Monday, June 29, 2009

gross, but funny

I've had an ingrown hair along my jawline for a long time now. I don't get ingrown hairs too often, and usually when I do it comes out with some fussing/scratching/picking. This little bastard had resisted all my weak attempts to free it, and just festered. It was also in a place that was difficult for me to see, so it was hard to see what could be done about it.

Early last week I had finally had enough and decided to actually take care of it, and to even try to do it the proper way to provide the best results. I scratched the dead skin off the top of it, then put a concerted effort into not touching it for several days except to clean it. I shaved carefully around that area, and let it rest a day. I waited until right after a hot shower, and then took a clean pin and gingerly poked at it. Immediately a small loop of hair popped out! I put the pin in the loop and popped the end out, and that little fucker was ~1/8" long. I left it, and figured I would leave it a day, shave then, and hopefully the issue would be resolved.

Two or three hours later it was still a bit sore, and similarly irritating. I went to the bathroom, and gave it a small pull, and a lot more hair came out! The whole thing came out and wasn't attached at the root anymore. In the end it was more like 1/2" than the originally exposed 1/8". It was such an odd feeling and sight that I snapped a pic.

Tuesday, June 23, 2009


Seminal spazzcore band Frodus, who broke up before I had the pleasure of listening to them, have regrouped almost 10 years later and are playing once again! On Saturday they played the Black Cat, and I went, all bright eyed and bushy tailed, excited to see them.

I showed up early enough to see the end of the first, and all of the second acts. The first act immediately made me think of the "space rock" stage at fun fun fun fest lat year, and I was left wondering what they were doing playing this show. My buddy said it sounded like they had tried really hard to write one good song, and then played it over and over again. We grabbed some beers and sat in the back and waited for the next act.

The next act was much the same, stylistically. If you go to a punk show, and see the guitarist of any of the bands "rocking out" by gently rotating his body back and forth while he nods, also gently, something is wrong. They sounded like they had grown up listening to Don Cabellero, and really, really wanted to be that good, but it was too hard so they added some lyrics and hoped no one would notice.

At this point I was getting nervous. I didn't own any Frodus records, could I have heard the only good songs and the rest sounded like these other guys? Had I made a grave error in judgement? I was actually jumpy as they were tuning up and taking the stage.

They came out and started off like a bomb exploding and I could feel waves of relief come crashing down on me. The first 3 songs were like one long crescendo building to an insane sonic peak. I tried to get some pics, but there was just too much movement for the camera in my phone to capture it.

you wouldn't even know it was Frodus if it weren't for the base drum

It was almost like it was planned to have oddly misplaced music as the intro, it made the aural assault of the headline seem that much more significant.

Another thing they did, which I REALLY thought was great was to eschew the "encore". Encores are total bullshit, and I think I've only ever seen one real one. Even that one was pretty expected.

At the end of the set, Frodus stopped, the singer said it was time for a period of reflection, cause encores are stupid, and they brought out chairs and sat there for a minute in silence. They then got up, played more, thanked everyone, then the show was over.

If you have the chance to see Frodus, do it.

Friday, June 19, 2009

another great scheme

Once again I'm at my desk trying to plow through ISI's weekly barrage of information, and I happened on this beauty:

Obviously not the worst one, but still has some nice features. Again we see the complete disposal of the typical left to right, top to bottom method of layout most people in the western world are familiar with. Who doesn't like to needlessly read charted information the goes up?

The first little loopy section has 3 different sizes of arrowheads, when one or two would have sufficed, and later in the scheme there are another two different styles of arrowheads used for no reason.

There is text above the arrows, below the arrows, and even some partially upside down text.

Perhaps the best part is that there are no structures for just over half the compounds. That always clarifies a scheme. I'm sure everyone reading the paper know what 1,2-dihydroreticulinium and salutaridine look like, but not tyrosine or morphine.

I suppose the strange part is that the structures are drawn pretty well, for an author that can't keep the font size and capitalization consistent.


I almost immediately found this one after posting:

All the lines around the piperidines are supposed to be hydrogens. I assume they used the cyclohexane drawing tool in ChemDraw and just left all the lines. For some reason they took them out in some of the other drawings that weren't in table form, and in at least one case used a drawing with all the extra lines, and actually put an H on the one they were specifically talking about without madifying ant of the rest. It's like some sort of odd selective vision on the author's part.

Sunday, June 14, 2009

xmas trip

I kept forgetting to post this, but better late than never.

This last holiday season my girlfriend and I went to visit my parents for a few days. My girlfriend and I live in different states, and see each other only once every two or three months. The though it's weird to have sex under my parents roof was a little disconcerting, but desperate times call for desperate measures.

On the flight there, my lady and I were discussing how we were going to pull this off with a minimum of fuss. We figured condoms were the way to go, so my mom wouldn't have to launder DNA impregnated sheets, and I grabbed a flight sickness bag so we could use it as our own personal trash bag for a later, surreptitious, disposal.

Everything went as planned, and I ended up packing the little goodie bag and bringing it back home with me. After I had landed and was commuting back, it occurred to me that I had inadvertently left a nice trap for the TSA. There wasn't a note in my bag indicating it had been searched, which actually surprised me a bit. In addition to packing the latex balloons of genetic material, I had a bunch of tools I had purchased on the trip as well.

Here is a series of me unpacking what I had flown back with.

bag full of dirty laundry

xmas socks and underwear from mom

there's some more interesting things

and the goods

In retrospect, I think it would have taken some actual effort to come up with a better trap for the TSA. Too bad they didn't fall for it.

Saturday, June 13, 2009

resolution step 2

I recrystallized the material from the resolution, and the ee went up to 98.9%. Perhaps I didn't use a sufficient volume of solvent or enough wash. In any case it will be easy to recrystallize again to get the ee up enough.

I took the mother liquor from the bulk resolution, which was heavily enriched in the diasteromer salt, and free based it. The opsque, dark brown, mixture was treated with D-tartaric acid, and crashed out to give the much more enriched salt. Interestingly, when the boiling solution of base was added to the boiling solution of acid, in similar concentration to the racemic case, the salt started to come out of solution even before I was done mixing the two. The already highly enriched enantiomer gave almost optically pure material (96.8% ee) that had only a hint of color. In a typical resolution of this compound from racemic I expect to get >75% ee, so this was a pleasant surprise.

I didn't add a pic of the mother liquor because it was on the rotovap when I took this, and I expect everyone is familiar with what a flask full of tar being stripped looks like.

I recrystallized the D-tartrate salt to get the ee up, and it took nearly twice the volume of solvent it would have if it were 75% ee, presumably due to the significantly higher optical purity.

Thursday, June 11, 2009


I was taking the products from the distillation and resolving them via their tartrate salts, and decided that was inefficient to do individually on a reaction by reaction basis. I saved up the products from all the remaining reactions I had, and started the resolution on a large scale today. On the left is all the product from the distillations of material in 7 volumes of solvent, and on the right is an equivalent of acid in about 7 volumes as well.

They are heated to boiling and then combined (adding the amine to the acid), and, when it works well, the salt starts to crystallize out immediately.

After cooling it is filtered and washed. One of the wonderful things about a good chiral resolution that is not often mentioned is that in addition to increasing diastereo purity, it increases chemical purity as well.

The product should be > 99.5% ee after one recrystallization, and I can take the dark mother liquor, free base the salt, and crystallize it with D-tartaric acid to get it with >99.5% ee.


I was distilling some material yesterday. At the end there was a small amount of tar left that was free flowing at the distillation temperature, and the last volatile material was coming over a drop at a time. I shut off the heat to the oil bath and left, and when I came back sometime later I was greeted with this.

At first it reminded me of Eddie VanHalen's guitar, Frankenstein:

But now I think it looks more like a Jackson Pollock knock-off.

Monday, June 8, 2009

nice set up

I'm pushing a bunch of material through a known reaction that, before my boss and I improved it, sucked. It worked very well on small scale and the yield and quality of the product dropped off precipitously as it was scaled up. Now the reaction can be performed on most any scale and yields of purified product are typically 90% or above.

Now there is only one small problem, the solvent for the reaction is triglyme. I run the reaction quite concentrated, but I still have hundreds of milliliters of solvent to deal with that has 50-100 g of crude product in it. Extraction on this scale is doable, but vacuum distillation is not only easier and faster in this case, it leads to significantly more pure product.

Herein lies the issue, triglyme is a bitch to distill. It has a relatively high boiling point, typically 80-100 centigrade with the vacuum my pump generates, and is prone to bumping. By prone to bumping I mean that the shit bumps almost continuously when contaminated with a product mixture, and treated in the fashion I usually treat short path distillations.

The first time I ran this reaction at 50 g scale in 500 mL of triglyme, I distilled a significant portion of the solvent off starting with the 1 L flask the reaction took place in, rinsed into a 250 mL flask, and removed the remaining solvent, rinsed into a 100 mL flask and distilled the product. There was some bumping over of the product, but not too much, and the reaction-purification sequence took all day. All in all not too bad for a 50 g reaction, but I still needed to put a few hundred more grams through it in the coming days.

I remembered a set up my boss had mentioned to me in another context once that he used for distillation of a heat sensitive compound. Many people are aware of the falling film distillation apparatus, and they are available from places like Aldrich for the low low price of $800 for the lovely 24/40 model.

an easily broken paper weight that cost almost as much as an ounce of gold

When my boss needed to do some sensitive distillation a long time ago, he made up an exceedingly useful contraption to effect very similar conditions using common lab glassware. My target compounds are plenty stable to heat, but I thought the apparatus would be usefull to deal with the bumping issue. Here is my practice run with the apparatus.


It's a 3-neck 250 mL rbf fitted with a stopper, a pressure equalizing addition funnel, and a short path. Notice that the addition funnel has a glass stopcock, teflon stopcocks do not work well at all for vacuum applications. The oil bath is heated to ~150 centigrade and the mixture is added to the hot flask a little at a time. It distills rapidly, and there is never a significant amount at any one time so the bumping is inconsequential, additionally I spin the shit out of it (1,000-1,200 rpm) which helps quite a bit. This pic is a practice run, and contains the solvent from the 50 g reaction containing a trace of product, hence the slight color. I was able to distill off 500 mL water white solvent leaving the crude product in 30-40 minutes this way.

When I ran the reaction on 100 g scale I was able to distill off all the solvent, and then distill the product in less than half the time the first 50 g reaction distillation took.

Tuesday, June 2, 2009

Waste Disposal

Let say that hypothetically you are a member of an organic research group at a well regarded department. What would you do with this form?

Yeah, I know it's complicated. Sure you are here to get a PhD in organic chemistry, but that doesn't mean that you can fill out one of these crazy hard waste disposal forms. Good thing that we keep these forms conveniently stored in a folder with easy to follow instructions.

Where can I find instructions to dispose of wastes of space?

Monday, June 1, 2009


Brandon, Tim, and I climbed dreamweaver yesterday. Dreamweaver is my most ambitious route to date, a 1600 ft ribbon of snow, ice, and rock that leads to the summit of Mt Meeker at 13,911 ft. We left Ft Collins at 2:30 am, were on the trail by 4 am, were on the summit around noon, and back to the car at 3 pm. Why don't I feel like moving today?