Monday, December 15, 2008

Blogging for Extra Credit

I don't normally give extra credit assignments in my classes.  I figure that rather than doing "extra" work, the class should focus on mastering the material we work on every day.  However, we have had a challenging semester and I wanted to give the class something fun to do that might help their morale (and grade)  and encourage them to read about science outside of class.  I asked them to write to me about something interesting that they had read about science, something from my blog or any thing else that strikes their fancy.  

It's always fun to see what students find interesting when they are left to choose the topic themselves.  Here is what I learned from my class:

Mikaela wrote:
Although my intentions were to look at one article and write about it, I seem to have got lost in the wonderful world of blogging and spent a little too much time on the day before exams surfing the web. Of the several I looked at, I enjoyed three in particular. First, I read about the study on caffeine versus napping. This was interesting to me because I am a firm believe of napping! I've never really been a caffeine person; I very rarely drink pop and maybe have a cup of coffee once a month. Caffeine does not really make me feel energized or more alert so I tend to just stay away from it. Napping, on the other hand, is probably the best part of my day. Although I don't nap as much as I'd like to, I always feel completely recharged and very alert once I wake up. I often nap before tests or quizzes instead of stressing and cramming minutes before because I do best when I am relaxed. After reading, I was curious to see the whole article and different experiments they did. 

The second article I read was on the glowing mushrooms. This was interesting to me because I like hearing about abnormal things that occur naturally. I love that nature has so many undiscovered features and that it encourages us to never stop exploring. 

The third article I liked was five reasons you should pick up a pencil and draw in "Getting Things Done in Academia." I have always found drawing as a release from all my other academics. I took four years in high school and it was my favorite part of the day because I got to unwind. I like the idea of linking art with sciences (particularly anatomy) because I think once you try sketching something, you look at the object your drawing in a different way than you ever thought you would. Noticing the small details makes the animal come alive, and that much more beautiful.

From Jenna:
I read through your blog and found a few interesting things. The first thing that stood out was on Mutagen, how drugs can be very effective, yet they can also have bad side effects. It is interesting that they can predict the toxicity of the compound before making it. Since I have started college, I have had many people ask me what courses I am taking. When they hear me say chemistry, they crinkle their noses and say "Yuck! I don't understand why anyone needs to take that! What good is that going to do to help you in the real world?" That's just it, many of them do not understand, or at least do not think about it. The first thing that comes to my mind is, "How do they think aspirin and other pain relievers came to work? Along with their cholesterol meds?" Since I began taking chemistry, especially organic, I have developed a deeper understanding of how chemicals work, and I think it is important to realize that chemists really do make an important impact on the world. Now, back to your blog, I agree with what you said about media portrayal. It seems every time you watch t.v. you see commercials for a new drug and they spend over half the commercial telling you all these horrible side effects it has. It's no wonder why so many people are afraid of chemistry. The media mostly portrays things like this involving chemistry, I think they don't portray the good things about it mostly because they are not well enough educated in chemistry to understand-most of them are biologists.

I also laughed about the high fructose corn syrup. Also, the brightly colored fruits and dark leafy green being defined as a fat. Even I know that's not true! I probably have my mother to thank for that!

I found an interesting article about Lions, Tigers, and DNA.  A scientist started studying feline leukemia in the 70's and found diseases. I find this interesting since I have worked for a few vets for the past 3 1/2 years and have done multiple feline leukemia tests on cats. These tests have been made possible because of scientists who have spent years studying it. I also find DNA and reproductive traits very interesting in animals. I hope to study animal genetics and reproduction more in depth when I go to vet school. The scientist also studied feline HIV to fine a gene that might help create immunization for people. This is another example of how scientists and veterinarians can to reasearch on animals to help understand and find treatments for people.  He also found genetic mishaps during migrations of felines, and he published his research in Science.

I found an interesting article about finding a new earth.  They have no real evidence but the star that they did find is one third of the mass of our sun, and when they first found the star there was a planet circling it and pulling the star at the speed of a jet plane.  Then they saw another planet rotating and it was pulling the star at the speed of a race car. After the most recent observations they found a third planet circling the star much more slowly, it rotated at the speed that a man could run!  I thought it was cool because they went on to say that the planet had a rocky content similar to ours. They also said that it is 15 million light years away, so the thought of a new planet is still far away, but really cool!  I think that we should try to keep our planet and restore it but the thought of other life forms is exciting.

I was searching online for articles about Organic Chemistry and came across a very interesting one that might be of a little interest or just a fun fact to learn about for you.

As the article says, "A discovery by a NASA scientist of sugar and several related organic compounds in two carbonaceous meteorites provides the first evidence that another fundamental building block of life on Earth may have come from outer space."

How interesting is that, that a fundamental building block of our life could come from outer space! I guess in previous research, researchers found that meteorites have organic compounds found on earth, like amino acids and carboxylic acids. This information is helping researchers understand that there could have been organic materials on earth before life. If you want to read more about it, the website is

I thought you all might like these topics… some relate strongly to organic chemistry and its affects and some deal with chemistry and physics and some are just plain interesting facts I thought you all might like to look into….so here is a list with links…

1. Is Carbon nanotubing… I first read about this material on an article that was titled “space Elevator” why it was call that is that the unique structure of this carbon sphere was a fraction the weight of steel and was around 10x the strength of steel, which made it a good candidate. 

2. This topic is a little hard to find…. Saw this on the history channel which was kind of cool how Hannibal in around 220 b.c. conquered Rome by attacking them through the mountain range the Alps. What made this so unique was Hannibal was said to be crazy to attempt this by taking 10,000 people and horses and war elephants on this trial over the mountain. He had no problem scaling the mountain where he ran into trouble was the descent. He ran into steep limestone rock faces they could go down and they couldn’t turn around either. As they sat there his chemist as you might call them found out if you heat limestone up and pour in their day was wine vinegar it would react and produce CO2 and H2O. Once cooled the rock became very brittle and they were able to make a zig zag path down the mountain face. As for a link with this I have looked for the story and havent found one you may be able to look up on and check for times the program maybe showing.

3. This topic is just rather interesting that relates to chemistry and slighty organic chemistry if you look up the term Browns Gas you will find an interesting topic. I heard about this at work they explained it to me in the simplest way as they thought it heated up any given material to the temperature at which it melts and does just that… I guess these links will explain it in more or more accurate detail. 

4. This topic is for anyone who wants to do some good with their computer and also get a viewing of a construction of a large carbon molecule from a simple core model. This is a program you can download called Folding@Home what it does is use your computer to fold organic molecules in an attempt to develop a molecule that can help them fight cancer. If you want to do this simply google the program name and go from there. It is a good way to view large organic molecules and how organized they are, I have had this program for a year I still run it to this day.

5. Well its not a big secret that there are more bio majors than chem majors so here is something interesting for bio majors. I don’t know if this relates to chem, but people tell me they have never heard this before so here ya go. There was these two Russians playing in a chess tournament Nikolai Titov and Vladimir Dobrynin and all of a sudden while Titov was in deep concentration on the board he screamed in pain and grabbed his temples and his head blew up like a fire cracker. Now I know you may think im pulling your chain but it’s a rare condition call HCE Hyper-Cerebral Electrosis. Now not getting into to great detail the gist of the story is not to think to hard or your head may blow up…Literally! …. If you want to read the article let me know and I will bring the book in.

Thursday, December 4, 2008

Chemistry Gift List

I know that everyone wants to keep-up with their chemistry studies over the holidays, and just in time the Make Blog site has a list of chemistry supplies for your Christmas list. The have descriptions of chemistry sets, as well as other chemistry-related things.

They include several chemistry sets, books about home chemistry experiments and suppliers for glassware. I had a Skilcraft chemistry set as a kid, but I don't remember much about it except that if you mixed certain chemicals together they would change colors. It is said that chemistry kits used to be much more interesting before all of the dangerous chemicals were removed. For an idea of what a do-it-yourself chemist could do in the Old Days, read Uncle Tungsten by Oliver Sacks.  

I really got a kick out of seeing The Golden Book of Chemistry Experiments, published in the 1960's. It's a collector's item now, but you can follow a link to download a pdf of the original book for free. Be aware, the file is 28 mb. There's a lot of good stuff there that would be familiar to any chemistry student. I'm not sure I would recommend making chlorine gas at home, but a lot of the experiments look like fun. You have to bear in mind how times have changed when reading this book - the list of where to buy supplies in the back of the book is pretty entertaining. I don't think I have ever seen carbon tetrachloride or manganese dioxide at a hardware store, or potassium permanganate at the drug store.

Also be sure to check out the youtube video of chemicals at a party, it's at the bottom of the page.

MAKE: Blog: The Chemistry gift guide - Celebrating chemistry and inspiring the next generation of chemists!

Tuesday, December 2, 2008

Need a Quick Pick Me Up? Take a Nap.

The New York Times has a short article about a study that compared caffeine with taking a short nap before doing mental and physical skills.  As it turns out, the people who took caffeine felt more awake, but they didn't score any better.  In fact the caffeine group performed worse than nappers on all three types of task that were studied:  motor skill, perceptual task, and verbal task.

I really like my coffee, but it is no substitute for getting enough sleep, and even a short nap in the afternoon will do more good for you than just caffeine.

The research paper itself is available online.  You can read the abstract for free, but to read the full paper you need to be a subscriber, or you can pay for it for $31.50.

Vital Signs - Regimens - For the Best Pick-Me-Up, Lie Down -

Monday, December 1, 2008

Cool Green Glowing Mushrooms

photo from

The Science-Fiction blog has an article about mushrooms that glow!  I knew about the jellyfish that glow, and I get fireflies in the backyard every summer, but I didn't know that there were mushrooms that glow.  

Apparently they are well known in Japan, and now National Geographic is reporting a new species from Brasil.

Hat tip to IO9:
Mega Biochemistry: Don't Eat the Glowing Mushrooms

National Geographic:

Friday, November 28, 2008

Thanksgiving with the Rents

Tetrabromo Anthracene from the Ground Up
Anthracene looks a lot like a big version of benzene, and to a large degree it is. If you wanted to make benzene with additional groups attached to it, such as bromine atoms, the chemistry is pretty well-established. If you want to add more than one group, and the exact positions of the groups are important, then it gets a little more complicated but it is still quite doable.

Anthracene on the other hand is rather less cooperative than benzene. The 9 and 10 positions on anthracene are very easy to modify, but the positions on the outer edges are a lot harder to get at with the same chemistry you would use on benzene. So how would you go about making anthracene with four bromines on the outer edges and not modify the 9 and 10 positions?

A recent article in the online Beilstein Journal of Organic Chemistry, the authors describe a synthesis of 2,3,6,7-tetrabromoanthracene in just four steps starting with benzene.

First they attach four iodines to benzene by reacting it overnight with I2, periodic acid and concentrated sulfuric acid. These seem like pretty forcing conditions, but they are necessary since iodine is the least reactive of the halogens. The periodic acid is necessary to oxidize the iodine to an "I+" species which then reacts with the benzene ring.

Next they use a coupling reaction to replace the iodines with tetramethylsilyl acetylene groups. The tetramethyl silyl (TMS)groups are protecting groups to prevent the acetylene from reacting at both ends. The coupling reaction itself is quite interesting and involves a palladium complex in which the palladium is effectively in the zero oxidation state - that is, chemically it is a palladium atom rather than being an ion. In the Sonogashira coupling reaction that they use, the Palladium complex and a Cu(I) ion interact with the pi-bonds to stitch together the acetylenes and the benzene ring in place of the iodines.

To remove the TMS groups they react the compound with a catalytic amount of Ag(I), which initially forms a silver acetylide compound. The acetylide ion does a nucleophilic attack on the bromine atom in N-bromo succinimide. In this case the bromine is effectively acting like Br+, with the succinimide acting as a leaving group.

At this point we have all the carbons and bromines needed for the tetrabromoanthracene, all that needs to be done is to make the rings on the ends. To do this they simply heat the compound in a high-pressure bomb. This is an example of a double Bergman cyclization, which can occur when you have an alkene with two alkyne groups attached to it - an "enediyne." This is a radical mechanism in which each of the alkynes donates one electron to make a new carbon carbon bond and close the ring. This produces a diradical. The cyclohexadiene is added as a hydrogen donor: when it donates two hydrogen atoms to the anthracene molecule the cyclohexadiene is converted to benzene.

Anthracene can undergo many of the same Electrophilic Aromatic Substitution reactions that are routine for benzene, but selectiviely modifying only the "end" positions is very difficult - the other positions on the rings are much more reactive - especially the middle 9 and 10 positions. So usually, any new additions end up in the 9 and 10 positions preferentially.  To get around this the somewhat counterintuitive solution is: don't start with anthracene.

Christian Schäfer, Friederike Herrmann, Jochen Mattay (2008). Synthesis of 2,3,6,7-tetrabromoanthracene Beilstein Journal of Organic Chemistry, 4 DOI: 10.3762/bjoc.4.41

Monday, November 24, 2008

Advice for Students

Have you ever had a hard time keeping up with all the things you need to do as a student?  Take a look at the Alpha Student web site.  It is run by a couple of college students in England.  The articles are listed in catagories: Academic, Career, Financial, Fun, Personal, Practical and Social.

Most of the articles are written by Ali Hale who is in a masters program in creative writing.  Take a look at this interview with Ali.  It makes me tired just reading about all of the different things she is doing while in graduate school - she writes for a bunch of blogs in addition to Alpha Student, and she did all of the coding for Alpha Student (html, css, and php).  

Why Do I Blog

I started this blog for the same reasons that I went to graduate school and that I teach. I think chemistry is really cool and would like to tell other people about it. As a lifelong science nerd and a chemist I've always been little frustrated the chemistry seems to get short shrift in the media. When you hear about science in the news it's seldom about chemistry. And when you DO hear about chemistry it's all about how bad chemicals are.

I have three main goals in writing for this blog. First of all I want to write about chemistry that I think is really interesting in a way that is accessible to anyone with an interest in science, in particular the students in my classes. Second, since I spend all of my time with college students, I'll write about things that I think might be helpful for them as students. Finally, for my own edification I plan to write about current research in chemistry.

Two sites that made a big impression on me in starting this blog are Mike Kaspari's blog Getting Things Done in Academia, and Dr. Kaspari is a biologist who writes advice for grad students in biology, but his advice is good for any student. Unfortunately he hasn't been posting much this semester, I hope to see more from him soon. is a web site that collects blog posts about peer-reviewed research in all areas of science.  I recommend both sites highly.

I'm still new at this and don't have many readers at the moment, but if you see something you like or have a suggestion I would like to hear from you.  Please leave a comment.

Sunday, November 23, 2008

Well, how did I get here?

A musical interlude courtesy of David Byrne.

I miss the big suit, but I'm glad he's enjoying himself now.

Monday, November 10, 2008

Ask Questions - Stepcase Lifehack

Ask Questions - Stepcase Lifehack

When I was an undergrad I tutored Organic Chemistry.  One of the students I tutored was a biology major and a friend - Kathy was also in the karate club,  but that's another story.  She was a challenging person for me to tutor - because she asked questions.  Specifically - "Why does that reaction happen?" and "How do you know that is the product?" and other inconvenient questions.  I could tell her the answers to her homework problems, but answering these questions took effort.

I'm grateful to her - she made me think.  And trying to answer her questions forced me to understand them myself.  Asking questions and trying to answer them is an important step in learning new things. Even asking yourself questions and trying to answer them yourself.  Don't be complacent!  Be curious!  Ask questions!

Saturday, November 8, 2008

How Do You Know It's a Mutagen?

How do you know if a compound will be a mutagen before you test it. Before you even make it?

Drug companies make lots of new molecules that they hope will be useful as drugs. But there are a lot of other things that can happen when a biologically active molecule gets inside you. A lot of potential drugs just don't work, or work poorly. Many work well enough for the task at hand, but have side effects that are unpleasant. Some side effects are inconvenient but tolerable, others are deal breakers. 

Making a new molecule and testing it is a time consuming process. Just making the molecule will involve several reactions run sequentially, and each step can require careful purification before you can go on to the next step in the process. Once the molecule has been made, there is a battery of tests to run both to see how well it works on the drug target, and to find out if it is likely to make the patient sicker through side effects.

It would be helpful if you could predict the toxicity of a compound before you go to the trouble of making it in the lab, or at least ruling out compounds that are likely to be highly toxic. In Accurate and Interpretable Computational Modeling of Chemical Mutagenicity, Langham and  Jain describe their work on predicting whether a compound is a mutagen just based on the types of atoms in the molecule. And they get pretty good results.

To do this properly you will have to look at lots of molecules, so you need a simple way to describe your molecules quickly without running lots of complex calculations. Langham and Jain had a computer program list all possible pairs of atoms in each molecule, and made a

 list of these atom pairs. The example they give in their paper is an atom pair found in aspirin described as O3_1_D5_C2_Ar2. This describes an sp3 hybridized oxygen attached to one heavy atom (not hydrogen) that is 5 bonds away from an aromatic carbon with two heavy neighbors.

Next you have to look for a pattern of atom pairs in a molecule that seems to be related to whether or not it is a mutagen. Just looking at the data would probably not be very effective, so the authors used three different Machine Learning techniques to look for a pattern: support vector machines (svm), RuleFit, and K-nearest neighbors (KNN). They analyzed a training set of 4337 diverse compounds, 2401 of which were mutagens and 1936 were not and found that the SVM method gave an accuracy of 0.77, and RuleFit was a little better with an accuracy of 0.79.

The real test is how well the model works in predicting the activity of completely new molecules. So next they used their SVM and RuleFit results to try to predict the mutagenicity of a completely different set of compounds taken from the Carcinogenic Potency Database (CPDB). With this new set of compounds, SVM (accuracy 0.770) worked a little better than RuleFit (accuracy 0.718).  This is far from ideal, but it's a pretty good start.  And it is interesting to see that such a simple criterion as pairs of atoms can be predictive of a complex behavior like causing mutations.

James J. Langham, Ajay N. Jain (2008). Accurate and Interpretable Computational Modeling of Chemical Mutagenicity Journal of Chemical Information and Modeling, 48 (9), 1833-1839 DOI: 10.1021/ci800094a

Saturday, November 1, 2008

More Eric, Plugged In This Time

Same song as the previous post, but electric.  Watch the bass player to Clapton's left about 40 seconds into the clip.

Friday, October 31, 2008

Take Time to Unplug Occasionally

I know I spend way too much time surfing the internet. It is a good idea to go unplugged every now and then in order to really get things done. I was reminded of this when I saw 10 Ways to Ungeek for Productivity Just the other day I took one of my classes to the library, so I could really relate to #5:

5. Do Research at the library

Despite what I’d like to think, Google can’t find me every detail on every topic. Depending on what I’m researching, I often go to the public library. Many libraries maintain subscriptions to databases that cost quite a bit to access, but they also have plenty of offline information. I make a habit of chatting to one of the librarians about what I’m working on. They can often point me to references that I might not have thought of or show me connections between my topic and another that I never would have found searching for keywords on the web.

And there are times when a change of scenery can do wonders for your attitude - get out of your room / office and go somewhere else to work. Besides, I like books.  

Finally an Unplugged interlude with Eric Clapton from back when MTV had music.

See if you can spot this one.

Thursday, October 30, 2008

Cool Three-In-One Reaction

ResearchBlogging.orgSince I teach sophomore organic chemistry, I'm always interested to see new research that involves basic organic reactions that I cover in class.  A new reaction using alkynyl halides produces alkynyl epoxides in a one pot procedure as a result of three different reactions.  At first glance, this looks like a complicated reaction, but everything involved is routinely taught in standard organic chem classes.  And it works well, this example gave 92% yield.

In a recent paper Trofimov, Chernyak and Gevorgyan describe their work with this reaction.  They report that it works quite well for aromatic ketones with a tertiary alpha-hydrogen, while other ketones give mixtures of products.  

The reaction starts with a deprotonation of the ketone to form the enolate, which performs nucleophilic attack on the alkynyl Bromine.  To a beginning student of organic chemistry this might look like a strange version of bromine, but mechanistically it is similar to brominating with Br2.  Next, the alkynyl anion attacks the carbonyl carbon.  This produces a halohydrin that simply closes to form the final epoxide product.  Pretty slick - three reactions all in one go.

Alexander Trofimov, Natalia Chernyak, Vladimir Gevorgyan (2008). Dual Role of Alkynyl Halides in One-Step Synthesis of Alkynyl Epoxides Journal of the American Chemical Society, 130 (41), 13538-13539 DOI: 10.1021/ja806178r

Saturday, October 25, 2008

Cyclobutanones and Antibiotic Resistance

Antibiotic resistance is a growing problem.  One way in which bacterial are able to resist antibiotics like penicillin is to use an enzyme called a beta-lactamase to react with the antibiotic and convert it into a form that does not work.

One strategy to overcome this is to inhibit the beta-lactamase before it gets a chance to deactivate the antibiotic molecule.  Compounds such as clavulanic acid have been used for just this purpose, but the bugs are starting to become resistant to this approach.  Beta-lactamases are not going away, so new compounds will need to be developed that inhibit them.

The center of activity in an enzyme is its active site - an openning in the enzyme where the substrate that is modified by the enzyme gets bound.  Typically the active site has a shape that complements the substrate, and has a number of catalytic groups inside which account for the chemical reaction that it catalyzes.  An inhibitor often binds to the active site of the enzyme and prevents the enzyme from binding to any of its "real" substrate.

When designing an inhibitor for an enzyme there are two things the molecule has to do.  First it has to have a shape that matches the active site.  Often enzymes are described as having a lock-and-key relationship with the substrate (or with an inhibitor).  Only a key with the right size and shape will fit into the keyhole of the lock.  Likewise, only a compound with the right shape will fit into the active site of the enzyme.  Secondly, the inhibitor should interact strongly with the catalytic groups inside the enzyme to help keep it lodged in the active site.  If the inhibitor comes out of the active site, the enzyme will no longer be inhibited.

A recent paper looks at a series of cyclobutanone-containing compounds as potential beta-lactamase inhibitors.  Beta-lactam antibiotics like penicillin , as well as the beta-lacatamse inhibitors clavulanic acid, sulbactam and tazobactam all contain the amide functionality.  Replacing the beta-lactam with a cyclobutanone is really interesting - it preserves the carbonyl and four-membered ring of the usual beta-lactamase substrates, and at the same time a ketone is very different from an amide.

When the beta-lactamase binds to penicillin it hydrolyzes the amide bond which leaves penicillin unable to act as an antibiotic.  Most beta-lactamases have a serine at the active site wich reacts with the beta lactam carbonyl.  After the serine OH attaches to the carbonyl carbon, the amide bond is broken to produce an acyl intermediate in which the penicillin molecule is covalently bound to the enzyme.  This is followed by a hydrolysis 
step which releases the resulting penicilloic acid.  
Currently used beta-lactam inhibitors do the same thing, except they get stuck at the acyl intermediate step.  With the inhibitors, the final hydrolysis step does not happen so the inhibitor remains covalently attached to the enzyme in its active site.  This prevents the enzyme from binding to penicillin and inactivating it.

The cyclobutanone analogs should also able to bind in the active site of the beta-lactamase enzymes.  Initially, the serine at the active site can attack the cyclobutanone carbonyl, which forms a hemi-ketal.  However, no further reaction can take place - there is amide group which can be broken to form the acyl intermediate.

Some beta-lactamases work through a different mechanism which involves two zinc ions at the active site.  Instead of a nucleophilic attack by serine, these metallo-enzymes use a hydroxide ion bound to one of the zinc ions as a nucleophile.  The substrate is never bound covalently to the enzyme and the acyl intermediate does not form.  Currently used beta-lactamase inhibitors are inactive against these metallo-enzymes.  The cyclobutanone analog can still react at the active site, forming a hydrate.  The hydrate can't react further, since there is no amide bond to be hydrolized.  In principle, the hydrate could remain bound to the zinc ions in the active site, and so inhibit the enzyme.

Since bacteria are developing resistance to beta-lactamase inhibitors, new strategies to counteract them are necessary.  Cyclobutanone-containing analogs show promise - since  they do not form a covalently bound acyl intermediate, they could inhibit the beta-lacatamase by a different mechanism than compounds like clavulanic acid and could be effective even in bacteria with resistance to clavulanic acid.  Furthermore, they could also be effective against metallo-enzymes which are not inhibited by the current crop of beta-lacatamase inhibitors.

Leo Kottke - Taxco Steps

I'm always amazed at how much sound Leo gets out of a single guitar.  And here he's only playing a six string.

Thursday, October 23, 2008

An Interesting Stable Oxonium Ion

The textbooks all say that hydronium ion is a strong acid, and the alkyl analog should also be very reactive. However, oxatriquinane turns out to be quite stable. One might think that it should be a powerful electrophile and react with even weak nucleophiles like water, but when boiled in water for 72 hours there was still no sign of decomposition.

Another thing I found rather satisfying is that all the chemistry used to prepare this compound is routine for a sophomore organic chemistry class. It starts with treating cyclonona-1,4,7-triene with MCPBA to form an epoxide. The epoxide is opened by reacting with LiAlH4 ( a nucleophilic hydride ion) . Reacting the resulting alcohol with iodine (I2) leads to an intramolecular halohydrin reaction. The iodine is removed with Raney Nickel. Finally, the compound is treated with HBr which protonates the remaining alkene. The oxygen bonds to the resulting carbocation to give the bromide salt of oxatriquinane.

The bromide salt could not be crystallized, so they used simple ion exchange to replace it with hexafluorophosphate ion or hexafluoroantimonate. The ion proved quite stable - they were able to measure the NMR in D2O, and even recrystallize from water. Weak nucleophiles such as water, alcohols or iodide ion did not react with oxatriquinane. On the other hand, nucleophiles like hydroxide, cyanide and azide quickly reacted.

Mark Mascal, Nema Hafezi, Nabin K Meher, James C Fettinger(2008) Oxatriquinane and Oxatriquinacene: Extraordinary Oxonium Ions J. Am. Chem. Soc., 130(41), 13532-13533. DOI: 10.1021/ja805686u

Tuesday, October 21, 2008

Exercise and Your Brain

It seems as if I have seen several news reports in the last year that show how exercise benefits the brain.  Now here are two more via Research Blogging.

In the first article, Neurotopia discusses a new paper that documents how exercise helps the brain recover from brain cancer.
But exercise is not just for stress relief. There are several studies out there which imply that exercise can make you THINK better, too. And this paper goes one step further, and implicates exercise in helping young animals recover from brain cancer.

The second article is discussed by Dr. Shock, and it describes the benefits of walking regularly for elderly women who are either overweight  or moderately depressed.  

Exercise isn't just for athletes.  

Wednesday, October 1, 2008

Is There Really Fat in Corn Syrup?!

Most people probably know more than they think they do about chemistry, but it can still take real effort to recognize non-sense.  Last weekend’s Parade magazine, which comes with our Sunday paper, had an article on arthritis.  The author is an MD, but I really wonder if he was paying attention when he wrote it because there are a number of really silly statements in the section on diet.  

#1 “Red meat and high-fructose corn syrup both are loaded with omega-6 fatty acids ....”

I don’t have any argument with saying there is fat in red meat, but fat in Corn Syrup?!?  This is the stuff used to sweeten almost everything.  Corn syrup, whether or not it is high in fructose, is pure sugar.  It is made from corn starch which is a carbohydrate, not a fat.

To a chemist, "sugar" refers to a whole class of related molecules.  Glucose is the most important fuel sugar in living organisms and most carbohydrates are converted into glucose when you digest them.  Starch is basically a bunch of glucose molecules strung together in a long chain.  Plants use starch as a way to store glucose, and animals use a similar compound called glycogen to store glucose in the liver and muscles.  

When you think of sugar, you probably think "sweet."  Despite being made of glucose, most people would not consider starch to be very sweet.  If you chew a piece of bread for a while and keep it in your mouth, you should notice a slight sweet taste as the enzymes in your mouth convert the starch to individual glucose molecules.   Table sugar is the molecule sucrose, which consists of one glucose and one fructose connected to one another to form a disaccharide.  In high fructose corn syrup, the corn starch has been disassembled into the individual glucose molecules and about half of the glucose turned into fructose.  The reason for doing this is that fructose is much sweeter than glucose or sucrose - you need less to produce the same level of sweetness.

I quite agree that you should not go overboard with a high sugar diet, but to claim that things like pepsi are an important source of any kind of fat in your diet is laughable.

#2 sources of omega-6 fatty acids: deep-sea fish, flaxseed, brightly colored fruits, dark green leafy vegetables, and olive oil

The health benefits of fish oil and olive oil are well known, but when I think of “brightly colored fruits” I think of things like oranges - not exactly known as a source of fat in the diet.  And “dark green leafy vegetables” are also known to be good for you, but I have my doubts about the fat content of things like spinach.  I won't dispute that you should eat these foods, but the claim about fat makes me scratch my head. A check on wikipedia for omega-3 fatty acid turns up a list of dietary sources that include meat, fish, flaxseed, some nuts.  Somehow brightly colored fruits and leafy greens vegetables don't seem to be a major source, unless you want to include krill and microalgae.

#3 “Our prehistoric ancestors, to whom arthritis was virtually unknown" 

According to the Arthritis Foundation  osteoarthritis, the most common kind of arthritis, is mostly a result of wear and tear on joints.  Am I to believe that arthritis is a purely modern condition?  That our prehistoric ancestors didn’t wear out their joints?  That is just plain silly, and a quick search for "arthritis archaeology" on PubMed turned up a free review article on the subject:  Skeletal evidence of osteoarthritis: a palaeopathological perspective.  This article discusses evidence for arthritis in archaeological finds, and even mentions arthritis observed in dinosaurs.

The general public is confused enough as it is about general health, but when experts publish such silliness it just compounds the problem.  This just points out the need to pay attention so that you notice when you read something that doesn't make sense, rather than swallowing misinformation without a second thought.

Sunday, September 28, 2008

Going to School for Fun

Wouldn't it be cool to go to school just for fun?  To take classes because you were interested in the subject, without having to worry about grades or money?  Turns out that Flea, the bassist for the Red Hot Chili Peppers is doing just that - at 45 he is a freshman music major at USC.  

Yesterday I heard an interview with Flea on NPR's All Things Considered.  Check it out.  As a chemist, and occasional musician, I especially liked this quote:

"Music is made up out of these building blocks," he says. "Studying how these blocks go together and what they consist of and the math of how it works — it's all the same stuff; it's just different aesthetics that we're talking about."

That could apply to almost any field.

I have to say that I'm envious.  As a teacher myself I do have a lot of freedom, as well as an obligation, to keep learning new stuff.  But I don't have the time to really immerse myself in quite the same way.  It would be fun to be a student again.

Thursday, September 25, 2008

James Bond Molecule bag

I saw this cool bag over at  I had to get a larger image to actually see what the picture is.  It shows the gun barrel shot seen at the start of the James Bond movies, with a molecule of some sort.  Being a geek, I had to figure out just what the molecule is.

Over at I was able to draw the structure in the editor and do a search.  The compound is called Sulforhodamine 101 acid chloride.  eMolecules provides a little info on the compound as well as links to chemical suppliers and listings in PubChem.

I just want to know what it's used for, so a quick search on Wikipedia turns up two listings:  one for Sulforhodamine 101 and another for Texas Red.  These are related compounds that are primarily used as biological dyes.  They are highly colored (red, in case you couldn't guess) because of the large amount of conjugation, and as it turns out they are also highly fluorescent. 

The difference between Texas Red (the acid chloride) and just plain sulforhodamine is the acid chloride has a chlorine in place of one of the OH groups.  This makes it very reactive with proteins especially - an NH2 on the protein acts as a nucleophile to replace the chlorine - leaving the protein with a bright red label attached to it.  Texas Red is especially convenient in that the acid chloride will also react with water, and the resulting compound is water soluble and can be rinsed away.  This means that only the dye molecules that are attached to the protein remain - excess dye can be washed away.  Other methods of labeling proteins aren't always so helpful - any excess dye may remain and obscure what you are interested in seeing.

Wednesday, September 24, 2008

Advice for Students

Most college students are so focused on the next assignment (or athletic event, or party) that planning ahead for post-graduation doesn't get much attention. Ironically, career planning can be rather like studying - you make it a habit to study every day and the exam will usually go well. If you procrastinate and cram at the last minute you will be stressed-out, not as prepared as you should be, and you probably will be disappointed in the results.

For some ideas to help you plan ahead, take a look at this post at I especially like #6 "Pay Attention!" Most things you see on self-help sites are really common-sense. But if you don't do anything about it, having common sense doesn't help much.

Thursday, September 18, 2008

Bee Vomit and Spider Silk

I rather like Bee Vomit, although I don't think I would put it on my peanut butter - I've always been a bit of a purist when it comes to peanut butter sandwiches. Spider silk is pretty cool too.

Wednesday, September 17, 2008

Sunday, September 7, 2008

Start of School

We're two weeks into the semester now and things are starting to settle into place again.  With the start of a new year there have been a bunch of changes, and of course not everything went smoothly.

First off, I have decided to try something new with my Organic Chemistry class. Lately I have been concerned that despite my best efforts, my students were not getting the most out of my lectures or the readings in the text. Using some student activities during lecture is something I have tried in the past, but I always drifted back to straight lecture. Over the summer I got two presents in my mail box:

  1. not one, but two copies of Organic Chemistry: A Guided Inquiry, which uses a POGIL approach

  2. a booklet on Using Pogil in the Classroom and Other Research Developments from last November's meeting of the Michigan College Chemistry Teachers Association

This seemed like too good an opportunity to miss. As a result, I am replacing my standard lecture format with POGIL. POGIL stands for Process-Oriented Guided Inquiry Learning and involves the students working in groups during class time, with me monitoring and guiding the groups when they have difficulties. The text is really more of a workbook which the students use during class that guides them through the process of learning each lesson. They need to have the book with them every day in class.

It is still a little early for me to tell, but the students seem to be adjusting – some better than others, but that is only to be expected. Of course, the students turned out to be the least of my problems in adopting POGIL. The second edition of Organic Chemistry: A Guided Inquiry, the POGIL text I am using, came out over the summer. When I went to our bookstore manager in July to ask about switching texts he told me there wouldn't be a problem and we should have the books before class started. Ha!

As it turns out, the publisher was out of stock and didn't expect more until Sept 5 – two weeks into the semester. This is at minimum a nuisance, but if the students NEED to have the book with them in class every day to do the lessons it makes it difficult to stick to a schedule. My bookstore manager was very helpful, he was able to get the first few sections of the book copied for me by the first day of class – so we were covered with about two weeks worth of class activities. The author, Andrei Straumanis, has a pretty active listserve on using his book and the POGIL system. He got permission to post pdf's of the first few weeks worth of the book on his web site.

Friday the bookstore called to say the books were in. Hurray!