What is a Bridgehead Carbon anyway?

It's the start of a new school year and I am going to try to post a little more regularly.  Since it has been a while since I posted on a regular basis, I thought it would be a good idea to re-introduce this blog.

What is a Bridgehead Carbon anyway?  I teach undergraduate chemistry and my main area of interest is Organic Chemistry.  I chose the name "Bridgehead Carbons" partly because I have always liked the look of bicyclic compounds like norbornane.  You can think of Norbornane as being a cyclohexane (in pink) with a CH2 unit (in black)that acts as a bridge connecting the top and the bottom of the pink ring.  The carbons that connect the "main ring" to the "bridge" are the Bridgehead Carbons.

Another reason for choosing this name is that Bridgehead Carbons serve to connect different rings within the same molecule, and I intend to write about a variety of topics that I none the less feel are connected to my experience with chemistry and teaching.

So, what is this blog all about?  Stuff that interests me as a chemistry teacher, especially organic and bio-organic chemistry, cheminformatics, things that might be helpful to college students in general, and anything else that strikes my fancy.

Science in the Library winner

Louise Peck posted this on the CHEMINF-L list serve

The Royal Society of Chemistry's RSC Publishing division recently ran an annual photograph competition with the theme 'Science in the Library'. 

The competition prize was that the winning photograph would be placed on the front cover of the 2012 RSC Publishing Catalogue and was voted for by over 115 RSC staff and the RSC Library Advisory Board.

image from RSCPublishing Blogs Home 

And the winner is Johns Hopkins University in Baltimore, MD,  home of the first PhD program in chemistry in the United States which was started by Ira Remsen if I recall correctly.

You can download a copy of the 2012 RSC Publishing Catalogue from their website.  All 17 libraries that were entered in the contest are shown on pages 2-5 of the catalogue.  See if you can guess which one I have visited.

End of the Year Writing Advice

It is the end of the school year and our seniors will be turning in their senior research papers soon.  I think that scientific writing in particular can be a big challenge, especially when writing about your own research.  When you work on a project for most of a year you become emotionally invested in it, and you loose sight of its complexity.  But in sharing your results with others, whether as a paper or an oral presentation, it is easy to assume that everyone knows what you know.  And when discussing complex ideas, you can try to say too much at a time.

The original list has seven rules, but I am only quoting the first three.  If you are a writer of any sort, go read the original post with all seven rules.

VS Naipaul’s Rules for Beginners 

1. Do not write long sentences. A sentence should not have more than ten or twelve words. 

2. Each sentence should make a clear statement. It should add to the statement that went before. A good paragraph is a series of clear, linked statements. 

3. Do not use big words. If your computer tells you that your average word is more than five letters long, there is something wrong. The use of small words compels you to think about what you are writing. Even difficult ideas can be broken down into small words.

The point is to use good judgement.  Use big words when they are necessary, not just to impress your reader.  Strive for short, direct and clear.  If the result is too simple, you can always revise.  But if your first draft is full of long, convoluted sentences it can be hard to make it concise.

Sometimes you don't really understand some of the details yourself.  Really good writing can help you to better understand the topic yourself.  It forces you to choose your words carefully and think about the meaning.  

VS Naipaul’s Advice To Writers - The India Uncut Blog - India Uncut via BoingBoing

Jmol test in Blogger

Here is a short test to see if I can display a Jmol applet in a blog post.  I don't currently have access to a server to host the jmol applet, so for this test I am linking to the applet, script and molecule files on the Jmol Samples page.

UI Controls example

Chiral Drugs on the Chemistry Blog

Yesterday we started Stereochemistry in my Organic Class, and on Monday Azmanam on the Chemistry Blog had a post on  Chiral Drugs.  Take a look at the structures below:

Both are used to treat gastroesophageal reflux desease (GERD, commonly known as acid reflux).  Can you see the difference in the structures?  Click the image to see a larger version.  Prilosec is sold as a racemic mixture: a 50-50 mix of the R and S enantiomers.  Nexium contains just one enantiomer - the S isomer.  This is an example of a chiral molecule whose stereogenic center is not a carbon, but rather a sulfur.  The fourth group attached to the sulfur - the one with the lowest priority - is a lone pair of electrons.  Read Azmanam 's post for a good discussion of the two.


Chemistry Blog - Nexium’s Dirty Little Secret

How Plants Use Caterpillar Spit for Protection

How do plants protect themselves from the bugs that chew on their leaves?  In the case of the wild tobacco Nicotiana attenuata, when tobacco hornworm (manduca sexta) caterpillars feed on the leaves a collection of molecules called Green Leaf Volatiles (GLV's) is released by the plant.  GLV's are released any time a leaf is damaged, but the interesting thing is that when the damage is done by chewing caterpillars, a different form of the GLV's are produced which attracts Big-Eyed Bugs (Geocoris spp) - a predator for the caterpillars.

Image via Wikipedia

Plants emit two main types of volatile molecules: terpenoids and Green Leaf Volatiles.  The terpenoids are emitted from the whole plant and usually after a delay - maybe as much as a day after the damage.  The green leaf volatiles are more specific - they are emitted from the damaged leaf itself and it looks like they are produced at the same time as the damage.

Green Leaf Volatiles are typically 6-carbon alcohols, aldehydes or esters.  In the case of Nicotiana Attenuata they seem to mostly consist of hexenal, hexenol and simple esters of hexenol.  The interesting bit is the alkene portion of these molecules.  Alkenes can have one of two basic geometries around the double bond: the Z (or cis) isomer is locked into a u-turn shape and the E (or trans) isomer is locked into a zigzag-like orientation.

Normally, Nicotiana attenuata produces mostly the Z isomer of these molecules and a relatively small amount of the E isomer.  However something unusual happens when the damage is caused by caterpillars chewing on the leaves:  in this case the plant produces roughly equal amounts of the Z isomer and the E isomer.  You and I would probably not notice a difference in the smell of the leaves, but apparently there are bugs that can.  When more E isomer is produced, more Big-Eyed Bugs are attracted to the plants.  And the big-eyed bug eats caterpillars and their eggs.  The E isomer GLV's are a plant distress call and the big-eyed bugs are the cavalry.

How exactly does the plant "decide" which GLV isomers to make?  After testing a variety of possible candidates, it looks as though there is an enzyme in the caterpillars' saliva that causes the Z isomers to isomerize to the corresponding E isomers.  It is the caterpillar spit that produces the distress call.

If you look closely at the Z molecules and the E molecules you will notice that there are actually two changes that take place.  First, the geometry around the alkene switches.   In general, the E isomer is more spread-out than the Z isomer and as a result it is lower in energy. Given a choice the alkene will usually adopt the E geometry.  If there is a catalyst available, this change is pretty easy to understand.

The second thing that changes is the location of the alkene, the  alkene moves closer to the oxygen end of the molecule.  Enzymes are very efficient molecules and they are very sensitive to shape.  My guess is that the "real" target for the isomerase in the caterpillar saliva is the aldehyde.  The aldehyde has a carbonyl group as well as the alkene and the most stable arrangement for these two functional groups is the one in hex-2-enal.  When the two double bonds are separated by only one single bond their orbitals are able to interact and form a conjugated system.  The conjugated version is more stable than the one where the two double bonds are farther apart and unable to interact with one another.

If improved conjugation in the product is the reason that the alkene moves from the 3-position to the 2-position, why does the alkene move in the alcohol and ester molecules too?  The alcohol has only one double bond since there is no C=O, so conjugation is not possible in this molecule.  And while the ester does have a C=O, it is too far away to interact with the 2-alkene to form a conjugated system.  What gives?

Enzymes can be very selective about the molecules that they react with, but they can also be forgiving if the structure is not exactly correct.  A lot of drugs affect specific enzymes in the body - the drug isn't exactly the correct shape, but it's close enough to bind to the enzyme.  In the case of the GLV's, the alcohol and ester molecules are close enough to the right shape to bind to the enzyme and react.  In the aldehyde the enzyme causes the alkene to migrate as well as change shape because it forms conjugated molecule.  Even though the alcohol and ester don't benefit from forming a product molecule that has conjugation, the enzyme treats them the same way it treats the aldehyde and the alkene migrates to the 2-position.

The other curious thing about this is the isomerase enzyme in the caterpillar saliva.  I would bet the reason the caterpillars make this enzyme has nothing to do with attracting big-eyed bugs to come eat the caterpillars, that would be counter productive. The plants probably evolved their GLV's to take advantage of this enzyme that the caterpillars make anyway.  So what is the isomerase "supposed" to do that benefits the caterpillars?

The smell of freshly-cut grass is actually a plant distress call | IO9.COM

Allmann S, & Baldwin IT (2010). Insects betray themselves in nature to predators by rapid isomerization of green leaf volatiles. Science (New York, N.Y.), 329 (5995), 1075-8 PMID: 20798319

How to safely put your hand into really scary liquids - fun with the Leidenfrost effect

Image via Wikipedia

Check out these two videos demonstrating the Leidenfrost effect.  If you have ever seen drops of water bounce around on a hot skillet, that's the Leidenfrost effect.



First Theo Gray puts his hand into liquid Nitrogen.  Liquid Nitrogen is really cold:  −196 °C, −321 °F.  You have probably seen demonstrations where something like a rubber ball or a rose is dipped in Liquid Nitrogen - on freezing at such a low temp most things will shatter if dropped or hit with a hammer.

Theo Gray dips his hand into a large container of liquid Nitrogen without developing a permanent case of frost bite by taking advantage of the Leidenfrost Effect.  Since his hand is much warmer than the liquid nitrogen, a very thin layer of gaseous nitrogen forms and acts as a protective barrier between the bulk liquid nitrogen and the surface of his hand.



Adam and Jamie demonstrated the same effect with molten lead on an episode of Mythbusters.  This is kind of the opposite of the liquid nitrogen case - instead of using an extremely cold liquid they are using a very hot liquid.  Lead melts at 621 °F, but they actually did the experiment at about 800 °F.

To be protected by the Leidenfrost effect they needed a thin layer of gas between their hands and the lead, so they dipped their hands in water and shook off the excess before putting their hands into the liquid lead.  The small amount of water on their hands vaporized to provide the thin, protective layer of gas between their skin and the liquid lead.  The fun starts about 2 minutes into the clip.



It goes without saying - making a mistake when doing this will have severe consequences. Don't try this at home.

You can safely stick your hand in liquid nitrogen...but you probably shouldn't | IO9.com

Gray Matter: In Which I Fully Submerge My Hand in Liquid Nitrogen | Popular Science