Tuesday, September 29, 2009

Tabla Periodica de los Elementos

Ever wondered what the Periodic Table would look like in a language other than English? The Chemistry site at About.com has one in Spanish. Look for the link to the PDF version underneath if you want a nice copy to print. It even includes the newly named element 112 Copernicio (Cp)

Tabla Periodica de los Elementos

Monday, September 28, 2009

Structure of Petroleum Gunk

C&EN's cover story last week discussed advances in understanding the structure of asphaltenes. The headline on the cover describes these compounds as "Petroleum's Gunk" because of the problems they cause the oil companies by clogging their pipelines. Asphaltenes greatly increase the viscosity of crude oil - more oil would be pumped from the wells but for these things. Take a look at the structure of one example from the C&EN article:

Monday, September 21, 2009

Walkingstick Molecules

ResearchBlogging.orgJohnny over at Ecographica has a post on defense molecules secreted by Walkingstick insects.  Head on over to Johnny's post for pictures of the Walkingsticks.

There are several species of Walkingstick, and the one described in this paper produces three different defense molecules that are stereoisomers of one another: anisomorphal, dolichodial, and peruphasmal.  Being an organic chemist, I wanted to know that these molecules look like so I did a little digging around.

The first place I tried was PubChem - only dolichodial was listed, although PubMed does have papers listed for all three compounds. Next I tried ChemSpider, and again only dolichodial was listed.  Time for a more specialized database.  Rich Apodaca is compiling a list of 64 free chemistry databases on his Zusammen Blog, and one of the databases he has profiled is a collection of pheromones and similar molecules called Pherobase.

Pherobase has a search box at the top of the page, and typing the name of each compound produced a list of google-search results.  The titles and descriptions of the search results were not completely obvious, but the pages with a file name containing "compounds-detail-" seemed a good place to look.  This gave me both a 2D drawing and a 3D structure for each of the compounds.  Go ahead an check out the Pherobase pages for anisomorphal, dolichodial, and peruphasmal.  The Pherobase page for each compound includes a 3D structure with the Jmol applet - if you want to turn of the auto-rotation, right-click in the molecule window and set Spin to "off."

Here are all three molecules side by side:

They are stereoisomers - the difference between them is the 3D orientation of the three side groups attached to the ring: dark wedges are "up" and dashed wedges are "down."  At a glance, I can't say why they might specifically be "defense" molecules.  However, much of molecular signalling just boils down to shape rather than chemical reactions - these compounds may just smell or taste bad to predators.

According to the article, the specific compounds produced by the bugs depends on their developmental stage, and even location.  The researchers raised 14 Walkingsticks and observed the types of defense molecules they produced as they grew.  The bugs they used produced a mixture of anisomorphal and dolichodial as hatchlings and the amount of  dolichodial increased after 2 months.  However, when they reached maturity they stopped producing either anisomorphal or dolichodial, and produced peruphasmal exclusively.  As adults, other populations of walkingsticks produce anisomorphal, or a mixture of anisomorphal and peruphasmal.  None of the adults produce dolichodial.

I'm a chemist, I don't know what all this means.  Something seems to happen at 2 months that changes the amount of  dolichodial they produce.  And something else happens when they reach maturity that they stop producing dolichodial.  It's interesting that adults produce one or both molecules that have the aldehydes on opposite sides of the ring - and the compound produced only by the immature insects is the compound with both aldehydes on the same side of the ring.

Dossey, A., Walse, S., & Edison, A. (2008). Developmental and Geographical Variation in the Chemical Defense of the Walkingstick Insect Anisomorpha buprestoides Journal of Chemical Ecology, 34 (5), 584-590 DOI: 10.1007/s10886-008-9457-8

Friday, September 18, 2009

Reactions Using Iodine Azide without Explosions

How do you carry out organic synthesis when the reagent has a tendency to blow up?  Brandt and Wirth constructed a microreactor to do the job.  In this case, one of the main benefits of a microreactor is that very small amounts of material are needed.  Once the reactants were mixed, they passed through a capillary with a volume of 0.196 mL where they were heated to promote the reaction.

The reaction of interest was between iodine azide and various derivatives of benzaldehyde.  Under these conditions, the weak iodine - nitrogen bond breaks and the reaction involves a free radical mechanism. The aldehyde Hydrogen gets abstracted and the resulting radical reacts with iodine azide to give an acyl azide and more Iodine atoms to continue the radical chain reaction.

The resulting Acyl Azide then undergoes a Curtius Rearrangement when heated.  N2 leaves, the benzene ring migrates from the carbonyl carbon to the first nitrogen, and a lone pair on the first nitrogen forms a pi-bond with the carbonyl carbon (replacing the bond from the benzene ring.) This produces an Isocyanate, which is quite reactive towards nucleophiles.  With excess azide ions present, the isocyanate reacts with a second azide ion (via an ionic mechanism this time) to produce the final product - a carbamoyl azide.

They don't report any explosions, but otherwise seem to have had disappointing results.  The reaction did work, but it was rather slow and gave low yields.  The yield did improve if they first distilled the benzaldehyde before the reaction, but it was still low.

Brandt, J., & Wirth, T. (2009). Controlling hazardous chemicals in microreactors: Synthesis with iodine azide Beilstein Journal of Organic Chemistry, 5 DOI: 10.3762/bjoc.5.30

Thursday, September 17, 2009

Amazing Molecule Movie

Cool movie showing some of the things computational chemists do by Jan Jensen and posted on his blog, Molecular Modeling Basics.

Saturday, September 12, 2009

Avogadro 0.9.8 Is Available

The latest update to Avogadro (0.9.8) is now ready.  The Avogadro Home Page doesn't mention it yet, but if you click on the "Get Avogadro" button, you will get version 0.9.8, or you could go to Sourceforge you can get the packages directly.

According to Tim Vandermeersch's blog there are no new features, but some bugs have been fixed.

via OB, Avogadro and Molecular Modelling: Avogadro 0.9.8

Friday, September 11, 2009

Visit Mr. Penumbra's 24 Hour Book Store - Wonderful Podcast

Escape Pod is a science fiction podcast magazine.  This week's episode is "Mr. Penumbra's 24 Hour Book Store" - a wonderful short story about a mysterious old book shop.  It was originally posted on Robin Sloan’s blog, and has been turned into an audio podcast by the people at Escape Pod. 

Just to give you a taste, here is the beginning:
I’m sitting in a book store next to a strip club.
Not that kind of book store. The inventory here is incredibly old and impossibly rare. And it has a secret—a secret that I might have just discovered.
I am alone in the store. And then, tap-tap, suddenly I’m not.
And now I’m pretty sure I’m about to snap my laptop shut, run screaming out the front door, and never return.

The audio runs about 45 minutes and is well worth the time.  You you can read the original.

EP215: Mr. Penumbra’s Twenty-Four-Hour Book Store
Via Boing Boing

Thursday, September 10, 2009

Head Music from Neurosonics Audiomedical Labs

Neurosonics Audiomedical Labs Inc. from Chris Cairns on Vimeo.

Cool video - reminds me of the Heads from the Nexus comic book.
via BoingBoing

Staying Safe Even When You Aren't in Lab

With the start of the school year, I spent a lot of time in Lab last week discussing safety.   Perhaps the first rule of being safe in the lab is to pay attention to what is going on around you, and that is true no matter what your situation.

Like the author of this article, I have studied karate.  I've been fortunate - the last time I was in a fight was eighth grade (long before I started taking karate), and I didn't start that fight.  I don't know if my martial arts training has had anything to do with it. It did help me feel a little more comfortable with myself, and self-confidence will make you less of a potential target of people with bad intentions.

How to Recognize Imminent Danger: 7 Essential Safety Rules - Stepcase Lifehack

Wednesday, September 9, 2009

CAS Hits 50 Million Compounds

Over the weekend, the Chemical Abstracts Service (CAS) registered its 50 millionth compound! Only 9 months ago they hit 40 million compounds. This stuff is so new that it isn't listed in PubChem of ChemSpider yet. For comparison, it took 33 years for CAS to record the first 10 million compounds.

According to the press release at CAS:

"The 50 millionth substance (CAS Registry Number 1181081-51-5) was uncovered by CAS scientists from the Examples section of a nearly 200-page patent issued by the World Intellectual Property Organization on August 13, 2009. According to the patent, "Few therapeutics are approved by the US Food and Drug Administration and other regulatory agencies for the treatment of neuropathic pain." To address this concern, a series of novel arylmethylidene heterocycles were synthesized, which included the most recent substance registered by CAS."

Check out the full press release at: 50 Millionth Unique Chemical Substance Recorded in CAS REGISTRY