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Department of Chemistry

University of Pittsburgh at Johnstown

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Energy Maps II

Task: Add search labels to isoprene

Time: 5 minutes

We'll set two search labels on the isoprene molecule.  One label will be the dihedral angle on the carbon backbone.  The second label will be the H-C-H bond angle on the CH2 group attached to carbon 2.

  1. Use the isoprene molecule built in the last lesson. If not already open, select File|Open and navigate to the file "isoprene".
  2. Select the atoms for the dihedral angle search.
    1. Choose the Select tool and click in the center of the carbon atom attached to three hydrogen atoms -- the one labeled 1 in the figure.
    2. Holding down the Shift key, click on the three remaining carbon atoms in the order shown in the figure. Note: the order in which you select the atoms is important. The first one selected is the one that moves as the value of the angle changes.
  3. Set the dihedral angle.
    1. Chose Adjust|Dihedral Angle.
    2. Select the Define Geometry Label box.
    3. Select the Search radio button.
    4. Set the Search range from -180.000000 to +180.000000 using 24 steps
    5. Select Apply
    6. Select OK
  4. You will see a search label which displays the current value of the dihedral angle and the letter S (for "search").
  5. Select the atoms for the bond angle.
    1. Choose the Select tool . Click anywhere in the workspace to select the whole molecule. 
    2. Click on one of the hydrogen atoms attached to carbon we didn't include in the dihedral angle search.
    3. Holding down the Shift key, select the carbon and the other hydrogen atom in the order shown in the figure.  As before, the order in which you select the atoms is important. The first one selected is the one that moves as the value of the angle changes.
  6. Set the bond angle.
    1. Chose Adjust|Bond Angle.
    2. Select the Define Geometry Label box.
    3. Select the Search radio button.
    4. Set the Search range from 105.000000 to 135.000000 using 6 steps.
    5. Select Apply
    6. Select OK
  7. You will see a search label which displays the current value of the dihedral angle and the letter S (for "search").
  8. Save the search labels: File|Save "isoprene"
 

Generate a .map file in the next lesson.