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DBL%20Hendrix%20small.png College chemistry, 1983

Derek Lowe The 2002 Model

Dbl%20new%20portrait%20B%26W.png After 10 years of blogging. . .

Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in Germany on a Humboldt Fellowship on his post-doc. He's worked for several major pharmaceutical companies since 1989 on drug discovery projects against schizophrenia, Alzheimer's, diabetes, osteoporosis and other diseases. To contact Derek email him directly: Twitter: Dereklowe

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September 22, 2009

Colorful Junk

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Posted by Derek

Last Saturday night I stayed out until 3:30 AM, then slept in the back of our van. Now, that may sound like a pretty good evening for some of you, but it might seem a little odd for a guy like me. There's a good reason, though - I was out at the Connecticut Star Party, a meeting of amateur astronomers out in the boonies of eastern CT. Fall is a good season for those get-togethers - there are a lot of interesting things in the sky, the weather tends to clear out as cold fronts come through (but it's still temperate, overall), and it gets dark at a reasonable hour. Conditions last weekend were about as good as they can get, actually - I won't go into what I observed, unless it turns out that there are a lot of readers to whom phrases like "Minkowski's Footprint" and "G-numbered globulars around M31" mean something.
There were good views of Jupiter, though, and that always reminds me of the lab. I didn't spend much time looking at the planet (it tends to ruin your night vision for a while!), but the colors of the cloud belts are striking: yellow, brown, orange, tan, and (of course) the Great Red Spot, which is sort of a light brick color these days. (That's about the right color there in the photo, although that's a lot higher-resolution than you can see with the naked eye, taken as it was from the Cassini spacecraft on its way to Saturn. The black dot is the shadow of one of the moons, giving anyone in Jupiter's cloud deck a total solar eclipse).

What it reminds me of are the reactions on my bench (and some of those older stored samples), which are turning the same colors. And they're doing that for the same reasons. Jupiter's a gigantic stew of organic chemicals, which are being run through all kinds of temperatures and pressures (including plenty of conditions that are too bizarre to reproduce - so far - on Earth), being irradiated by the Sun and constantly zapped by huge lightning storms. The side reactions in my lab tend to make yellow, orange, red, and brown stuff, and Jupiter is nothing but side reactions.

So what is all that stuff? It's rather hard to characterize it, naturally, but I've always assumed that they're some sort of high-molecular-weight condensation products. (There's been some work done on trying to figure out what the astronomical versions of it, called tholins, must be). There must be a fair number of double bonds and a lot of conjugation in there, to get all those chromophores which push the transmitted light down to the yellow-orange part of the spectrum. All the higher-energy wavelengths of light, the purple/blue/green stuff, are being soaked up. No organic compound in my experience has ever decomposed to anything colored blue. They start by going yellow and then head down through orange and red, towards deep brown and thence to black.

So when I purify these things, and all the colorful stuff sticks to the top of the chromatography column and makes bands of who-knows-what up there, I often glance up at the stuff I'm throwing away, and think "Jupiter". And that's probably accurate.

Comments (10) + TrackBacks (0) | Category: Life in the Drug Labs


1. GA on September 22, 2009 8:38 AM writes...

Nice, Derek! What equipment were you carrying, if you don't mind me asking?

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2. Derek Lowe on September 22, 2009 9:19 AM writes...

I have an 11-inch Dobsonian scope, and an equatorial tracking platform (from Round Table Platforms) to put it on. No fancy eyepieces, just a couple of Tele-Vue Plössls - that's probably going to be my next upgrade. I've also copied and enlarged all the finder charts from my copies of the Night Sky Observer's Guide and put those in plastic sleeves, so I can put them on the scope's tube next to the eyepiece.

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3. Hap on September 22, 2009 10:05 AM writes...

One of the reactions (a model of a reaction occurring in proteins for which my advisor was trying to determine the products) I ran in grad school gave a rainbow - the products were a variety of colors (green, yellow, orange, red) which changed over time and which I wasn't able (or clueful enough) to characterize. [I assume they equilibrated over time and either decomposed or converted to a mess which I didn't understand.] Most of my reactions didn't give colors, though, even when they failed - a simple alkylation with KOH in DMSO gave a deepening yellow solution as I wondered how I could ever get my stuff out of it and finally gave up. Other people's reasearch yielded pretty fluorescent red crystals which, of course, were bricks. I don't miss my grad research.

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4. Sili on September 22, 2009 11:42 AM writes...

That's a big'un. I had no idea you liked space. Haven't been reading long enough, I guess. Now I feel bad for not even getting out too look with the naked eye over the Summer. Do you read Universe Today?

I once contributed to an article by asking a contemporary master's student what that lovely blue band on his column was. They'd always just thrown it out as a byproduct from a simple alkylation making some starting materials. He was kind enough to isolate it and crystallise it. Not all that interesting, I gather, but at least now they know what happens to that 1% of the product. (And it really was a very pretty blue.)

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5. ap08 on September 22, 2009 12:41 PM writes...

Here is a very blue organic compound:

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6. alig on September 22, 2009 1:52 PM writes...

I did some indole chemistry for a few months that gave lots of blue and purple side-products.

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7. John Beutler on September 22, 2009 2:47 PM writes...

Just yesterday I inadvertantly decomposed a sesquiterpene lactone to an stuff. The OHs were set up just right that when a touch of acid from some old CDCl3 got to it, more double bonds were generated and it started to turn blue....even in natural products, blue is rare, though.

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8. Dave on September 23, 2009 2:42 PM writes...

Trippy man, trippy......

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9. A Pocess chemist on September 24, 2009 3:32 PM writes...

If you really want blue compounds go for Anthroquinone derivatives. there are some nice disperse blue dyes.

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10. milkshake on September 24, 2009 3:45 PM writes...

amino substituted quinones are also deep blue. The corresponding amino-hydroquinones and catechols are so electron rich that they promptly oxidize on air and turn blue as soon as you filter off the Pd-C hydrogenation catalyst. I was in a lab where a guy was making these, and he was purifying them on Chromatron radial prep-TLC machine, and he produced all colors of the spectra in the react mix and the various colorful zoned crept apart this thing was spinning - Hollywood would totally love to have this in a mad scientist movie

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