Bridgehead Carbons

SOPA/PIPA and the Internet Blackout

2012-01-18T08:57:00.000-05:00

Apparently there are some people on twitter who are confused and upset that Wikipedia (in English) has been blacked-out for the day.

If you haven't done so already, take a look at the announcements on Google, and Wikipedia. Follow the links for a more detailed explanation. Also, Wikipedia's pages on the bills in congress, SOPA (in the House) and PIPA (in the Senate) are not blocked.

Two other sites I'll recommend are this post at the Electronic Frontier Foundation, and this post at Mashable that breaks down the actual text of SOPA.

These bills are poorly written and will probably not even prevent the real sources of online piracy.

Wordclouds of Chemistry Texts

2011-10-12T08:28:00.000-04:00

After stumbling across a post on One R Tip A Day about building Wordclouds using R, I thought I would try it out myself. I have been subjecting my undergrad chemistry students to R, so this seemed like a good opportunity to use R for a little fun. I decided that it would be interesting to look at some old chemistry books. I picked three works from Project Gutenberg:

The Sceptical Chymist (1661) by Robert Boyle
Elements of Chemistry (1789) by Antoine Lavoisier
An Elementary Study of Chemistry (1905)

by William McPherson and William Edwards Henderson

The Sceptical Chymist (1661) Robert Boyle

Elements of Chemistry (1789) Antoine Lavoisier

An Elementary Study of Chemistry (1905) McPherson and Henderson

It's no surprise that Boyle's wordcloud is so different from the other two. The influence of Alchemy was still quite strong in 1661, and Boyle's vocabulary reflects this. It is perhaps more interesting to see how similar Lavoisier is to McPherson and Henderson despite their being 116 years apart.

Robert Boyle and Antoine Lavoisier were both instrumental in developing modern Chemistry, William McPherson was a chemistry professor at Ohio State University and one of the chemistry buildings there is named for him.

I adapted Paolo's code from Wordclouds using R. You will need the R packages tm, wordcloud and RColorBrewer. I downloaded the books as plain text from Project Gutenberg and saved them in a directory called chemtxt.


library(tm)
library(wordcloud)
library(RColorBrewer)

#reads all files in the directory chemtxt
chemtexts <- Corpus(DirSource("chemtxt/"))

book <- Corpus(VectorSource(chemtexts[["boyle.txt"]]))
book <- tm_map(book, removePunctuation)
book <- tm_map(book, tolower)
book <- tm_map(book, stripWhitespace)
book <- tm_map(book, function(x) removeWords(x, stopwords("english")))

# format as a dataframe with words and their frequencies
book.tdm <- TermDocumentMatrix(book)
book.m <- as.matrix(book.tdm)
book.v <- sort(rowSums(book.m),decreasing=TRUE)
book.d <- data.frame(word = names(book.v),freq=book.v)

#color scheme
pal2 <- brewer.pal(8,"Dark2")

# uncomment this line to save wordcloud as an image file #png("wordcloud_boyle.png", width=600,height=600)

#I picked just the 60 most frequent words

# to show ALL the words in the wordcloud use max.words=Inf wordcloud(book.d$word,book.d$freq, scale=c(8,.2),min.freq=3,max.words=60, random.order=FALSE, rot.per=.15, colors=pal2)

dev.off()

What is public science, and why do you need it?

2011-09-20T21:14:00.000-04:00

Image via Wikipedia

Did you use a browser to zoom around on the internet today? Have you ever been vaccinated? If you answered yes to either of those questions, your life has already been made better through publicly-funded science in America. Public science is basic scientific research funded by governments, and just in America alone it's led to breakthroughs in everything from medicine to clean energy. But now public science is under threat. Here's why — and why we can't afford to lose it.

The Science Fiction blog IO9.com has a nice overview on the value of basic research funded by the US government and some of the myths about science funding. Don't rely on know-nothing blowhards who tell you the US should cut funding for science. Check it out.

What is public science, and why do you need it?

Animated sheet music - So What

2011-09-17T08:00:00.011-04:00

So What

via Kottke.org Animated sheet music

Nano "Motor" Powered by Chemistry

2011-09-14T08:11:00.000-04:00

We have been hearing about nanotechnology in the media and in science fiction for a long time now. I have always been a little skeptical about how realistic an idea "nano-machines" are. This new research has me rethinking that skepticism.

A communication published online in Angewandte Chemie describes what you could call a working nano-motor. Ayusman Sen and his coworkers at Pennsylvania State University have prepared little spheres less than a micrometer across - one side of the sphere is gold and the other side is silica (SiO2). On the silica side they have attached a Ruthenium compound known as a Grubbs Catalyst. The Grubbs Catalyst reacts with alkenes which are the "fuel" for the motor.

Image via Angewandte Chemie

When they place their motor-particles in a solution containing norbornene, the catalyst group on the silica side of the particle polymerizes the norbornene, and the amount of unreacted norbornene molecules on the silica side of the particle decreases. This causes a concentration gradient - the concentration of norbornene on the gold side is higher than the concentration of norbornene on the silica side.

It is this difference in concentration of "fuel" molecules that makes the particle move. Osmosis involves solvent molecules moving from a region where concentration is low, to a region where concentration is high. As a result, solvent molecules flow around the "nano-motor" from the silica side (less norbornene - because the Grubbs cayalyst polymerized it) to the gold side (lots of norbornene). And this causes the particle to move in the opposite direction.

Professor Sen anticipates that eventually you could redesign his nano-motor to use a "fuel" like glucose and doctors could use it in the bloodstream to repair damaged tissue. Just like something out of Fantastic Voyage.

Image via Wikipedia

Self-directed microspider could repair blood vessels - New Scientist

Original research article: A Polymerization-Powered Motor DOI: 10.1002/anie.201103565

What is a Bridgehead Carbon anyway?

2011-09-07T08:55:00.001-04:00

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

2011-09-07T07:56:00.000-04:00

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

2011-04-25T08:42:00.003-04:00

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

2010-11-02T11:59:00.001-04:00

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

2010-10-22T08:52:00.001-04:00

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

2010-09-07T08:38:00.001-04:00

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

2010-09-05T19:54:00.000-04:00

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

Laboratory Disaster Stories

2010-09-03T14:12:00.000-04:00

Do you need some good reasons to wear your lab goggles? Check out the Lab Horror Stories thread on Reddit.

Image via Wikipedia

Here's one short and sweet example from an organic chemistry lab:

When I was in organic lab, my TA closed my heating reaction flask a little too tightly. It blew up. I pulled three pieces of glass out of my forehead right above my right eyebrow. The stopper hit my partner in the head. We lived long enough for the department to let us graduate.

Yay for goggles!

For educational and entertainment purposes only, please don't do any of these things yourself.

Link from Boingboing:
Or does it explode?: Reddit collection of laboratory disaster stories - Boing Boing

ChemSketch on Linux Again

2010-08-11T21:39:00.000-04:00

Last year I wrote about using ChemSketch on Linux. It is about the only Windows program that I regularly use these days. Since switching to Linux I have not completely settled on a chemical structure drawing program. Sometimes I still use ChemSketch on Windows and then copy the image into OpenOffice, sometimes use another program on Linux - usually MarvinSketch.

Thanks to a comment left by Dragly on my original ChemSketch post in January, I can now reliably use ChemSketch on Linux.

ChemSketch is a Windows program, so I have to use Wine in order to run ChemSketch. The problem was that ChemSketch would run fine the first time it is started after installation, but every other time I tried to run the program it would hang-up without the ChemSketch window ever appearing.

Dragly's comment referred me to:

http://markmail.org/message/grddjlgsn3dh5kqp

And he also pointed out that the program could be run with the window maximized by using this command, provided that the file path to the program is correct:

wine start /MAX C:\\WINDOWS\\TEMP\\ACDFREE12\\CHEMSK.EXE

This works, but it behaves a bit flakey for me running Ubuntu 10.04 and Wine 1.1.42. First the ACD/Lab Products panel appears (very slowly) - after clicking the "OK" button, the program itself loads on the workspace to the right of the one I am working on. The 3D View program behaves the same way - you need to use:

wine start /MAX C:\\WINDOWS\\TEMP\\ACDFREE12\\SHOW3D.EXE

to get it to open normally, and then it shifts one workspace to the right.

After digging around a bit, it turns out that the problem is in the Wine registry file, which for me is at

/home/steve/.wine/user.reg

This file is updated every time you close a program that is running under Wine. The quick and dirty solution would be to delete this file before running ChemSketch. Except for losing all the settings for every program you run with Wine, this works pretty well. The program starts normally - if a bit slowly compared to Windows.

The clever thing to do would be to edit user.reg to delete the offending setting, which starts with

[Software\\Advanced Chemistry Development (ACD)\\Size]

and is followed by a bunch of numbers. Deleting this setting allows you to run ChemSketch and the 3DViewer "normally." This is a bit tedious but do-able. To be really clever I should write a program to do it for me every time I run ChemSketch.

Under Windows, you can open the 3DViewer from ChemSketch by using the ACD/Labs menu. Unfortunately, when I run under Linux, this menu does not have any of the labels visible. The first menu item is the 3DViewer. Or you can right-click the ACD/Labs icon in the Gnome panel at the top of the screen and select the 3D Viewer to open it.

Copying between the ChemSketch and 3D Viewer windows works, and so do the Database search options. The only remaining problem is getting the figure into an Open Office document. You can't simply copy the image, nor can you insert an OLE object the way you would in Windows. Instead you will need to save the figure as an image and import the image into the Open Office document. The downsides of this are adding an extra step to save the image, and not being able to edit the image easily unless you also saved the original ChemSketch file.

Finding Buckyballs in Space

2010-08-10T18:58:00.002-04:00

When you hear about molecules in interstellar space or on the moons of Saturn they tend to be small molecules like methane, ammonia or water. A big organic molecule would be something like glycine, the simplest amino acid, with only 5 "big" atoms (carbon, oxygen and nitrogen) and 5 Hydrogen atoms. So finding buckyballs with 60 or 70 carbon atoms is really quite extraordinary. It's a big difference, and buckyballs contain only carbon atoms - no other elements not even hydrogen, the most common element in the universe.

Buckminsterfullerene - C60

Image via Wikipedia

Using the Spitzer Space Telescope, an international reseach group has recently observed the buckminsterfullerenes C60 and C70 in Tc 1, a young Planetary Nebula (PN) with a white dwarf at the center. The inner region of the nebula is carbon-rich, hydrogen-poor and dusty and this seems to be an important reason that they were able to see buckyballs there - buckyballs need lots of carbon in order to form, and they don't have any hydrogen in them at all.

The Hourglass Nebula

Image via Wikipedia

Most planetary nebulae have strong emissions from polycyclic aromatic hydrocarbons (PAH's) but not Tc 1. Also missing, there are almost no simple hydrogen-containing molecules like HCN or C2H2. A PAH would be like a small piece of a buckyball with hydrogens around the outside edge. Once a buckyball started to form if there was any hydrogen around, hydrogen atoms could attach to the carbons on the edges resulting in a PAH instead of a buckyball.

from the research article:

On Earth, fullerenes can be synthesized by vaporizing graphite in a hydrogen-poor atmosphere that contains helium as a buffer gas. The fullerene formation process is very efficient, and C60 is by far the dominant and most stable species among the large cluster population formed in these experiments, followed by C70. However, fullerene formation is inhibited by the presence of hydrogen. The circumstellar environment of Tc 1 seems to be the astrophysical analog of such a laboratory setup.

They used Infra-Red (IR) spectroscopy to identify the buckyballs. It's especially useful in this context because it tells you what kinds of bonds there are in a molecule. Visible light doesn't usually give a lot of useful information except for individual atoms, or maybe certain types of large, complex molecules. But IR gives you a lot of information about the bonds in a molecule. IR spectra can be quite complex - the nifty thing with C60 is that for as large as it is, it has a very simple IR spectrum.

I had a difficult time finding an IR spectrum for C60 at the usual online chemistry databases (NIST Webbook, ChemSpider, SDBS). But this web page has a small image of the IR spectrum of C60. It's a very simple spectrum with just 4 absorptions. The molecular structure of C60 it looks intimidating, but it turns out that there are really only two kinds of bonds: bonds that are shared between two 6-membered rings, and bonds shared between a 5-membered ring and a 6-membered ring. And the thing about IR spectroscopy is that it is highly dependent on symmetry. C60 is highly symmetrical, so you only see 4 absorptions for it. C70 is the second most common buckyball. It's not as symmetrical as C60, and as a result its spectrum is more complex that that of C60.

Cami, J., Bernard-Salas, J., Peeters, E., & Malek, S. (2010). Detection of C60 and C70 in a Young Planetary Nebula Science DOI: 10.1126/science.1192035

The Chemistry of Cthulhu?

2010-08-01T14:07:00.001-04:00

I write like
H. P. Lovecraft

I Write Like by Mémoires, Mac journal software. Analyze your writing!

I haven't posted in a while - is this the reason?

Was I tottering on the brink of cosmic horrors beyond man's power to hear?

I suppose that some people might say of Organic Chemistry that

... there is no language for such abysms of shrieking and immemorial lunacy, such eldrich contradictions of all matter, force, and cosmic order.

Image via Wikipedia

Thinking about Simplicity

2010-05-04T09:12:00.000-04:00

Harvard Organic Chemistry professor George Whitesides takes a stab at defining "simplicity." Here's a wonderful, thoughtful talk for the end of the school year.

Top 30 Science Blogs at Times Online - Eureka Zone

2010-02-08T07:00:00.000-05:00

The Eureka Zone science blog at the NY Times has a list of their top 30 science blogs. If you are looking for science reading this is a great place to start. I only wish there was a Chemistry blog or two on their list.

Times Online - Eureka Zone: Eureka's Top 30 Science Blogs

Gypsy Bach Jazz

2010-02-06T08:00:00.001-05:00

George Whitesides Discusses Designing a "Lab on a Stamp"

2010-02-05T11:23:00.000-05:00

This talk is listed at the Ted.com site as "A Lab the Size of a Postage Stamp," but it should really be "A ON a Postage Stamp." He talks about the ingenious way his group has designed "devices" for medical diagnostics from paper. This makes it very inexpensive as well as easily disposable - no sharps or bio-waste to worry about, you can just burn the device when you are done.

George Whitesides is an Organic Chemist from Harvard - I would love to hear him talk about his work on Self-Assembly, but this is pretty cool too. To quote from his Bio at Ted:

He's co-founded a nonprofit called Diagnostics for All that aims to provide dirt-cheap diagnostic devices, to provide healthcare in a world where cost is everything.

While sharing some of his experience, he also has some interesting observations of the nature of our society, given that the cost of healthcare has been such a topic of discussion lately.

Moebius Strip Bach Canon

2010-01-17T08:20:00.001-05:00

A little MatheMusical fun for Sunday.

via BoingBoing Bach canon played as a moebius strip - Boing Boing

Fun With Dimensional Analysis

2010-01-11T20:53:00.001-05:00

It's amazing what you can do if you can just get the units to cancel.

xkcd - A webcomic of romance, sarcasm, math, and language - By Randall Munroe

Sugary Antifreeze Molecule Found In Alaskan Beetle

2009-12-28T17:24:00.000-05:00

image: Carl Gustav Calwer - wikimediacommons

I've been visiting family out of town - we got here just in time to be snowed-in for Christmas. So I thought some wintry chemistry would be appropriate.

Slashdot recently had a listing about a new anti-freeze molecule that has recently been found in the Alaskan beetle, Upis ceramboides. Anti-freeze molecules have been observed in a variety of plants and animals that help them resist damage from the formation of ice crystals in their tissues. All previous anti-freeze molecules have been proteins, but this new one is a sugar. It may also have a lipid component, but that isn't clear.

The sugar, xylomannan, is a polymer of mannose and xylose. Originally the researchers assumed that the anti-freeze compound in their beetles was a protein, like other known anti-freeze compounds. However they couldn't visualize it with electrophoresis, and the UV-vis and NMR spectra didn't show any sign of peptide bonds or aromatic sidechains like tyrosine or phenylalanine. Instead, the NMR was consistent with a sugar molecule, which was confirmed by GC/MS.

Research Article: A nonprotein thermal hysteresis-producing xylomannan antifreeze in the freeze-tolerant Alaskan beetle Upis ceramboides

Slashdot Science Story | New Antifreeze Molecule Isolated In Alaskan Beetle

Blondie Christmas Carol

2009-12-25T08:00:00.002-05:00

A little Christmas music before going back to some cool chemistry.

Via Blondie - We Three Kings Music Video (2009) Boing Boing

Atomic Cookies

2009-12-24T08:57:00.000-05:00

I've been away for a while. Here's a little treat for the holidays:

Courtesy of Not So Humble Pie, a cooking blog that has been posting recipes for science themed treats recently.

Via Not So Humble Pie: Science Cookies: Atom

Blue Sun

2009-11-07T21:48:00.000-05:00

The Astronomy Picture of the Day site has this cool image of the sun. The visible spectrum of hydrogen has 4 lines called the Balmer Series. I can see at least three of them myself, but the fourth is on the edge of my eyesight. To me the lines have the colors Red (656 nm), Blue (486 nm), Violet (434 nm) and Violet (410). This picture was take using a filter that only lets through the Hydrogen Alpha line, and then color inverted to appear blue. I'm not sure why they changed the color, but it looks cool. Take a look at the larger version of this picture at the link.

Image Credit & Copyright: Alan Friedman (Averted Imagination)
Link APOD: 2009 November 4 - Blue Sun Bristling

Guitar Duet with only One Guitar

2009-11-01T11:15:00.002-05:00

This looks a little awkward, but the amazing thing is that some times his left hand is fretting the strings that she is playing, and she is fretting the strings that he is playing. When I play, both hands are working in synch - I would think it would be hard to NOT have both hands playing the same strings.

via Neatorama

Symmetry is Not A Spectator Sport

2009-10-30T08:46:00.000-04:00

We just finished discussing Stereochemistry in my Organic class. Since stereochemistry ultimately boils down to a matter of symmetry, this seems like an opportune time to show this video.

32 Years Without Small Pox

2009-10-26T21:49:00.001-04:00

It has been 32 years since a case of Small Pox was last diagnosed. According to Wikipedia:

The last naturally occurring case of indigenous smallpox (Variola minor) was diagnosed in Ali Maow Maalin, a hospital cook in Merca, Somalia, on 26 October 1977. The last naturally occurring case of the more deadly Variola major had been detected in October 1975 in a two-year-old Bangladeshi girl, Rahima Banu.

We have heard a lot about vaccines in the last few years. The fact is: vaccines work. The Variola major version of Small Pox has (had?) a mortality rate of 30-35% - out of every three people who got the virus, one died. In the 20th century, it is estimated that 300-500 million deaths were caused by small pox. Because of the small pox vaccine, no one gets this disease. Anywhere in the world.

(Image: wikimedia commons)

Via An Anniversary Worth Celebrating – Neatorama

A Timely Video for Lab Day: Safety Song

2009-10-22T07:40:00.000-04:00

Made by some UC Berkeley Grad students. See more of their work at The Sounds of Science.

via Safety Song: musical number about lab safety - Boing Boing

Drug Microscopy from the Wellcome Image Awards

2009-10-17T14:54:00.000-04:00

Image: Annie Cavanagh and Dave McCarthy

Cool image of polymer-coated drug particles taken with an electron microscope. It looks like some sort of modern art piece. Originally in black and white, the color was added later: the drug is orange and the polymer blue. From this year's Wellcome Image Awards.

According to judging panel member Catherine Draycotte:

"One of the reasons this image stood out as extraordinary is because it doesn't look like a natural image. It doesn't look as though it could possibly come from a microscope - it looks as though it must be computer-generated.

"This is because the particles - and those within them - are so smooth: they are artificial and have virtually no texture. The image really shows what technology can do in targeting drugs to specific purposes. This system is designed to delay the release of the drug that is contained in the smaller particles until it reaches the large intestine, where it will treat inflammatory bowel disease."

Wellcome Image Awards 2009 | Winners' gallery | Scientific and medical images

Commercial green fuel from algae still years away

2009-10-11T19:35:00.000-04:00

Scientists and investors are lured by the pond scum's natural oils that can be extracted and refined into fuel.

Algae grows fast and absorbs greenhouse gases along the way. Plus, the lowly lifeform uses less land, water and other resources than the corn or soybeans used in first generation biofuels, alleviating concerns that those renewable fuels would cause food shortages.

It's disappointing that this may take a decade to be practical, but it seems like a no-brainer to use algae rather than terrestrial plants as a source for renewable bio-fuels.

via Slashdot: Commercial green fuel from algae still years away | Reuters

Desktop Electron Microscope

2009-10-11T19:21:00.000-04:00

From SlashDot:

Wired previewed the desktop-sized Hitachi TM-1000 Electron Microscope a while back. Light microscopes can magnify up to 400X (1,000X at lower quality) — just enough to see bacteria as shapes — but this one offers 20X to 10,000X, giving some amazing pictures. Unlike traditional electron microscopes, this one plugs into a domestic power socket and specimens don't need any special preparation; it's point-and-shoot, much like your typical digital camera.

Cool! But what I would really like is a desktop NMR!

Slashdot Science Story | An Electron Microscope For Your Home?

Aberranone - an Unusual Gorgonian Molecule

2009-10-04T21:05:00.002-04:00

The Caribbean Sea Whip, or Gorgonian, has been the source of a myriad of unusual natural products. The latest example being Aberrarone, which has a unique carbon skeleton, not observed before.

Aberrarone gets its name from the Latin word aberrare, meaning "not typical or usual." The authors suggest that the aberrarane skeleton may be formed via a rearrangement from other gorgonian compounds such as Elisapterosin A or Colombiasin A. All three compounds show anti-malarial activity.

It's hard to really see the structure of these compounds in 2D. Elisapterosin A and Colombiasin A are listed at ChemSpider and if you click the 3D tab above the strucure there you can see them in 3D.

Rodríguez, I., Rodríguez, A., & Zhao, H. (2009). Aberrarone: A Gorgonian-Derived Diterpene from

The Journal of Organic Chemistry, 74 (19), 7581-7584 DOI: 10.1021/jo901578r

Fires spread FAST!

2009-10-03T10:42:00.003-04:00

A couple of minutes into this video they start a fire in a simulated dorm room to show how quickly a fire can spread. This is really impressive, and a little scary.

A good reason to make sure your fire alarm is working, and pay attention when it goes off.

When I was a post doc, the house next door to us burned down late at night in the middle of winter - it was frightening how quickly it happened. We were lucky it didn't spread to our house, in the middle of Pittsburgh the houses are very close together.

Thanks to Debbie Decker on the DCHAS-L list.

Tabla Periodica de los Elementos

2009-09-29T21:42:00.000-04:00

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

Structure of Petroleum Gunk

2009-09-28T20:48:00.000-04:00

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:

Walkingstick Molecules

2009-09-21T21:09:00.003-04:00

Johnny 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

From TED: John Lloyd and Things We Can't See

2009-09-19T08:45:00.000-04:00

Reactions Using Iodine Azide without Explosions

2009-09-18T20:46:00.001-04:00

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

Amazing Molecule Movie

2009-09-17T20:32:00.002-04:00

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

Avogadro 0.9.8 Is Available

2009-09-12T09:22:00.001-04:00

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

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

2009-09-11T19:40:00.000-04:00

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:

IT’S 2:02 A.M. ON A COLD SUMMER NIGHT.

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

Head Music from Neurosonics Audiomedical Labs

2009-09-10T22:16:00.000-04:00

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

2009-09-10T21:44:00.000-04:00

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

CAS Hits 50 Million Compounds

2009-09-09T11:41:00.004-04:00

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

Come On and Meet the Elements

2009-09-08T19:17:00.003-04:00

They Might Be Giants, from their new album of kids' music: "Here Comes Science."

via They Might Be Giants: "Meet the Elements" music video (BB Video) - Boing Boing

A Video History of Movie Special Effects

2009-09-02T20:45:00.001-04:00

A cool compilation of movie special effects over the last hundred years.

via IO9.com 100 Years of Visual Effects From Kong To Tron, And On - visual effects - io9

ChemSketch on Linux? Maybe not ...

2009-08-30T17:40:00.000-04:00

Ever since I started using Ubuntu last Spring I have been looking for a Chemical Structure Drawing program that runs on Linux. On Windows, I have been using ACDLabs ChemSketch ever since version 1.0 in the 1990's. They are up to version 12, and every new release has lots of good stuff. It's available as a free download for educational use, I recommend it to my students for writing their lab reports.

When I realized that they had put out a Linux-compatible version I was really excited. ChemSketch is about the only program I use that I need Windows to run. Unfortunately it doesn't look like that's going to work out.

After you register to download the Linux installation program, you get an exe file. Unless you read carefully you may have missed the reference to CodeWeavers Crossover. EXE files don't run on Linux systems, but you can run them with a Windows Emulator which is what Crossover does. Crossover is not a free program, but it is based on a program called Wine, which is free.

I have tried both Wine and Crossover (as a free trial version) and ChemSketch seems to work pretty well with both. There is a problem though: After installing ChemSketch I can run the program just once. When you start ChemSketch you see a splash screen displayed, then a CheckBox describing ACDLabs products appears. Once you click the OK button, the CheckBox goes away and the ChemSketch window opens. In addition to the ChemSketch window, the ACDHost runs as an icon in the top panel.

The second time (and every other time) I try to run ChemSketch on Ubuntu, that icon is the only sign that ChemSketch has started. I see the splash page and CheckBox as usual, then nothing happens. I get the same result whether I use Crossover or Wine to install and run ChemSketch. The only thing I can do is right click the ACDHost icon and choose "Close All" to exit the program.

It's puzzling and quite frustrating. Obviously the program will run (once) and everything seems to work the way it does under Windows. The System Monitor shows processes for ACDHost and ChemSketch with their status listed as Sleeping. What do I have to do to wake them up? There may be a simple answer to this, but I'm still really new to Linux and I haven't figured it out yet.

Test Your News IQ - Pew Research Center

2009-08-25T21:37:00.003-04:00

The Pew Research Center has a Science Knowledge Quiz. Go ahead and take it now, there are only 12 questions. I'll wait.

As a professional, life long science geek I expected to do well. I helps that I teach chemistry, and I'm interested in medical research, astronomy and space science.

If you look at the breakdown by question, it's not too surprising which questions most people answered correctly. And it's understandable that about half the people who took the quiz didn't know how big an electron is - that's not something most people have any personal experience with.

The question that disappointed me most was the one on antibiotics and viruses. Every time you get a cold and ask for antibiotics your doctor should tell you the answer to this one. Antibiotics don't affect viruses. When you are feeling crummy, it may seem unfair but the antibiotics won't make you feel any better except by the placebo effect. Fewer than half answered correctly. Everyone should know this, for two reasons:

it's wasteful and a waste of time to take drugs that don't work
it contributes to bacterial resistance to antibiotics, which is bad for everyone

Test Your News IQ - Pew Research Center
via Greg Laden's Blog

Internet Profile: Bridgehead Carbons

2009-08-19T14:10:00.000-04:00

My "seemingly authoritative personal profile" courtesy of Personas, which is part of an exhibit at the MIT Museum. When you enter your name, Personas searches the web for information about you according to a set of categories which it uses to generate a profile like the one above.

I tried with my real name a couple of different ways. Apparently I share my name several other people who have much bigger internet presences than I do - including a golfer and a CEO. The "profile" I get doesn't fit the real me at all. Since the profiles I got didn't seem to reflect me as well as a bunch of other people, I decided to enter "Bridgehead Carbons" as my "Name."

I'm amazed - the largest category is Sports. WTF! Ok so here's my sports-related comment: I can't believe that my hometown Minnesota Vikings actually signed Brett Favre - I may have to root for the Lions this season, because there is no way I can root for that bozo. If they win the Super Bowl with that clown I might be able to live it down. But I don't expect him to play any better with the Vikes than he did with the Jets last year - the hapless Dolphins kept them out of the playoffs with the QB that Farve replaced. For every 3 TD passes, Favre throws 2 interceptions and he's almost as old as I am. The last time he was in the Super Bowl was more than 10 years ago and he LOST.

via Personas - Miss Cellania -

CRC History

2009-08-18T21:06:00.000-04:00

The three reference books I use the most often are the Sigma-Aldrich catalog, the Merck Index and the CRC Handbook of Chemistry and Physics. The first one is a catalog and the second started as a catalog. As it turns out, the CRC was also started by a chemical supplier - it wasn't a catalog but was provided as a marketing tool by the Chemical Rubber Company. The first edition, published in 1913, was so popular that it has been revised almost every year since.

The Chemical Information division of the American Chemical Society has an interview with Dr. David Lide , who has edited the CRC Handbook of Chemistry and Physics since 1989. The interview was published in the Fall 2009 Chemical Information Bulletin.

You can also access the interview directly at
http://acscinf.org/docs/publications/Interviews/Lide/2009/CIB2009_61-2_Lide.pdf

Cyclization Reactions and Angelmarin Synthesis

2009-08-13T21:30:00.000-04:00

The first total synthesis of (+)-Angelmarin includes some neat cyclization reactions. They started with Umbelliferone which you can buy, and synthesized angelmarin by way of columbianetin.

I'm always curious about where the names of these compounds come from. The systematic names are probably rather cumbersome, so these common names are useful. Umbelliferone is found in plants of the Umbelliferae family - which includes carrots. Also named for plant species, angelmarin was isolated from Angelica pubescens, and columbianetin from Lomatium columbianum.

The first cyclization step is a Claisen rearrangement - three bonds all move in a circle, which causes the allyl group to migrate to the aromatic ring. The resulting ketone tautomerizes to the more stable phenol structure.

After an olefin cross-metathesis to introduce two methyl groups, the next step was in effect a double cyclization. First a stereoselective Shi epoxidation. Then the epoxide is opened during the second cyclization to form columbianetin.

This last cyclization is an an example of a 5-exo-tet cyclization according to Baldwin's Rules for ring formation. The resulting ring is a 5-membered ring. The bond broken to make the new ring is not part of the new ring (exo). And when the new ring is formed, the nucleophile is forming a bond to a tetrahedral atom (tet).
To convert columbianetin into the final product required the formation of an ester. This proved to be challenging - many standard esterification strategies either did not work, or it caused side reactions that destroyed the columbianetin portion of the molecule.

To get around this, they first converted it to a malonate ester under mild conditions. This was reacted with p-hydroxybenzaldehyde and catalytic piperidine to generate the final product by way of a Doebner-Knoevenagel condensation. In effect building the hydroxycinnamate group instead of adding it as a single piece.

Magolan, J., & Coster, M. (2009). Total Synthesis of (+)-Angelmarin The Journal of Organic Chemistry, 74 (14), 5083-5086 DOI: 10.1021/jo900613u

Hubble Deep Field in 3D

2009-08-13T19:23:00.000-04:00

According to the Hitchhiker's Guide to the Galaxy:

Space is big. Really big. You just won't believe how vastly hugely mind-bogglingly big it is. I mean, you may think it's a long way down the road to the chemist, but that's just peanuts to space.

I think this starts to give you a hint at how big space is.

link to video via BoingBoing

July Weather: Local vs Global

2009-08-12T20:00:00.001-04:00

From AccuWeather:

NASA's Goddard Institute of Space Studies (GISS) has determined that July of 2009 was the second warmest July globally, since records were kept going back well over a hundred years.

The map above compares July 2009 with "normal" - July from 1951 through 1980. Blue is cooler than "normal" and red is warmer. There are some blue bits, but there sure is a whole lot of red - more than enough to compensate for the smaller regions of cooler temperatures.

In fact most of the eastern US was blue in July, with the darkest blue in the Great Lakes region where I live. I know I'll be hearing people say, "Gosh it's been cold this summer. That proves there's no Global Warming!"

The thing about Global Warming is that the Earth warms unevenly - that is one of the things that causes winds. Change the winds and you change the weather. Change the temperature - up or down - and the amount of rainfall and you can have big problems for the farmers.

It's not just an issue of having warmer weather - some people would like that. I have lived in Tennessee and Georgia and I prefer to live in a place that gets snow in the winter, I kind of like the weather as it is. The real issue isn't so much creature comforts but food. Considering all the red in the polar regions, if I lived in Miami I would be a little worried about sea level too.

via AccuWeather.com: Global Warming News, Science, Myths, Articles

Drawing Molecules with SMILES

2009-08-10T22:40:00.001-04:00

Lately I have discovered that when drawing 2D or 3D chemical structures, it is often a lot easier to input a SMILES string than to draw it with the GUI. It reminds me of when I first started using Windows (v. 3) - at times I thought it was easier to type a command to tell the computer what I wanted to do instead of hunting through menus and dialogs to find the thing I needed to click.

SMILES is a way of describing a chemical structure on a single line - a LOT like a conventional condensed formula except without the Hydrogens. It is commonly used in database and chemical informatics applications. In an earlier post on Surfactants, I wanted to include the structures of a couple of perfluorinated surfactants. Drawing all 15 fluorines individually was just too tedious, it was much simpler - believe it or not - to type: FC(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(=O)O

Drawing large and complex compounds "by hand" is also a hassle - and in some cases very difficult to get a good looking structure. Fortunately, many on line resources (e.g. Wikipedia, PubChem, ChemSpider) list the SMILES string for compounds like morphine:
Earlier in the summer I decided to install Ubuntu on my laptop in addition to Windows so I could run either operating system. One difficulty I have had in moving to Ubuntu is finding chemistry software to replace the programs I usually use on Windows. It turns out that several of the structure programs that I have been using lately will allow me to input a SMILES string.

One program I have been experimenting with lately is Avogadro - an open source project for building and studying 3D chemical structures. Avogadro is available on both Windows and Linux (as well as Mac), which is pretty convenient for me right now. It is a very nice program, they are at version 0.9.7 and plan to release 1.0 in September.

For drawing 2D structures on Windows I use ChemSketch, available as freeware from ACDlabs. On Ubuntu I have tried several 2D structure programs, none that match up to ChemSketch. One that I have used most is BKChem, which I used for the structure of Morphine above.

The Pentatonic Scale from the World Science Festival

2009-08-09T20:50:00.002-04:00

World Science Festival 2009: Bobby McFerrin Demonstrates the Power of the Pentatonic Scale from World Science Festival on Vimeo.

via The Pentatonic Scale - Neatorama

Chemistry Graphics Hassle on Ubuntu

2009-08-01T19:42:00.001-04:00

Lately I have been using Ubuntu Linux instead of Windows, and on the whole I think I prefer Ubuntu:

Ubuntu starts-up and shuts-down faster than Windows
Open Office is faster with Ubuntu (I never use MS Word even on Windows)
security is much less of a problem (although I do use a virus scan package with Ubuntu)
FREE SOFTWARE
and the geek factor of using Linux probably appeals to me as well

One difficulty for me has been finding chemistry-specific software to take the place of the Windows programs I am used to using. That situation improved a little bit today.

Avogadro and Ghemical are two programs I have been playing around with for building and doing simple calculations on 3D molecular structures. They both have a window that displays the molecule in 3D, and up until today that has been a problem for me. Frequently the desktop would "bleed through" so I couldn't see the molecule being displayed. Depending on what I was doing it was either inconvenient or a major annoyance. It would be so much easier to do things in Windows. That would involve re-booting the computer and starting Windows - something I try to avoid doing these days.

It turns out the solution was pretty simple, but I'm still a newbie with Linux and it took me a while. If I turn off the fancy graphics for the desktop, the problem goes away. The first time this idea occurred to me I went into the Compiz control panel and didn't know where to even start - and I wanted to be able to turn everything back on again if that didn't work. Compiz has LOTS of settings, I tried a few things without making matters any better.

Instead, what I should have done was go to the System Preferences and select "None" on the Visual Effects tab. Problem solved! The Visual Effects aren't all that important to me, but it's nice that I can turn them on and off so easily.

Now I can spend some time playing around with Avogadro and Ghemical to figure out what they do.

Blue Food Dye Does NOT Treat Spine Injury in Rats

2009-07-31T11:59:00.003-04:00

You have probably seen those cute pictures of the blue mice by now. I first saw it on Neatorama, which linked to an article at Wired. Both said in their headlines that a Food Dye was responsible for reducing the damage from spinal cord injuries. To be fair, both sites mentioned in the articles themselves that the actual molecule used was similar to the food dye FD&C blue No. 1, but it was not in fact the dye used in blue M&M's.

The compound used in the Spinal Injury study was Coomassie Brilliant Blue G, which is commonly used as a protein stain for gel electrophoresis and in the Bradford protein assay. As you can see, they are not quite the same - Coomassie has a couple of extra methyl groups, and the substituent on the "top" benzene in this image is different.

The interesting thing to me is how it "works." According to the research article published in PNAS, the initial injury to the spinal cord is followed by a secondary injury. Over time, the area of damaged tissue expands from the original site of injury and the researchers reasoned that this expansion should be preventable.

The P2X7 receptor is a membrane channel that opens in response to increased ATP. In the injuries studied, the traumatized tissue releases a lot of ATP which in turn activates the P2X7 channels causing them to open. This has been linked to the spread of the injury, so anything that prevented the opening of the P2X7 channel could be expected to reduce or eliminate the secondary injury.

The Coomassie Blue acts as an antagonist for the P2X7 receptor. It binds to the receptor but does not activate the receptor - so the channel remains closed. Presumably Coomassie Blue and ATP both bind to the same site on P2X7 and only one can occupy the binding site at a time. Because the receptor is bound to the Coomassie Blue, ATP is unable to bind and activate the receptor. Since the opening of the channel is what leads to the expansion of the injury, keeping it closed will limit this expansion.

This is an exciting discovery, but it is likely to be only the first step. In the study, they treated the spinal cord injuries after 15 minutes. People who suffer spinal cord injuries might be helped by treatment with Coomassie Blue, but it is unlikely that they would receive treatment within 15 minutes.

Peng, W., Cotrina, M., Han, X., Yu, H., Bekar, L., Blum, L., Takano, T., Tian, G., Goldman, S., & Nedergaard, M. (2009). From the Cover: Systemic administration of an antagonist of the ATP-sensitive receptor P2X7 improves recovery after spinal cord injury Proceedings of the National Academy of Sciences, 106 (30), 12489-12493 DOI: 10.1073/pnas.0902531106

Blue Man Group video

2009-07-30T22:00:00.000-04:00

Blue Thousand and One from Blue Man Group HD on Vimeo.

With the news about Blue Mice lately, here's a cool video from the Blue Man Group.

via The Daily Dish | By Andrew Sullivan

Steven Chu on The Daily Show

2009-07-22T09:38:00.003-04:00

John Stewart reveals Energy Secretary Steven Chu's secret identity as a super-hero who combats climate change.

The Daily Show With Jon Stewart

Mon - Thurs 11p / 10c

Steven Chu

www.thedailyshow.com

Daily Show
Full Episodes

Political Humor

Joke of the Day

Science Tattoos

2009-07-20T11:05:00.000-04:00

Here's the neurotransmitter Seratonin from the Science Tattoo Emporium at Discover Magazine

Learning makes your brain happy

2009-07-20T10:55:00.000-04:00

Ed Yong at Not Rocket Science writes about a research paper showing a link between learning and thirst in rhesus monkeys. In

Why information is its own reward - same neurons signal thirst for water, knowledge:

he writes:

To me, and I suspect many readers, the quest for information can be an intensely rewarding experience. Discovering a previously elusive fact or soaking up a finely crafted argument can be as pleasurable as eating a fine meal when hungry or dousing a thirst with drink. This isn't just a fanciful analogy - a new study suggests that the same neurons that process the primitive physical rewards of food and water also signal the more abstract mental rewards of information.

As commenter oscarzoalaster puts it:

So there is actual objective evidence that curiosity can be as important a desire as food and water! I feel more normal now!!! Thank you!

If only teaching were so easy.

via Learning makes your brain happy - Boing Boing

Element 112 - Copernicium

2009-07-17T10:00:00.000-04:00

Goodbye Ununbium.

Thirteen years after it was first discovered, Element 112 has been officially added to the Periodic Table and its discoverers have suggested the name Copernicium (Cp) in honor of Polish astronomer Nicolaus Copernicus who proposed the heliocentric model of the solar system.

Of course, IUPAC is cautious and the name isn't official yet.

Image: Wikimedia Commons

BBC NEWS | Science & Environment | New element named 'copernicium'

Lipase-Catalyzed Synthesis of a "Green" Surfactant

2009-07-13T19:45:00.000-04:00

Surfactants are molecules that lower the surface tension in water. They behave this way because of their dual nature: a long, hydrophobic carbon tail attached to an ionic end, typically an acid or ammonium group. Surfactants are used in a variety of industrial applications including detergents and wetting agents. A number of widely used surfactants are problematic in that they are non-biodegradable and toxic. PFOA and PFOS are perfluorinated compounds (all hydrogens replaced with fluorines) – the fluorines make the compounds very good surfactants, but also very unreactive (and not biodegradable). They are also known carcinogens. SDS and SLES are not so bad, but still they are irritants and contain sulfonate groups that make them not as easily biodegradable as other compounds.

This article describes the synthesis of an alternative surfactant that is both more biologically friendly (non-toxic and biodegradable) and uses “green” chemistry methods that improve the efficiency of the synthesis and reduce hazardous waste products. N-Acyl palmitoyl ethanolamine is derived from two common constituents of biological lipids: the fatty acid palmitic acid and ethanolamine. Like soap, this surfactant is cheap, non-toxic and biodegradable. Like many industrial surfactants, and unlike soap, it is not prone to forming soap scum with hard water.

They used the enzyme Lipase to catalyze the reaction between ethanolamine and a fatty acid (or its ethyl ester). There are two possible products depending on which end of the ethanolamine reacts: either a hydroxy amide or an amino ester. Perhaps not too surprisingly, the hydroxy amide is formed exclusively. Amides are generally more stable than esters, amines are stronger nucleophiles than alcohols, and as the authors point out themselves amino esters with only two carbons between the N and O will rearrange on their own to the more stable amide form. Lipase was chosen because it is a flexible catalyst and the reaction takes place under mild conditions (no strong acids or bases to neutralize at the end).

They investigated three different sets of reaction conditions:

reactants in solution, conventional heat source
reactants in solution, microwave heating
reactants in solid state, microwave heating

The enzyme itself was attached to porous resin beads. For the solution-phase experiments, the enzyme and reactants were added to dioxane. For the solid-phase experiment, the reactants were dissolved in a small amount of solvent which was added to the enzyme and then evaporated to leave the reactants as a film on the enzyme-containing beads. Both microwave-heated reactions went considerably faster than conventional heating, and the solid-phase reaction was faster that the solution.

What exactly makes this "green?" While dioxane is not the most desirable solvent, it can be recovered afterwards and re-used. Otherwise, there is little waste. If fatty acids are used as the starting material instead of the corresponding ester there are no waste byproducts (such as ethanol) to separate and dispose of safely, and no strong acids or bases to neutralize. Even the enzyme is re-usable. And the product hydroxy amide is of low toxicity and should be biodegradable as well. If the solid-phase reaction with microwave heating turns out to be practical, it would greatly improve the efficiency of the process by speeding-up the reaction and improving the yield and purity of the products.

Kidwai, M., Poddar, R., & Mothsra, P. (2009). N-acylation of ethanolamine using lipase: a chemoselective catalyst. Beilstein Journal of Organic Chemistry, 5 DOI: 10.3762/bjoc.5.10

Quantum Kitteh

2009-07-12T17:19:00.004-04:00

see more Lolcats and funny pictures

Antimony for Good Digestion?!

2009-07-11T20:25:00.002-04:00

Scribal Terror has an article on "The Everlasting Pill," which was apparently an item you could buy in the past as an aid to good digestion. It was a small "bullet" of metallic antimony that you swallowed as a purgative agent. Not only that, it was meant to be re-used: once it had passed all the way through your digestive system it could be recovered, cleaned off and used again!

The original source is the Medico-Pharmaceutical Critic and Guide (1907), edited by William J. Robinson, which goes on to say:

This, as Dr. J. A. Paris says, was economy in right earnest, for a single pill would serve a whole family during their lives and might be transmitted as an heirloom to their posterity. We have heard of a lady, says the Doctor, who, having swallowed one of these pills became seriously alarmed at its not passing. "Madam," said her physician, "fear not. It has already passed thru a hundred patients without any difficulty."

And then finishes with this keen observation:

We do not think that the everlasting pill would be popular at the present time.

I wonder why antimony was chosen? Antimony and its compounds have been used in treating parasites, but I don't know it that would have anything to do with the supposed "cathartic" properties of the "Everlasting Pill." Of course, antimony is toxic. According to wikipedia, antimony poisoning is similar to arsenic poisoning, which only makes sense since antimony is right below arsenic in the periodic table. I don't know how much metallic antimony you would absorb through the gut, but I doubt it would be a good idea to use this device.

You can read the original, and many other interesting articles in the Medico-Pharmaceutical Critic and Guide which is available by way of Google Books. This book is out of copyright, so you can read the whole thing for free on line, or download a PDF copy for yourself. As a bonus, you can also search and copy selections on line - which is how I got the quote above. Since the PDF version is just a scanned image it can't be searched or copied so easily.

Image: Wikimedia commons

Scribal Terror: The everlasting pill by way of Neatorama,

Anticancer Compound from a Tumor-Promoter

2009-07-06T21:20:00.000-04:00

The title of this article caught my eye because of the irony of designing an anticancer drug by modifying a known tumor promoter. Aplysiatoxin is a tumor promoter, while Compound 1 from the paper is not. In fact, Compound 1 is just a simpler version of Aplysiatoxin: the hemiacetal has become an ether and several side groups have been lost. There are also fewer stereocenters in Compound 1 than in Aplysiatoxin.

First a little background. Both compounds affect cancerous cells the way they do because they bind to Protein Kinase C (PKC). PKC is an enzyme that contributes to a number of signaling pathways within the cell, particularly having to do with cell differentiation, proliferation and apoptosis. PKC's involvement in cellular growth cycles also results in its involvement in carcinogenesis, and it has been a target for developing anti-cancer drugs for this reason.

The curious thing about PKC is that some molecules that bind to PKC activate the enzyme, while others de-activate it. Even stranger, some activators promote tumor formation and other activators do not.

PKC activators have shown some promise for treating diseases such as Alzheimers or AIDS, but their tumor-promoting behavior is a big drawback. Ideally you would want to find a PKC activator that was also non-tumor promoting. Bryostatins fit this description, but the compounds are too complex to be easily made in the laboratory. In nature, bryostatins are made by a coral-like organism but in extremely small amounts. According to Wikipedia, you would need a ton (2000 lb) of bryozoans to obtain just one gram of bryostatin.

Aplysiatoxin binds to PCK as a tumor promoting activator. Compound 1 was designed as a simpler version of aplysiatoxin that might be a PKC activator without also being a tumor promoter. As it turns out, compound 1 shows minimal tumor-promoting activity, and it counteracts the effects of the tumor-promoter 12-O-tetradecanoylphorbol-13 acetate. It's anti-cancer activity as well as it's mode of binding to PKC seems to be comparable to the bryostatins. The authors report that they can make Compound 1 in only 22 steps, which makes it a promising alternative to bryostatins as a potential therapeutic agent.

Nakagawa, Y., Yanagita, R., Hamada, N., Murakami, A., Takahashi, H., Saito, N., Nagai, H., & Irie, K. (2009). A Simple Analogue of Tumor-Promoting Aplysiatoxin Is an Antineoplastic Agent Rather Than a Tumor Promoter: Development of a Synthetically Accessible Protein Kinase C Activator with Bryostatin-like Activity Journal of the American Chemical Society, 131 (22), 7573-7579 DOI: 10.1021/ja808447r

Lord of the Rings Webcomic

2009-07-05T08:00:00.000-04:00

I came across "DM of the Rings" on Neatorama the other day and had to read all 155 installments. It's a hilarious web comic by Shamus Young that uses scenes from the Peter Jackson Lord of the Ring movies to imagine a group of Dungeons & Dragons players reenacting the Lord of the Rings. Needless to say the players haven't read the book (or seen the movies), and while D&D is a role-playing game, the players have a hard time staying in character.

The first episode is a good place to start. As a science geek, I particularly liked Schrödinger’s Familiar. If you aren't familiar with the gazillion monsters character might run into, a Lich is a sort of undead sorcerer.

The Chemistry of Firework Displays

2009-07-04T03:22:00.000-04:00

photo credit Dori (Wikimedia Commons)

Slashdot has links to some cool articles on the chemistry of Fireworks.

Slashdot News Story | The Chemistry of Firework Displays

Ridiculous Fellows: Amazing Organ Performance

2009-06-27T12:48:00.002-04:00

"Ridiculous Fellows," from Prokofiev's "The Love for Three Oranges" orchestral suite. Qi Zhang playing a Yamaha Electone Stagea, which she programmed herself.

Quorum-Sensing Molecules

2009-06-19T08:00:00.001-04:00

I was fascinated by Bonnie Brasler's TED talk on Quorum-Sensing, and being a chemist I wanted to know more about the molecules involved. She did put up a slide with structures during the talk, but I wanted more so I did a search on PubMed and found this Perspective written by Brassler and Michael Federle.

My only experience with the notion of a “quorum” is our Faculty Assembly where we sometimes have difficulty achieving a quorum. In order for the meeting to be “official” and for any votes taken to be valid we need to have a minimum number of faculty present, a “quorum.” For bacteria, quorum sensing is the way the bacteria “count” one another. The bacterium releases a particular molecule, called an autoinducer - if there are lots of the molecules, then there are a lot of bacteria. If there are very few autoinducer molecules, then there are few bacteria present. The bacteria has a protein receptor that binds to the autoinducer molecule – so the bacteria can “sense” the presence or absence of autoinducer molecules depending on whether or not the receptor protein has detected any. In this way the bacteria can change their behavior depending on the number of bacteria present, as measured by the number of autoinducer molecules it finds. As a group, the bacteria behave one way when there is a low density of bacteria present and a different way when there is a high density of bacteria present.

In the simplest examples, quorum-sensing allows the bacteria to switch between two different behaviors depending on the number of bacteria present. One example would be the staphylococcus aureus bacteria – at low density they adhere to the surface of the cells of the host organism where they can grow and produce more bacteria. Once they reach a “quorum” there are enough bacteria present to be able to invade the host cells Their metabolism then shifts from producing the proteins that allow attachment to the outside of host cells and starts to produce proteins and toxins that allow the bacteria to enter the host cells. The light-producing bacteria from Bonnie Brassler's TED talk produce light when there are a lot of bacteria present, and stop producing light when there are few bacteria present.

Enough about biology, what about the molecules involved? In this Perspective, two categories of autoinducers are discussed, and one “special case.” Gram negative bacteria produce a type of autoinducer referred to as AHL for Acyl Homocysteine Lactone. Different types of bacteria will have different acyl groups attached to the homocysteine, and only recognize their own type of AHL. Gram positive bacteria do not use AHL's, instead they produce specialized proteins called AIP for AutoInducing Peptides, which consist of a string of 5 to 17 amino acids, some of which may be modified. The two types of autoinducer (AI) are detected by the bacteria when the AI binds to a receptor molecule in the bacteria. The details differ, but when enough AI's are around to bind to their receptors, the receptor causes a change in gene expression in the bacteria, which leads to a different behavior by the bacteria.

The AHL's and AIP's are species specific: each type of bacteria produces only one AI and only recognizes it's own AI. The third type of molecule discussed is an unusual boron-containing molecule that may have a role for communication between different species of bacteria. The light-producing bacterium vibrio harveyi produces two different autoinducer molecules. The first is referred to as AI-1. AI-1 is an AHL molecule used for communication only among the V. harveyi bacteria. The other autoinducer is AI-2 which, on the other hand, may have a role in allowing different species of bacteria to communicate with one another.

AI-2 is synthesized by the bacteria in three steps from S-adenosyl methionine. The enzyme for the final step in this synthesis is called LuxS and as it turns out the gene for LuxS is found in many different bacteria, which all seem to both make and respond to the presence of AI-2. The implication of this is that perhaps AI-2 serves as some sort of generic autoinducer that allows bacteria to sense not only their own species, but also all other species of bacteria that produce AI-2.

The really interesting thing is that if we understand how bacteria communicate, we can find ways to short-circuit that communication. Many pathogens use quorum-sensing to regulate their virulence. In the example I mentioned earlier about S. aureus, the bacteria depend on reaching a “quorum” before they begin to “invade” the host cells. If their ability to sense one another is prevented, then perhaps their ability to invade the host and cause disease could be reduced.

Federle, M. (2003). Interspecies communication in bacteria Journal of Clinical Investigation, 112 (9), 1291-1299 DOI: 10.1172/jci200320195

How Bacteria Use Molecules to Keep Track of Each Other

2009-06-15T10:34:00.002-04:00

About Bonnie Bassler at Ted.com

Cosmetic Toxicity Database

2009-06-13T07:30:00.004-04:00

Wouldn't you like to know what's in the products you put on your skin? Skin Deep is an online database that brings together safety information on the ingredients in a wide variety cosmetics. They pull their information from many sources, including US EPA, EU, Canadian government, and a number that look like they are probably public interest groups.

You can search by product name, product category, manufacturer, or ingredient. All ingredients in the product are listed along with a safety rating of 0-10 and what type of hazard may caused by the ingredient, as well as a “Data Gap” which indicates the lack of safety information on the ingredient as a percent.

Of course, toxicity is a complex issue and not simple to nail down precisely. It depends on the dosage and the route of exposure (skin, oral ingestion, inhalation, etc). It would be nice to see the actual test data that they used to develop their ratings. Many ingredients are listed as (possible) carcinogens or as neurotoxins, but I can't tell how this was determined. If the actual test were based on oral ingestion or whole cell screens they may not be very informative about how the compound would behave when applied to the skin.

The other problem is dosage – most of the compounds in a cosmetic are likely to be found in small amounts – were the tests done with low concentrations to accurately reflect the “dosage” in a cosmetic? The pigments in particular seem to get the higher toxicity ratings – the thing about pigments is that it only takes a small amount of pigment to get a significant color. It may be difficult to measure the behavior of really small amounts accurately, higher dosages would be easier to measure but may not be good indications of the effects when exposed to only small amounts.

Particularly telling is the “Data Gap” rating which is "is a measure of how much is unknown about an ingredient. " A search for a common shampoo listed one of the ingredients as "Fragrance," which was given a hazard score of 8 (out of 10) with concerns about "Neurotoxicity, Allergies/immunotoxicity, Miscellaneous " and a Data Gap of 100%. The Data Gap score suggests to me that their toxicity rating is a not at all reliable. Most fragrances in commercial products are fairly simple compounds of a floral nature, and probably only present in a fairly small concentration. Although allergy concerns are probably sensible, I really doubt that washing my hair with shampoo is much of a risk for neurotoxic or immunotoxic side effects. Most people with a little common sense would probably tell you the same thing.

Skin Deep is probably a good place to start looking for information about the substances found in cosmetic products, but I don't know how much you should really trust the toxicity ratings that are given.

via BoingBoing

Too Funny: Roche xCELLigence Rock Video

2009-06-10T09:00:00.002-04:00

I saw an ad for this in Science a while back. Cell Biology isn't my area, so I'm not too sure what xCELLigence IS, but the music video is entertaining.

They also have a Rock Ballad video.

Roche xCELLigence Rock Video

Bendable Crystals

2009-06-09T16:45:00.002-04:00

Crystals are generally rigid and brittle, but this paper describes microcrystals of dimethylamino trans azobenzene that bend into a semicircle when a light is shined on them. That the azobenzene molecule responds to light is no real surprize, but the fact that the whole crystal changes shape, and reversibly to boot, was pretty cool.

Take a look at the video's of this that are provided, for free, in the supplemental information for the paper. The movie 002 shows the bending motion most clearly. This crystal is about 0.5 mm by 0.28 mm and 0.005 mm thick, so it is really tiny. A larger crystal probably would not do this.

So what's going on? The N=N double bond can be in either the trans orientation or the cis orientation. The trans version is preferred - the cis version suffers from steric crowding as the two benzene rings bump into one another. By shining light with the proper wavelength on the molecule, you can convert the trans into the cis molecule. Turn off the light, and the molecule can revert back the the trans version.

The authors were able to confirm that when they shine light on their crystals they convert about 1% of the molecules from the trans form to the cis form. This was readily apparent in proton NMR, but evidence could also be seen in changes in the UV-vis spectrum and the melting point of the crystals. After turning off the light source, the molecules in the crystal return slowly to all-trans.

So, how does this cause the crystal to bend almost in half? It seems to have to do with the way the molecules arrange themselves in the crystal lattice. The trans molecules are flat and stack into a very regular herring-bone type of pattern. The cis molecules don't fit this pattern - in addition to the U-shape, the cis molecules have a twist in them to reduce some of the steric strain between the benzene rings. The twist make the molecules much bulkier than the flat trans form As a result the cis molecules don't fit into the crystal lattice and cause the unit cell to be longer than the unit cell for only the trans molecules.

When the light source converts some of the molecules to the cis form, the side of the crystal nearest the light source appears to expand - because of the larger unit cell of the cis molecules. The side of the crystal away from the light source does not experience this and stays the same size. To accommodate the expanding surface facing the light source, the whole crystal bends away from the light source. When the light is turned off, the cis molecules slowly revert to the (more stable) trans form and the crystal un-bends.

Koshima, H., Ojima, N., & Uchimoto, H. (2009). Mechanical Motion of Azobenzene Crystals upon Photoirradiation Journal of the American Chemical Society, 131 (20), 6890-6891 DOI: 10.1021/ja8098596

Visualizing Data in the AlloSphere

2009-06-09T09:00:00.000-04:00

How do I get one of these?

Structure of a Viral Protein Coat

2009-06-08T11:55:00.000-04:00

The June issue of Popular Science has an image of the 3D molecular structure of the protein capsid for the Penicillium stoloniferum virus (PsV-F). This is the protein outer shell of the virus that acts as a container for the genetic information of the virus. The image doesn't appear to be on the Popular Science web site, so I went looking for the protein structure at the Protein Databank.

The image above comes from the PDB entry for structure 3es5 which is the crystal structure of the dimeric capsid protein (CP). The image above shows the biological unit which consists of 60 copies of the CP dimer in a roughly spherical arrangement. In Atomic Structure Reveals the Unique Capsid Organization of a dsRNA Virus, Pan et. al. used electron cryomicroscopy to compute a 3D reconstruction of the entire 120-mer of the protein capsid. The image in PopSci and the images in the original paper are much cooler than the one above, but this gives you an idea of what it would look like.

If you can't find a copy of Popular Science, you can see the original article at PNAS or Pubmed Central in September, since PNAS makes articles available for free 6 months after print publication.

More Fun with Mercury

2009-06-07T09:30:00.003-04:00

See how to make solid Fishes, Turtles and Frogs out of Mercury. Pretty cool, but don't try this at home.

via BoingBoing

Hot Blues from the Homemade Jamz Blues Band

2009-06-05T14:50:00.004-04:00

These kids are great! I first heard of them on NPR last summer - check out the profile from NPR including several clips. Today I learned that they have a new CD coming out on Monday.

Exploring Ubuntu

2009-04-23T11:23:00.002-04:00

I've had a mild curiosity about the Linux operating system as an alternative to Windows for a long time. Actually installing it always seemed like more trouble than I cared to bother with, but recently I have seen a few things that convinced me to look into it.

This post from Lifehacker about Portable Ubuntu convinced me that I could take a look at the Ubuntu version of Linux without doing anything more complicated than installing another program under Windows. Portable Ubuntu installs everything it needs into a single folder on Windows, so it doesn't affect the regular Windows operating system at all. You run Portable Ubuntu just like any other Windows program. It appears as a toolbar with menus for Programs, Places (the file system) and System settings. Although in most cases it doesn't run the same programs you would use in Windows, it does have programs that do all the same things I would normally do in Windows. The only immediate problem I have is drawing 2D chemical structures, which I'll save for another post.

Portable Ubuntu convinced me that there's nothing scary, or even all that unfamiliar, in using Ubuntu instead of Windows. But I have found that my Windows machine is increasingly a memory hog and running Portable Ubuntu at the same time only makes this worse. I decided to take the next step and install Ubuntu outright.

The Ubuntu version of Linux is designed to be REALLY easy to use, especially for newbies. You have lots of options for installing Ubuntu:

turn on your computer with a Live CD in the diskdrive and you can run Ubuntu from the CD without installing anything on your hard drive. Of course you can't save anything this way, and it is slow because the operating system has to read everything from the CD first.
use the Live CD to install over Windows - if you don't want Windows anymore you can go to a Linux-only machine.
If you still want to have the option of running Windows you can partition the hard drive, leaving Windows intact one one partition and installing Linux into the other partition.
If you don't want to partition you can use Wubi, which is what I decided to do. Wubi installs Ubuntu into a folder - no partitioning required - and Windows is not affected. When you turn on your computer, you will get a screen asking which operating system you want to run: Windows or Ubuntu. One nice thing about Wubi, if you have internet access you don't even need the CD. Wubi will download everything for you - of course downloading 700+ MB will take some time.

If you are a fan of Manga, check out this Manga Comic to see exactly how easy it is to install Ubuntu. Why do the people in Manga look like they have fangs? Link via BoingBoing.

Personally, I like to have the instructions to read. Or at least a nice tutorial. If you do too, take a look at the free Linux Starter Kit, from Linux Format magazine. Link via Greg Ladens blog.

More Easter Egg Fun on Your Computer

2009-04-12T17:10:00.000-04:00

Check out some of the "goodies" hidden in the software you use.

I even got to look at the Linux Easter Eggs myself, since I had just installed Portable Ubuntu so that I could try-out a Linux operating system as easily as running a program on my Windows machine. The "doctor" hidden in emacs really takes me back. The first time I saw this program I was in college - in the pre-PC days when we all had accounts on the school's Vax mainframe computer. Then it was called Eliza, but the program itself is even older than that.

Lifehacker - Top 10 Software Easter Eggs

Video: Watch 10 terrific 'Easter eggs' in action at Computerworld.com

There's some overlap between the two sites. The Computerworld page has video clips of all the Easter Eggs so you can see what they look like even if you don't have the program or operating system involved.

Fun with Mercury

2009-04-09T15:35:00.000-04:00

The start of this clip may be a little confusing. He's talking about mercury barometers being portable because they are short. If you used water in your barometer it would have to be something like 32 feet tall. Mercury barometers can be under a meter tall.

I don't recommend keeping vats of mercury like the one shown here. Mercury is 13 times heavier than water and quite volatile, the mercury vapors are not good for your brain. Mercury poisoning is responsible for the expression "Mad as a hatter," since mercury was used in the making of felt.

via Cannonball floating in mercury - Boing Boing

Science Fun and Easter Eggs

2009-04-09T15:00:00.001-04:00

No classes today and Friday, so I thought I would post a couple of Easter Egg links.

Lifehacker has a post on an online egg timer for the uber-geek: just select the temperature of your egg (Celsius), it's circumference (in cm), your elevation above sea level (meters) and how well done you would like your egg and it will calculate the time needed to cook. Oh, and be forwarned, the site is in Norwegian. If you are that eager to input the necessary variables to accurately calculate your cooking time, I'm sure that a little thing like not knowing the language won't be a problem.

And as an added bonus, how often do you see the Angstrom symbol used in acutal words?

Kunsten å koke et egg (translation: Art of cooking an egg) [University of Oslo]

via Lifehacker - Cook the Perfect Boiled Egg with the Power of Science - Holidays

Once you have cooked your Easter eggs, surely you will want to add a little color to them. Of course, if you dye the shell you have to remove the decorative part before you can eat the egg. Neatorama has a neat link to a way to decorate the egg that's inside the shell.

Edible Easter Eggs - Neatorama

Molecular Frameworks in Wired

2009-03-14T18:45:00.000-04:00

The latest issue of Wired magazine has a chart of the top 30 molecular shapes in the Chemical Abstracts Service database of more than 24 million compounds. Their definition of shape is based on rings and linkers which connect the rings, nothing else is considered: not the side chains attached to the rings or their connectors, presence of multiple bonds, or the elements involved.

As they point out many of the compounds listed are naturally occuring, or synthesized with natural compounds as the starting point or inspiration. Not surprisingly, the most common shape they identify is a hexagon and the second most common is the pentagon. The preferred bond angles for most organic compounds are around either 109 degrees or 120 degrees. Four- and three-membered rings (squares and triangles) aren't that common in nature - they do not appear in any of the top 30 shapes. These small rings have much smaller bond angles, and feel a lot of strain when forced to have such compressed bond angles. 5- and 6-membered rings have effectively zero ring strain and are very common in nature. Larger rings can also have ring strain issues.

About half of the top 30 shapes include a pentagon, but there is one or more hexagons in every one of the top 30 shapes except for shape #2 which is a simple pentagon.

Wired: Molecular Frameworks, the Building Blocks of All Life

Watch: Sita Sings the Blues

2009-03-14T18:15:00.000-04:00

image by Nina Paley

The Ramayana is a Hindu epic that tells the story of Rama, a prince from the city of Ayodhya. Sita Sings the Blues is a wonderful re-telling of the Ramayana told from the perspective of Rama's wife Sita. It isn't a happy story: Sita goes into exile with Rama, she is kidnapped and rescued and her faithfulness questioned more than once.

Nina Paley has put together a marvelous presentation of this story using several different styles of animation and music. The story is interwoven with commentary by three shadow puppets as well as scenes from Ms. Paley's own life. An integral part is the music of Annette Hanshaw, who made recordings in the 1920's and 30's. It makes for a strange combination, Indian legend and Jazz Age music, but it works delightfully.

Nina Paley has made Sita Sings the Blues available for download, or you can watch the streaming video at www.thirteen.org The artwork is beautiful, and the music is wonderful. Make yourself comfortable, it's almost an hour and a half long, and worth every minute.

Sita Sings the Blues

Science Literacy Survey

2009-03-13T22:00:00.000-04:00

The California Academy of Sciences, www.calacademy.org, recently conducted a telephone survey of scientific literacy. There are 6 questions listed on their web site if you want to test yourself - I don't know if they asked other questions or just those 6.

I came across this by way of the links below at Slashdot.org and ScientificBlogging.com. The results of the survey aren't too surprising: a lot of Americans don't know some very basic facts about the earth. However, I was especially interested in the readers' comments left at both of the posts. I recommend reading them yourself. A complaint of many was that the questions in the survey don't really measure any understanding of science, but rather they amount to mere trivia. Understanding science, they argue, requires an understanding of the scientific method, experimental design and generally being skeptical and knowing how to judge the evidence.

Personally, I like (some) trivia. But I understand the point - it isn't enough to just know some facts. Given the importance of scientific knowledge and discoveries in everyday life, I think it is important for the public to have an understanding of how scientists figure out how things work. Advertisers often tout some product as "clinically proven," or "scientifically tested." The public should know what this means - and I would hope they could make a guess at when it is pure bullshit.

However, I think it is also important to know things. And for that reason, trivia like the questions asked in the CalAcademy survey are worthwhile. They probably have little impact on your daily life, but if you are to have any hope at judging the reliablity of what scientists (or politicians or advertisers) have to say, you need to know some of the relevant facts as well.

Slashdot | US Adults Fail Basic Science Literacy

Science Literacy - American Adults 'Flunk' Basic Science, Says Survey

Boom: So You'd Like To Be An Explosion Scientist

2009-03-13T21:20:00.000-04:00

Cool article at IO9.com about New Mexico Tech's Energetic Materials Research and Testing Center (EMRTC) in Socorro, NM. They are even starting a summer "Explosives Camp" for High School students. I'm jealous!

Cool Science: So You'd Like To Be An Explosion Scientist

Understanding the Financial Crisis in Everyday Language

2009-03-07T15:58:00.003-05:00

We have all heard about the banking crisis and Toxic Assets, but what is it really all about? This affects everyone and you should be informed - and the regular media doesn't seem inclined to be as clear as they could be.

This American Life is a radio show on National Public Radio, they have put together a 59 minute program that explains the whole thing in easy to understand language. I highly recommend listening to the show.

Via Lifehacker.com:

Money: This American Life Explains the Financial Crisis in 59 Minutes

Also, you can get a transcript or download the podcast at This American Life.

Concertos and Chemistry

2009-03-01T19:25:00.004-05:00

Like any specialized field, chemistry has its share of technical jargon, but often technical terms have their roots in more ordinary language. I like to emphasize the connection between "normal" usage and the more technical use to help my students remember them better.

One example is the "concerted reaction." In many chemical reactions, more than one thing happens as reactants are transformed into products. One possibility is these events happen in a set order: step-wise. Another possibility is that they occur simultaneously and the reaction is said to be concerted.

The word "concerted" isn't exactly an everyday word, but it isn't especially unusual. Wiktionary gives the following definition for concerted:

Performed through a concert of effort; done by agreement or in combination.

Since my students may not be familiar with this usage, I usually make reference to a musical concert, or the concerto form - musicians playing all together. Certainly "done by agreement," and "in combination."

The Concerto of Baroque and Classical music typically has a soloist playing with a group of musicians. Here are two Concertos from different eras.

Antonio Vivaldi is probably best known now for his concertos, in particular The Four Seasons which consist of four of the twelve movements in his opus #8, which in English is entitled: "The Contest between Harmony and Invention."

The clip below is from a different work than The Four Seasons and features the lute as the solo instrument: Concerto in D Major for Lute.

My second featured concerto is Concerto for Cootie, composed by Duke Ellington. It was originally composed as an instrumental piece for trumpeter Cootie Williams. Later words were added, the tune may be more familiar as "Do Nothing til You Hear from Me." This is the instrumental version.

ATP-Synthase Modeled in Glass

2009-02-25T08:00:00.000-05:00

The Medical Museion at the University of Copenhagen has this interesting sculpture of ATP-Synthase entirely in glass. Take a look at their site. Scroll down to the comments where the artist, Colin Rennie, shares some of his thoughts on the scuplture. It's difficult to really see what it looks like from the photos. I would love to got there to see it myself.

ATP-Synthase is the enzyme responsible for making most of the ATP formed in cells - the main form of stored cellular "energy." The sculpture is based on a crystal structure published in 1999 and available at the Protien Data Bank, PDB ID 1QO1.

By way of IO9.com

Tycho's Supernova

2009-02-24T19:21:00.008-05:00

In 1572, the Danish nobleman Tycho Brahe observed a "new star" in the sky in the constellation Cassiopeia. He published a small book on his observations of this new star called "De Nova Stella," and thus coined the term nova. We now know that Tycho's star was actually a supernova and it is still being studied today. Both novae and supernovae involve explosions by stars that cause them to become much brighter than normal.

This is a composite image from NASA's Chandra X-ray Observatory and the Spitzer Space Telescope. The green and yellow are from x-rays emitted by the expanding shell of gas from the original explosion more than 400 years ago. The blue represents the shock wave from the explosion, also from x-ray emissions. The red is dust observed in infrared wavelengths.

You can get this image and more from the Chandra Observatory's web site. There are desktop patterns and wallpapers in several sizes, and a lot of other cool stuff. Take a look at the photo album for more details about this image.

via IO9.com

Science Careers Booklet from AAAS

2009-02-24T08:45:00.001-05:00

The Association for the Advancement of Science (AAAS), publishers of Science magazine, have put together a booklet of advice for people planning on a career in science. There are chapters on graduate school, skills for scientists, resumes and networking, non-traditional careers, diversity issues and others.

The articles were originally written for their careers web site and have been collected into an 88-page booklet. You can see the original articles, individual chapters, or download the whole booklet as a PDF file. And it's FREE.

Career Basics Booklet - Biotech, Pharmaceutical, Faculty, Postdoc jobs on Science Careers

Musical Interlude from Venezuela

2009-02-21T18:25:00.003-05:00

Gustavo Dudamel and the Teresa Carreño Youth Orchestra

From this year's Ted conference. These are high-school aged kids and absolutely incredible.

Viewing 3D Structures at PubChem

2009-02-16T14:37:00.006-05:00

PubChem is now providing 3D structures which you can view or download. PubChem3D generates a single conformer for molecules which are not too large or too flexible. You can view the results of this on the compound summary pages. The Compound Summary page shows the structure of the compound with two tabs at the top: you can choose either the customary 2D view, or a 3D image by clicking the appropriate tab.

You also have the option of an interactive view by clicking either the tetrahedral molecule icon

or the image of the 3D molecule. There are two options for viewing the molecule.

The first is a web-based viewer that opens a new window and generates an animated gif on the fly. This web-based viewer takes a little getting used to, and strikes me as rather clumsy. I don't understand why they did not use a java applet such as Jmol instead. In fact, Rajarshi Guha's Pub3D site does just this. Enter a PubChem cid and you can see the 3d structure using Jmol.

The second option for viewing the structure in 3D is to download and install the PubChem 3D Viewer. Windows, Linux and Mac versions are available. The graphics are nice, but it is limited to the file formats used by PubChem: pc3d, asn, and sdf for multiple molecule files. You can load more than one molecule at a time by either opening a multi-molecule sdf file or using the Import option. With more than one molecule loaded you can toggle between a panel-view which displays all the molecules in a table format, or an overlay mode. Select which molecules to overlay in the Molecules tab in the right-hand panel.

In addition, the right-hand panel has controls for changing the way the molecule(s) are displayed. Oddly there is no Save function. There might be no particular need to save the molecular data files from the viewer, but they seem to have gone to some trouble to give a lot of graphics display options. It's too bad that you cannot save images from the PubChem 3D Viewer.

Kodo Drummers!

2009-02-14T11:24:00.002-05:00

We saw Kodo last night in Ann Arbor. You really have experience Kodo in person, but this clip gives you a sense of their power and precision.

Create a Chemical-Free Dryer Satchel ... and Be Sure to Proofread Carefully

2009-02-10T18:20:00.000-05:00

Lifehacker.com has a link to a Do It Yourself site for making a sachet you can put in the clothes dryer to make your clothes smell nice. This one is fun to read just for the comments that other readers have left. Several point out in amusing ways the absurdity of anything being "Chemical-Free." It's nice to know I'm not the only person out there who is annoyed by such willful ignorance.

Some of the other comments suggest that you probably want to make a "sachet," and not a "satchel" for this project as the Lifehacker title puts it. This would probably make a big difference in terms of the cost and effectiveness of the project.

In response to the article's suggestion that minty-smelling sheets would be pleasant, one commenter says, "If my sheets smelled like mint, I would probably eat them in my sleep."

Take a look for yourself, and be sure to read the comments too.

DIY: Create a Chemical-Free Dryer Satchel

CN7 - An Anion that Goes Boom

2009-02-08T22:04:00.001-05:00

How could I pass up reading this article when the abstract had a picture of an explosion? But seriously, the molecule is cool and has an interesting structure.

The tetrazole ring looks like it ought to be aromatic. It resembles pyrrole: a five-membered ring with two double bonds and a lone pair on the NH nitrogen so you would think it would be aromatic. In addition, the tetrazolate anion is typically written with an aromatic symbolism having a circle inside the ring rather than showing double and single bonds.

The tetrazole ring itself is used in biological chemistry because it is acidic like a carboxylate group but it will not do the same reactions as a carboxylate, like form amide or ester bonds. In designing drugs, a carboxylate can be replaced with a tetrazole group. It is roughly the same size and will have a negative charge like a carboxylate, but since it cannot react chemically like a carboxylate it can get stuck without reacting and thus serve as an inhibitor.

Of course that is not what the present authors are interested in. They like the fact that it blows up. Be reassured, not all tetrazole compounds are explosive, especially not those used in the pharmaceutical industry.

In this paper, the authors react CHN7 with different bases to prepare a number of different salts of the CN7 anion paired with different cations. All of these compounds are explosive. The authors' interests are in developing "green explosives," such as explosives which do not contain toxic elements like lead (found in many primers) or perchlorate (used in rocket fuel.)

They prepared CN7 salts with both metal counter ions (Li, Na, K, Cs and Ca) and ammonium-type ions (NH4, N2H5, CH6N3 and CH7N4). The nitrogen salts were relatively stable, but the metal salts required a LOT of care given the description in the paper. The lithium and sodium salts were "relatively" stable - quotes in the original. Of the potassium salt, the paper says that even small amounts explode violently. They managed to isolate three crystals of the cesium salt and "a few hours later the whole preparation exploded spontaneously." These compounds are not to be taken lightly.

The next time a student asks if we can make something that explodes, I may just share with them the caution from this paper:

5-Azido-1H-tetrazole as well as its salts ... are extremely energetic compounds with increased sensitivities towards various stimuli. Therefore proper protective measures(safety glasses, face shield, leather coat, earthened equipment and shoes, Kevlar gloves and ear plugs) should be used at all time during work .... All compounds should be stored in explosive cases since they can explode spontaneously.

Once they safely obtained crystals of the salts, they determined their crystal structures. Hydrogen bonding seems to play a role in stabilizing these compounds. All of the nitrogen-cation salts were fairly stable, and their crystal structures show a fair amount of hydrogen bonding between the CN7 ions and the counter ions. The Li and Na salts crystallized with one water of hydration. The presence of water in these crystals seems to stabilize them through hydrogen bonds. The most reactive salts, K and Cs, have no waters of hydration and make no hydrogen bonds in the crystal. The other metal salt studied was Calcium. The Ca salt was also relatively stable, and co-crystallized with about 4.3 waters of hydration per Ca so there will be a lot of hydrogen bonding here as well.

The authors measured a number of properties of these compounds which had not been done previously. However, in the end they concluded that they are probably too sensitive for practical applications.

Thomas M. Klapötke, Jörg Stierstorfer (2009). The CN Anion Journal of the American Chemical Society, 131 (3), 1122-1134 DOI: 10.1021/ja8077522

Scott McCloud on comics | Video on TED.com

2009-02-07T09:45:00.001-05:00

A fascinating look at the world and story telling from the perspective of a comic book artist.

Games to Exercise Your Brain

2009-02-05T09:00:00.000-05:00

Check out these online games for exercising your brain:

In Assembler you have to move objects around to solve the puzzle. There are boxes, boards and barrels and they all obey the laws of physics. Each level is a little harder than the last.

FreeRice quizes you on vocabulary, adjusting to your skill level. Might be good practice for preparing for the GRE. There are other quizes too: Math, Foreign languages, Atomic Symbols, Geography and even paintings.

GeoSense tests your knowledge of geography. You have to click on the location of a city within 10 seconds. Your score depends on both speed and accuracy. You can choose US cities, European cities or World cities.