Archive for May, 2007

I’m very excited to announce what is shaping up to become a regular feature on ChemBark: The Rip Van Winkle Files.  These posts will be penned by “Retread,” a commenter who recently rediscovered his chemical roots when he stumbled upon the chemical blogosphere.  If you pay attention to comment threads at Totally Synthetic and here, on The Wall, you may already be familiar with his story.

I’ll let Retread introduce himself properly; his first post is below.  Given his participation in what was perhaps the most exciting environment for organic chemistry in history and his unique story, I am really looking forward to these posts and his perspective on the modern chemistry “scene”.  As far as my participation is concerned, I am merely a messenger—Retread sends me his essays and I post them, uncensored, in all their original glory (with minor HTML reformatting).

For those of you interested in following the series, his posts will be filed under “The Rip Van Winkle Files”.

Enjoy.

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What’s all this about?  Well it started like this when I posted the following on The Wall:

24 Apr ‘07

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Let’s say you were a graduate student in organic chemistry at Harvard ‘60 - ‘62 (I was), and that you passed 8 of the first 9 cumes (I did) and that you talked Woodward into letting you work on you own idea 9 months after you got there because passing 8 cumes was all you needed to start your PhD work (also true) and were remembered by most concerned as arrogant unfortunately true) and that you were god-awful in the lab (true) and left organic chemistry to go back to medicine. Further suppose that organic chemistry always seemed natural and fun, and that you happened to see a squib in the 12 April Nature about the total synthesis of Lyconadin B, Googled it and found the structure and commentary in TotallySynthetic.Com and fell back in love with organic chemistry, and wished to get up to speed so you could enjoy reading about the field again.

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How and where would you start? What are the best introductory texts for organic chemistry, physical organic chemistry? Are there still texts, or is everything on the web now? What is the best place to read about NMR and structure determination (just beginning back then), computational chemistry (practically nonexistent back then — they were still sweating H2+). Also is Debye Huckel theory still what we used to think about it — good for slightly impure distilled water, but not much else. Something better is needed for
cell water which is .3 molar.

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I love the irreverance of the chemical blogs. Have at it folks.

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and

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Thanks

I got this back the same day from Excimer:

I’ll bite: my favorite introductory chem text is by Jones- it has pretty widespread use throughout undergraduate classes still, and I like Anslyn and Dougherty’s “Modern Physical Organic Chemistry” for that subject.

and from Paul:

Excimer mentions my two favorite undergraduate organic texts. I would also consider ordering the solutions manual to Jones, then working out some of the problems. There are few things more satisfying than being able to solve problems to convince yourself you understand what’s going on. If you’re super-excited, what about enrolling in an orgo course at a local community college? Taking courses on a subject always gives me extra motivation to learn things, since you have to stick to a schedule.

So I bought the above (the solution manual hasn’t arrived yet) and started working through Jones ‘04.  Anslyn looks like something I should read after Jones.   I was impressed with how different Jones is than how I remembered my first Organic text (English & Cassidy 2nd Ed. ‘56) so I managed to find a copy on the net and it arrived today.  The next post will contrast the two books.

So this series will be sort of “Rip Van Winkle meets Modern Organic Chemistry”.  Why should you bother reading what’s coming?   Just imagine quitting grad school with what you know and spending the next 45 years reading molecular biology and biochemistry with the background you currently have (in your spare time while going to med school and practicing neurology that is).  I guarantee you’d find it primitive and rather simplistic but would have no problem understanding what’s going on.   So there will be tidbits here and there that you’re unlikely to find elsewhere (such as why Jones is wrong about Strychnine poisoning — I saw a case, and how the cell lets potassium inside while excluding the smaller sodium ion — if you don’t know the answer think of how you’d design a protein to do it — MacKinnon won a Nobel for it — if you can’t wait.  I can assure you that no one had a clue until the structure was solved.  There was a lot of handwaving about differential absorption of Na and K to proteins, and that great fudge factor that no one could calculate — the activity coefficient.

Stay tuned,

Retread

In the course of running experiments today, one of my labmates happened across a small mercury spill in our instrument room. Well, we’re not 100% sure it was mercury, but the material was both liquid and metallic. Our lab just finished a massive clean up and it has taken only a week for someone to soil a common area with a nasty chemical THEN SIMPLY WALK AWAY. I really hate some of the people here—I just wish I knew who.

This being our first venture into using the handy-dandy mercury spill kit, we decided to film the event and preserve it for the historical record. Enjoy: Part I, Part II.

Director’s Note: These videos are long and not particularly instructive or entertaining.

I picked up an old issue of the New England Journal of Medicine and came across a couple of interesting picture stories. The first was on a serious HF accident (free access). The poor victim was cleaning an old facility used for glass etching when a pipe containing 70% HF burst on him. The treatment involved pumping Mg²⁺ and Ca²⁺ into his veins and arteries.  You can actually see the calcified precipitates on his skin. Yum: 

The second pict-o-story was based on a tub of fluorescent urine.  When admitted to the ER, the urinator was believed to have ingested anti-freeze.  The doctors noted that the patient’s pee fluoresced under UV light, and they concluded that this was probably the result of the anti-freeze’s being spiked with dye.  The wording of the paper made it seem like the doctors suspected the chromaphore was fluorescein, which is often added to anti-freeze to aid in the detection of radiator leaks.

The only problem is that the fluorescence was blue, not green, which is the color you’d expect from fluorescein.  Some other guys noticed the same thing and sent a letter to the editor, so who knows what’s going on?  In their defense, the doctors noted that there are plenty of opportunities for false negatives and false positives if this were to actually be used as a test for anti-freeze ingestion, so it appears the only reason this story was published was as an excuse to run a pretty picture of glowing urine.  I can respect that.

Lastly, I should add that both of the patients survived and apologize for ruining your appetites.

ChemBark has obtained the covers to the next two issues of Chemical and Engineering News.  Sources tell us that they may change at the last minute, but given the juicy nature of the featured stories, you will appreciate seeing them now:

May 28th:

June 4th:

Anyone interested in “discovering” future covers of C&EN should use this handy PowerPoint file.  It will prove especially useful for finding headlines like “My Hoodmate Smells like Cheese” or “Advisor of the Year”.  For decent conversion to j-peg, “print” your cover using the highest quality setting into a PDF file, then cut and paste it into an image editor like Photoshop.  You’ll have to adjust some things (colors, fonts, spacing) if you want a color print (directly from PPT) to look right.  I’ll be sure to tell Bill Gates about this problem when he comes here next month.

P.S.  When I said “big, Big, BIG…”, I was lying.

P.P.S.  Be sure to share your efforts with the rest of us.

As you know by now, I’m a C&E News superfan. In this week’s edition, editor-in-chief Rudy Baum discusses how he spices up the cover of our favorite chemistry magazine by insisting on variety.  That’s why I like it when he cuts the leash and lets the art editors (directors?) play with the covers. On May 7th, we saw the third (by my count) fancy cover since the 2006 redesign.  The blue and white title bar made a triumphant return, and the cover sported the most centrally-located address label that I can remember (yet required no ugly white box):

Now is probably as good a time as any to unload all of the comments and suggestions I’ve been saving for C&EN: 

— As much as I hate to say it, I’ve really liked the new ”C&EN Photo Gallery” section.  I’m torn, because while I like nice pictures, I am also troubled by some PI’s insistance on finding a pretty picture FOR EVERYTHING. That said, there are times when the crux of an experiment can be explained by a nice picture. Also, some pictures bankrupt of scientific value still have artistic merit.

— I think a regular reader/commenter on ChemBark took one of the pictures featured in this week’s gallery. I don’t want to out him/her, but would the mystery photographer enter and sign in, please?

— I’d like to see more opinion in C&EN, especially the point-counterpoint pieces. There is a simple method for selecting good pairs of chemists to fight in print. First, the people have to be recognized experts on the subject in question.  You can’t pick a random idiot, but you also can’t pick a big name in a tangential field just because he’s a big name. Second, it’s best if the people you pick are jerks who don’t care about upsetting anyone. Don’t pick writers who mince words—diplomatic writing is less informative and less entertaining.  Give us a duel.  We want to know why someone is wrong, and we don’t want to sift through BS to find out.

— My most radical suggestion: C&EN should sponsor a chemical song parody contest.  They could run a full-page call for submissions over several weeks, then post the best songs (top 50?) online and give prizes to the top 5.  I’m sure the contest would drive plenty of traffic to the online edition, and the feature would stand a good chance of getting picked up by Fark, Slashdot, and Boing-Boing.  If money is what motivates the powers that be, think about how this would increase site traffic, and consequently, ad revenue.

That’s it for now, but prepare for a big Big BIG BIG C&E News post on Friday.  Big.

BIG. 

Regular commenter CET sent along an interesting picture from a gen-chem textbook at his school. Start the week out right by determining what the chemist below is doing wrong:

Read the rest of this entry »

As a grad student, most of the time you’re a chemist, but sometimes you’re a teacher, a secretary, a copy editor, a graphics artist, or even a repairman. Our group has some pretty old lab space—and it shows. Over the last 25 years, work areas have been abused, storage areas have been neglected, and machines have deteriorated due to wear and tear. You can stumble into some pretty gross situations, as I did two weeks ago when I needed to cool down a flask. I opened the lid to our ice machine and was greeted by an arctic sea instead of the usual pillowy mounds of crushed ice:

There’s a drain at the bottom of the ice chest so that the water won’t build up as the ice melts. Obviously, something was clogged. The first order of business was to bail out all of the ice. This took a while and was no fun (read: brrrrrr). Once the ice was gone, we were left with 30 gallons or so of water with nasty gobs of slimy, black mold. It was at this point that I unearthed the following items:

• 1 bottle of Poland Spring water
• 1 can of Sierra Mist
• 2 bottles of fruit-flavored Snapple Iced Tea (1 half-consumed)
• 1 collapsed box of horchata (sweetened rice beverage)

You can click that picture to enlarge it. Be sure to notice the floaters. Gross. To my dismay, it turned out that the drain grating was clear, meaning the obstruction was in the drain line.  I enlisted the help of the building’s plumber, who conveniently, was busy installing the successor to the DG3000. After some handy wet-vac work followed by a thorough cleaning and bleaching, we were back in business. And since I was already in a tidying mood, I decided to conduct a little preventative maintenance by backflushing the air filter. It was a good thing, too. Just look at the number of grody dirt balls that came out of there:

After popping the filter back into place and starting the compressor, the machine was churning out ice within ten minutes. Instant gratification. Thanks to the magic of the Internet, you can check out the action on video.

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