenching your protein with the reactive compound and hope it doesn’t land anywhere that it will get in the way. Thiols show up as cysteine residues, and unlike primary amines tend to be much rarer and quite a few proteins have none at all naturally. If you know the site where you want something attached, it is fairly easy to engineer a cysteine there for site specificity.


Methods for modifying thiols tend to come down to two options: forming a thioether, or forming a disulfide. The most popular groups for the first are iodoacetamides, and maleamides. The third usually uses a thiosulfonyl. However, thioethers are pretty irreversible, and disulfides usually get reduced somewhere along the line. So how do you nail something onto a thiol but leave yourself the option of selectively removing it later?


That’s phenylmercury, baby! Stuck to Alexa Fluor® 488. This autism campaigner’s wet dream of a chromophore is available from Invitrogen. That S-Hg bond will stand up to TCEP reduction, but can be knocked off by DTT or 0.1 M HCl.

Can’t say I have any plans to rush out and use this thing though. I’ve got much better means of killing brain cells.

Here I Am

February 9, 2009

Well Here I am, starting my own chemistry blog. I don’t forsee having any central point beyond chemistry in general. Since I consider myself an organic chemist first, things around here will probably be mainly involved there, but I don’t see myself getting super focused on any one topic. I mostly see myself posting whatever happens to amuse me at the time.

See you all around.

P.S I know my spelling is terrible


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