Sunday, August 30, 2009

ChemSketch on Linux? Maybe not ...

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.

Tuesday, August 25, 2009

Test Your News IQ - Pew Research Center

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

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

Wednesday, August 19, 2009

Internet Profile: Bridgehead Carbons

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 -

Tuesday, August 18, 2009

CRC History

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

Thursday, August 13, 2009

Cyclization Reactions and Angelmarin Synthesis

ResearchBlogging.orgThe 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

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

Wednesday, August 12, 2009

July Weather: Local vs Global

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 Global Warming News, Science, Myths, Articles

Monday, August 10, 2009

Drawing Molecules with SMILES

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.

Saturday, August 1, 2009

Chemistry Graphics Hassle on Ubuntu

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)
  • 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.