Everybody should read this

I read a story on Wired news about garage chemistry. I wish they still sold chemistry sets that I thought would be fun to use. Like all the chemicals and equipment necessary to isolate and characterize natural products. I think I would specialize in marine natural products, they don't seem to be a passing fad.

Organic chemistry_, Cutting edge literature_

The Golden Run

Last night's run was what we analytical chemists call a golden run. This means that all the analytes that I needed to analyze for, for each sample, had the yellow highlighter run over them on the cover page of the lab report. The yellow highlighter means that the result is good to go and I don't need to reanalyze. This has only happened one other time in the year I have been running the mass spec.
Talk about staying steady, the mass spec was on point for at least 12 to 14 hours. Now, sales people for mass specs say their instruments can stay "in cal." for like 2 or 3 days. What they don't tell is they are analyzing nice clean pretty sample in D.I. water. Get some real samples in there with loads of salt or suspended solids and your instrument might not make it past the first sample like that.

In the lab_,

Backwards chromatography with Mass Spec

I've been trying to run the FIAS analysis for three days now, the column just doesn't seem to be doing its job. I think the problem might be that I have it backwards. I believe the way the flow should be is into the large end and out the small end. This way, the front of the column will bind the most metals, then, when the flow reverses to rinse the metals off the column with dilute acid, the metals will be at the end of the column, so they come off together.

More from the blogosphere

I've been reading a few other chemistry blogs around the web.

The Sceptical Chymist
This blog is from the editors of Nature. They have several different authors and many chemstry topics. Somehow they know about In the pipeline and Tenderblog. Powered by Moveable Type.

TotallySynthetic.com
This blog must be from some grad student trying to keep up on "the literature." I do enjoy the review natural product molecules in current literature I can't read about due to enormous subscription fees.

The Endless Frontier
Ph.D student at Harvard.

Interfacial Science
California post-doc.

post doc ergo propter doc
Canadian post-doc.

Check them out and enjoy.

In the blogosphere_

Busy as Hell

Sometimes you're waiting around for the chemistry to happen, but I haven't been. It goes like this, I run the mass spec everyday which includes first, turning it on. Sometimes the plasma flickers, arcs, and starts melting the torch. This pisses me off, and it pisses my boss off because they are over $300 bucks. I still use them if they didn't melt all the way through.

Then, I move on to "optimizing" the "signal." This consists of aspirating a "tuning" solution and looking at a real time graph of "intensity" vs. time. And basically, you just move some voltages around to create high intensity of what you want, while creating low intensity for things you don't want.

Getting mid-way throught the morning now, I need to find some time to review the run from last night and prepare all the data in a type of lab report. The best time to start this is right after I start the calibration. I usually see some drift during the first calibration, so I restart it right about lunch time, so the lab keeps working while I'm off the clock.

Getting back from lunch, I have to quickly check the calibration and find some samples to run because there is no point in even thinking of running any samples until I know the instrument is going to work right. So I type in a sample sequence, make sure the QC is kosher, and then start making dilutions for pretty much everything but freshwater samples.

Now it's about 4pm and I have to finish reviewing yesterdays data, make any solutions that need to be made, and deal with email. Then I just schedule the MS to shutdown when it's done, which is usually between midnight and 3 in the morning.

In my backyard

I grow the herb Wormwood in my backyard just because it synthesizes the psychedelic compound Thujone.

These goodies are used to make absinthe.

Copper in seawater

This is the worst analysis ever, it's called Time Transient Resolved Analysis (TTRA) or Flow Injection Analysis of Seawater (FIAS). The methods are the same, they remove the salt from the seawater so I can measure the concentration of copper. The problem is the flow, there are two pumps, two valves, four lines, a 5mL loop, column, and six way valve, and the flow has got to be steady. A simple calculation reveals 7 to the 10th ways for it to screw up.

I have to use a bunch of para-film to keep the tube joints together because the pump builds up so much pressure in the peri pump tube to push everything throught the column.

The sample flows through a tube, mixes with a buffer (the whole shabang is pH sensitive), and flows onto the column. The metals, including copper and sodium, stick to the resin in the column. The column is rinsed with water, supposedly, the sodium washes off. Then the column is rinsed with diluted nitric acid and the copper comes off and goes into the spectrometer. The metals binding strength to the iminodiacetate resin in the column depends on pH.

Mass Spec at home?

There is a reason why you can't have a mass spec at your house. It's not because it's so big, it's because they cost so much to fix. I had a service technician come out the other day and his visit to fix one part for one day was a cool $25,000. Ya, thats just to fix it. You could buy a pretty nice house for what they can cost new.

Parts break all the time, and you can't just keep running it like a car, a mass spec has to be fully optimized at all times to work properly. The technology is always pushed to the furthest point. If old designers of mass specs stuck with the original design and just improved on it, like a clothes washer, maybe they could last 30 years. But, then it would have run off of DOS.

The picture is not me or the mass spec I run, that thing is huge. And whats with all the multi-colored lights.

Ophiobolin C

I worked on the synthesis of this molecule while in school at FSU as an undergraduate. It was one of my better academic experiences in Tallahassee. I had my own lab bench, my own glassware, and my own chemicals. I guess it was a taste of graduate school without the 80 hours a week. I met a lot of great people in there; post docs and graduate students who have all dispersed across the world from England to China. When I retire, I'm going to build a
laboratory and make natural products.