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Department of Chemistry

University of Pittsburgh at Johnstown

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Visualizing Steric Interactions -- III

Task: Generate the van der Waals surface of 1,2-dichlorethane and compare with the Ball & Stick rendering.

Time: 2 minutes

  1. Begin with the Workspace you had at the end of the last lesson:

  2. Generate the van der Waals surface:
    1. Select Experiment|New  
    2. Property of: chemical sample
    3. Property: Van der Waals surface
    4. Using: PM5 geometry with PM5 wavefunction
    5. Click Start.
    6. When the experiment is finished, click in the molecule window to bring it to the foreground.
    7. Save the file. File|Save "12Cl2ethane-PM5"
  3. Visualize the surface:
    1. Select Analyze|Show Surfaces from the Menu bar.
    2. In the Displayed surfaces box, select 12Cl2ethane-PM5.csf.VonD (a check mark appears next to the name).
    3. Click OK.
    4. The van der Waals surface appears on both renderings.
  4. Initially, the surface will be transparent; you can see the molecule "inside" the surface.  Clicking anywhere in the Workspace (no bonds or atoms) selects the surface.
  5. A question to think about: Right after you select Show Surfaces, you can see the individual atoms of the molecule. Based on the the two images, which surface, the van der Waals surface or the space filling model, better approximates the "space" the molecule occupies?

The next lesson you will introduce you to the basics of electrostatics and charge distribution.