The Molecular Universe

For the last few days I have been posting links to news articles which mention the term molecule. If you take a look at the articles which make this list (I only keep the latest 100 on the page), you will invariably see some interesting stories. (See Molecules in the News).

Why are the stories interesting? Well, partly because molecules are interesting. Molecules are tiny. In general their existence needs to be inferred rather that directly appreciated. Molecules are hard to make, chemists need to carry out complex syntheses to put the atoms of a molecule into a specific configuration. Yet, despite these caveats, molecules are often in the news and molecular images are included in adverts for the latest pharmaceuticals.

The stories are also interesting because they present so many different points of view. There are stories about the cancer causing effects of moisturizing creams and suntan lotions, among other items. Stories like these are invariably alarmist and convolute the original scientific research from which they are based to achieve a degree of sensationalism. Why is that? Sensationalism makes for more interesting stories and more interesting stories make for more readers and more readers make for more advertising revenue.

Then there are the stories which contain interesting inaccuracies. Some of these are trivial, like calling 'radiation' 'irradiation' (see this article on irradiating food) and this article which says 'A molecule you can barely see...' (when, in reality, you cannot see a molecule because they are far too small).

So, there is some good news. Molecules are generally understood by the news article writers and the readers that they write for. There is some bad news too. Often the information is a little misleading and this spreads and perpetuates various falsehoods. Additionally, the news sound bite leaves little scope for an explanation of cause and effect, and statistical analysis, which would help reduce the more alarmist articles to an informational level.

However, all in and all, I have been very pleasantly surprised by how frequently articles mentioning molecules are published these days. Hopefully the trend will continue and, if so, there is a likelihood that the inaccuracies and missed opportunities for detailed explanations will decline with time. To examine the current state of molecules in the news, here is the appropriate link: (See Molecules in the News).

If you ever need to know the structure of a given molecule, use the eMolecules (http://www.emolecules.com) site to obtain all the information that you need.

I have found this site extremely useful for obtaining chemical information rapidly. The site has a large database of chemical information, obtained from the suppliers of a range of chemicals and chemical intermediates. You can query the database using an effective Java sketching tool, by SMILES string, or by common names.

Once you have obtained your hit you will see the various suppliers of the compound, so if you are a chemist you will be able to buy the appropriate amount, you will also be able to obtain additional information on the compound. The additional information includes the SMILES string, and using the SMILES string you can obtain a chemical connectivity file (.mol file) from the InChi site: http://inchi.info/converter_en.html.

So, if you are interested in the structure of Aspirin, for example, head over to eMolecules to obtain a SMILES string for Aspirin (e.g., CC(=O)Oc1ccccc1C(=O)O), then go to the InChi site, to obtain a .mol file. Then you can read the .mol file into PyMol, or your favorite molecular viewer, to see the structure of Aspirin.

These sites will give you a good idea of the structure of a range of molecules. The procedure above does not include a treatment of the lower energy confirmation of the shape of the molecule, and it does not include adding hydrogen atoms to the molecule. I will cover those steps in a future posting.

The Structure of Aspirin

Having restarted The Molecular Universe after a year or two off, I thought that now would be a good time to start up a blog as well!

Naturally, this involves an interesting search for suitable a suitable blogging engine, and after checking for a day or two on the various options, I selected 'NanoBlogger'.

NanoBlogger is a blogging engine written in the Bash scripting language. It produces a blog which is composed of simple html pages, so there is no database, or server side technology to maintain. The downside is that adding comments to the blog is not completely trivial - so for now, please email me at the address on the navigation panel if you have comments or questions.

One of the things that I was worried about was how the pages would look in a variety of browsers. So, I tested appearances with http://browsershots.org which uses a bank of web clients and screenshots of the results, to give a sense of how different browsers render the pages on a site. So far, the results are quite encouraging!