Welcome to the CAChe Molecular Modeling Tutorials

Department of Chemistry

University of Pittsburgh at Johnstown

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Ferrocene

Use a molecule from the Fragment Library to build another molecule

Task: Build -- Part 1

Time: 10 minutes

  1. Select File|Open and open the Fragment Library folder
  2. Open the Cyclic folder.
  3. Choose cyclopentane.csf and click Open.  A document window opens with a model of cyclopentane.
  4. Before making any changes, we want to save our molecule, and we want to be sure to save it with its new name in the appropriate folder.
    1. Select File|Save as
    2. Locate the folder where you want to store the molecule. 
    3. Name the file "nitrocyclo". Click Save.
  5. Change the two C-C single bonds to C=C double bonds. 
    1. Using the select tool, click on one bond.
    2. Hold down the shift key and click on the second bond (see picture above).
    3.  Select in Bond Type box.
  6. Change the hybridization of the carbon atoms with C=C double bonds.
    1. Using the select tool, click on one carbon atom.
    2. Hold down the shift key and click on the other carbon atoms in the double bonds.
    3. Select in Hybridization box.
  7. Click in the Workspace (no atoms or bonds) to select the whole molecule Select Beautify|Comprehensive.
  8. Save the changes you have made so far.  Select File|Save.
  9. We want to add a nitro group.  We could just build it by replacing one of the hydrogen atoms with a nitrogen and then adding the oxygen atoms.  OR, we could use the nitro group from the Fragment Library.
In the next lesson we will add a nitro group from the Fragment Library to the cyclopentadiene fragment we just made.