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Learning to Speak OCHemese

Bond-Line Notation and SMILES

In order to complete this exercise, as well as many that will follow, you must learn how to use a structural drawing program that is capable of converting the bond-line representation of a molecule into a text string called a SMILES ( Simplified Molecular Input Line Entry Specification). Several drawing programs are available. We will use one called CS-Chem Draw Net™. (It's free.) To use this program you must use one of the Macintosh computers in either the Portland or Gorham micro labs or in Room 351 of the Science Building: Double click on each of the following icons in turn- PML5.VOL1/MACAPPS/Course Materials/Chy251-254/CS Chem Draw Net/CS-ChemDraw NetTM. Double clicking the last icon in this sequence opens the drawing program called CS-ChemDraw NetTM. Use the drawing tools to draw each of the condensed structures below in bond-line notation. To learn how to use the program select CS ChemDraw Help from the Help menu. Once you have drawn the structure, use the lasso tool to select it. Then choose SMILES from the Copy as sub-menu of the Edit menu. Click on this window and paste the SMILES into the text field beneath the appropriate structure.

N.B. One of the most common mistakes that beginners make when using a structural drawing program is failure to join atoms together correctly. While the drawing may look like a proper structure, if the atoms are not joined properly, the SMILES string that the program generates will not be the correct string. If you want to check to see if a SMILES string that you created corresponds to the structure you believe to be the correct answer to a particular question, there is a program called DEPICT which generates graphical images of structures when you give it a SMILES string. If you would like to learn more about SMILES, you can go to the SMILES Tutorial. (Select Back from the Go menu to restore this page once you have checked your answer with DEPICT or explored the SMILES Tutorial.)


Exercise 1 Make a bond-line drawing of each of the following condensed structures. Then paste the corresponding SMILES into the text field beneath the structure. (Systematic and/or common names of each compound are included for your edification.)

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