Chemistry on the Desktop

So far, I've just been describing building up a molecule. In the rest of the screenshots here I'm using a simple benzene ring to discuss the chemistry you can do with BKChem.

You can get basic information about your structure by clicking on Chemistry→Info, which will pop up a new window with items like the chemical formula, molecular weight and composition.

Figure 6. You can get a list of basic chemical information about your structure.

If you want to check to see whether the structure you've built makes sense, you can select it and click on the Chemistry→Check chemistry menu item. If everything makes sense, you'll see a new window telling you that everything is okay. Otherwise, you'll get an error message highlighting what doesn't quite work from a chemical point of view. This is where you may need to dig into the grittier items available from the Edit menu when you click on an element with the middle mouse button. You may need to change the type of atom or change its valency. As an example of the type of error you might encounter, see what happened when I changed one of the carbon atoms to an oxygen atom in the benzene ring (Figure 7).

Figure 7. Sometimes, the chemistry doesn't work out.

At the far right side of the menu bar, there is an entry for available plugins. One of these plugins allows you to calculate bond angles. You can select two connected bonds by holding down the Shift key and clicking them one after the other. Then you can click on the Plugins→Angle between bonds menu item to calculate the angle.

Figure 8. You can calculate bond angles for your molecule.

When you've finished all of the work of creating your new molecular structure, you'll want to save it for further analysis or to share with other researchers. The default file format that structures are saved in is an SVG (Scalable Vector Graphics) file. If you want to save your work using a different file format, click on File→Export to get a list of all the supported file formats. Most of them are simply other graphics file formats, but a few are specifically used for storing chemical information.

You can select CML or CML2 (Chemical Markup Language) to save more of the chemical information for your structure. You also can save your structure in the molfile file format, which was created by MDL Information Systems to store more detailed information about a chemical structure. If you just want an easily shared image of your molecular structure, you can export it into either a PDF or PNG file.

As you have seen here, you can use BKChem to build molecular structures in a way similar to many other chemistry applications. What is slightly different with BKChem is that you can do some basic chemistry with your newly created structure directly from BKChem. This added functionality might be enough to make BKChem a tool you'll want to add to your arsenal.

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Joey Bernard has a background in both physics and computer science. This serves him well in his day job as a computational research consultant at the University of New Brunswick. He also teaches computational physics and parallel programming.