Chirality

read any good books lately?

2009-12-18T19:54:00.000-08:00

I'm looking ahead to next term, when some of my Organic students will once again need to write a term paper. Last term's topic was Green Chemistry and the Presidential Green Chemistry Challenge awards.

For the past few years I have had students read Carl Djerassi's autobiography, The Pill, Pygmy Chimps and Degas' Horse, but for a variety of reasons I may not assign it this year. The problem is finding another book that fits the bill: I need something that is ideally focused on organic or synthetic chemistry, I need something that is a narrative of sorts (not a text), and I want a book that brings up things that don't get brought up in class. These are reasons I have enjoyed assigning Djerassi's book. It's a great window into the life of a synthetic organic chemist.

I'm running up to the library tomorrow to pick up a copy of a book called the Carbon Age by Eric Roston, which sounds like it has some potential. But I'm looking for other possibilities. Have you read anything good? Is it about Chemistry? I'd be delighted to hear your suggestions--or warnings about books that wouldn't be suitable.

oh, chirality!

2009-11-19T21:14:00.000-08:00

You can scroll back to an entry from January 2009 to find the article I wrote on chirality. For those who are in my class this year, and who weren't last, this could be interesting.

For those of you who have been in the fan club for a while, go ahead and disregard this note.

let go of the side of the pool

2009-11-18T20:06:00.000-08:00

Thanks to my undergraduate advisor Cathy for noticing t his link at Scientific American. Don't fear your mistakes! Share them with others and use them to focus your mind and attention. There are indications that you will learn better (and I promise I won't judge you for making an error in front of me).

As the ever-wise Zelda says, you can't swim until you let go of the side of the pool.

Circium Pitcheri

2009-11-12T19:56:00.000-08:00

Many many many many years ago (it was the 90s) I spent about 1.5 years' worth of Thursday mornings in the lab at Chicago Botanic Garden, working with Kayri Havens genetically typing a number of rare plants including the Pitcher's Thistle. We usually talked about our samples using their Latin names. In this case it was Circium pitcheri.

What a great blast from the past to see them in the New York Times! As I was digging into the article I was thinking, "oh my gosh I think this is work done by people I know!" then "oh my gosh I think I know that project!" then "oh my gosh I think this is a plant I have worked on myself!"

Working with the scientists at ChiBot taught me that there is a lot more in museums, beyond displays for the public to look at. I gained a deep and persistent appreciation for plants, for their ability to adapt to specific environments and expand their territories.

I also learned that my lab skills allowed me to make contributions in areas far outside my specific field of expertise. After all, what business did I have in their lab? Was I a plant expert? Nope. But life is like this: sometimes we imagine we have less to offer than we really do have. Speaking up is the first step to being in on some great stuff.

Is the periodic table the same around the world?

2009-11-12T19:17:00.000-08:00

I was asked this question last week. I answered incorrectly. I stand corrected. I said yes, thinking only about how the element symbols and arrangement are universal. But the names are different in different languages, even though many are derived from latin so come out very similar in different languages. But to get a taste for the variety out there, check out these different variations, many of which are produced by the same people:

In Spanish

In French

In German

In Dutch (because I have a special place in my heart for the Dutch)

In Arabic

In Swahili

In Russian, the language of Mendeleev

It is somewhat surprising that the languages that use different alphabets would use our alphabet characters for their elemental symbols. Can you imagine learning element symbols with an alphabet different than your own? It sure would seem more cryptic.

While some element names are very different (check out Sulfur, for instance), others seem quite universal (the Noble Gases). I wonder why? Perhaps those elements that have been discovered and named more recently, since communication across the world has become easy, have internationally-agreed upon names. Hydrogen appears to have its name translated literally in German and Dutch....to wasserstof. Funny!

To top it off (if you're still reading) there is always the Periodic Table of Comic Books . I know it's not a language, but it's funny and creative so I'm including it here anyhow.

Deuterium

2009-11-08T16:03:00.000-08:00

I spent a lot of after-school time watching Hogan's Heroes as I was growing up. Sargeant Schultz was always good for a laugh, and I can remember his references to "heavy vasser" and a red bucket that was labelled so. Many years later I learned that heavy water was of some concern during the war, as the Germans appeared to be experimenting with it as a moderator for nuclear reactions. To the allies, this indicated an interest in developing nuclear weapons. Heavy water is water containing deuterium (D) the isotope of hydrogen that contains a neutron and hence that has an atomic mass of 2 rather than one. So heavy water weighs 20 amu/molecule, or 20 grams per mole: a modest 10% more than regular water.

Disrupting the development included a really dramatic destruction of a supply of heavy water, which was all produced during that time in Norway. The PBS series Nova has described both the sinking of a ferry carrying the stuff on "Hitler's Sunken Secret," as well as an attack on the plant that manufactured the stuff in the first place. The plant made use of a series of multiple distillations, if I recall correctly, to enrich samples of water, which naturally contains a small amount of D2O.

Gilbert Lewis (of Lewis structure fame) was the first person to isolate D2O, incidentally.

Heavy water is actually a little more dense than regular water, since deuterium weighs a little more than hydrogen. But the effect is fairly modest and wouldn't be noticeable if you were carrying a little flask of the stuff.

The drywall problem continues

2009-10-29T16:27:00.000-07:00

The Chinese drywall story is back in the news. National Public Radio has an update.

My dog has quite the lifestyle

2009-10-13T11:16:00.000-07:00

Molecule of the Day points out how easy it ought to be to put our dogs on diets. Feed them less, right? So why are there diet drugs for dogs? Maybe it's about our inability to control our interactions with food, even to ask our dogs to abstain. Or maybe it's about sharing our concerns about weight with the family members that so far have been blissfully unaware of this American obsession. Or maybe there are drugs out there that could have use in people but just haven't made it through FDA approval.

Whatever the reasons may be I have to laugh as I think about these as lifestyle drugs for dogs. My dog has quite the lifestyle. No work, free food and drink, lots of affirmation and attention, and no responsibilities to anybody.

That was fun.

2009-10-09T15:40:00.000-07:00

A helpless audience of GS199 students were subjected to 50 minutes of joy-filled rambling by me today, on the subject of Green Chemistry. Oooh I had fun! I hope that they did, too. It was an interesting experience, explaining this to a general audience. I appreciated their interest. It is a very fun story to tell, optimistic and varied and full of good characters.

Featured tales of Green Chemistry successes were the ibuprofen synthesis, TAML oxidant activators, and Non-fluorous, highly CO2-soluble materials.

Links are to the EPA summaries of the projects.

Now it's time to get out and enjoy the weekend.

What are they looking for?

2009-10-09T15:31:00.000-07:00

Tis the season that recommendation letter-writing is beginning to wind down, just as the school year is beginning to wind up. I think this week is the first time in about 3 months that I haven't had somebody's letter request sitting on my to-do list. I'll admit it: I am relieved.

It's not that it's a job I don't like, it's just that it is a job. Crafting a letter that is honest, professional, and that gets the message right can be a difficult thing to do.

As I look out over the sea of expectant faces in my new classes I know that this coming year will bring more requests. I'm already watching for the qualities of character I hope to be able to write about later. Those would include things like flexibility, honesty, drive, and the abilities to both listen carefully and act decisively.

Students out there who know or think they know that they'll be seeking admission to medical or other professional health programs, studentdoctor.net has an article that does a good job of explaining how to think about and manage your presentation of yourself in your personal essay. Much of what is here is also relevant to how you might want to be perceived for letters of recommendation. This might be valuable reading.

Why I adore Hans Rosling....

2009-08-27T08:26:00.000-07:00

It's not entirely explainable with words or simple graphs. It's best understood by actually watching him operate with his animated data. See his new TED talk here.

OSU pals make the Oregonian!

2009-06-19T13:40:00.000-07:00

...this work brought to you by my favorite peeps at OSU. These folks have previously brought us wonderful research on air quality at our very own Mt. Bachelor Observatory, with help from some great students at COCC.

glycosides in my garden

2009-05-23T15:36:00.000-07:00

Memorial Day always has felt like an odd holiday for me. Growing up the only real memorial thing that would happen is that my mom and dad would each take their mothers to the cemetery to put flowers on the headstones of their spouses. There wasn't much for direct links to the military, it seems. But Memorial Day was always a day to work on some project outdoors. As an adult I still find myself planning for and doing work around the house during the holiday weekend.

So today I went to the nursery and bought some plants and tree bark for my yard.

I knew I wanted to get some digitalis, because there was some growing here when I moved in and I find it gorgeous in a showy kind of way. But I also love it that digitialis is the source of commonly prescribed cardiac glycoside digoxin. I didn't realize until I did a little web searching today that the plant actually is not just a little poisonous--it contains enough of the glycoside to really mess you up bad even if small amounts are ingested.

I also picked up some kinnickkinnick, which is Arctostaphylos. I bought it because it will look good and do well where it needed to go, but it turns out to be darned interesting, too. Turns out it is a relative of the familiar manzanita, and like digitalis, it contains a glycoside compound that is biologically active. In this case the glycoside is named arbutin. It inhibits the formation of melanin and has been used in herbal treatments for urinary tract problems. But these extracts have been the subject of some concern since they may be carcinogenic.

a new blog to watch

2009-04-16T12:25:00.000-07:00

Emily Monosson has a blog that has been recommended to me, called the Neighborhood Toxicologist. I'm linking it from here, from the list of Stuff I Like that is in the right-hand corner of my page. I haven't had a chance to give it a close inspection but I have reason to believe it'll be good.

Meanwhile, in Ochem the current topic is Electrophilic Aromatic Substitution. In an email conversation with a student, I was drawn in to a discussion about polycyclic aromatic hydrocarbons, or PAHs. There is so much descriptive chemistry I would like to include in my courses, but there just isn't much time and it is often the kind of information that is accessible to my students anyway, if I just point out to them where to look.

So with that said, I once again can plug Wikipedia, which has an excellent article on PAHs.

biology meets chemistry meets physics meets engineering

2009-04-04T15:56:00.000-07:00

This is one of the best cross-disciplinary stories I have seen in a while. Who'da thunk this would work? What a creative idea! Biological systems are so cool, since over time they are often optimized to utilize available materials and make the best possible use of what is in the environment.

is your drywall off-gassing poisons?

2009-03-26T17:56:00.000-07:00

ABC News ran a story this evening about a woman in Florida who is claiming her house has made her sick, and that Chinese drywall may be to blame. The story included no details worth mentioning--it was a classic case of little information but lots of "two sides" reporting.

CNN does a much better job, reporting that the materials have been tested and shown to contain some strontium sulfide, which potentially could lead to the production of H2S, explaining both a sulfurous smell and problems with corrosion of pipes and wires in the house, which is quite new.

You can read more here.

mmmmmmeta

2009-03-24T10:22:00.000-07:00

Science News reports on a group that has devised an efficient way to substitute at the normally-resistant meta position on aromatic rings. Thanks to Sean for the link.

MSRA among the piggies

2009-03-12T20:29:00.000-07:00

Thanks to my college advisor for posting a link to this article about drug-resistant staph in pigs. And of course, thanks also to Nicholas Kristof for researching and writing it in the first place.

SciAm on Sustainability

2009-03-09T19:28:00.000-07:00

I was tipped off to this article today, and although I haven't read it I'd bet you a dollar it's good.
So I'm posting it without a pre-read. Meanwhile, out in the news, the conversation about changes in funding for research involving embryonic stem cells is heating up rapidly.

nuclear forensics

2009-03-09T08:45:00.000-07:00

National Geographic News has posted an article describing the emerging field of nuclear forensics. The article appears to suggest that the nuclear decay products of an unknown sample were used to determine its origin, which happens to be the first nuclear bomb test.

Oregonian reports on Chromium Exposure Among National Guard Troops

2009-03-08T09:19:00.001-07:00

The link is here.

EJ Corey and Retrosynthesis

2009-03-03T19:35:00.001-08:00

Check out this little gem of a synthesis, credited to EJ Corey, the esteemed developer of retrosynthesis: Trabectedin (from Wikipedia). Astounding.

My Synthesis professor in grad school used Corey's book as a foundation for our course and told us his (not Corey's) 9 days in jail for a BUI offense provided a stretch of uninterrupted time for reading. The book is called The Logic of Chemical Synthesis, and it's becoming a classic.

a tragic accident

2009-03-03T19:22:00.000-08:00

It is unfortunately too easy for any of us to forget the hazards associated with some of the stuff we work with. The LA Times reports that this recent fatal accident involved tert-butyllithium, an organometallic reagent that is used as a base, but that has similarities to the organolithium reagents used for generating carbon nucleophiles in organic synthesis reactions.

10 best?

2009-03-02T21:47:00.000-08:00

While poking around the web looking for full-text versions of Djerassi's original papers I discovered this list of the "10 best organic chemists of all time." I couldn't help but notice that many of you, Readers, will know the reasons for nomination if not the actual names.

I smile as I read these names and their contributions. They are an amazing bunch of minds. I can't comment about the drinking: I have no first hand experience with any of them.

I didn't find the Djereassi papers, by the way, but I think I have them in my office. Somewhere.

doublets of doublets: I'm beggining to see!

2009-02-26T19:22:00.000-08:00

Poking around in some books on nmr today I found someone who directly addresses the doublet of doublets phenomenon. You can't imagine how happy I was to see this.

I'm beginning to get it. As usual, Straumanis is right. The book explains that in most situations, nearest neighbor hydrogens are similar enough to one another that the splitting occurs in a way that follows the rules for splitting we have learned. In a few situations, though, when the neighbors are very different from one another (as expressed by something called their coupling constant), they split the signal sort of separately and generate a doublet of doublets.

The book provides an example that looks a lot like the fluorinated benze we were examining, except it has a nitro (NO2) group across from the F.

The fluorine is the reason for the different coupling constant in our molecule, but I am still sorting out the details of what role it plays. I also still don't have complete clarity about why these coupling constants could vary when the coupling has all been explained to me using the quantized spin states (as I tried to describe in my earlier post).