Welcome to the CAChe Molecular Modeling Tutorials

Department of Chemistry

University of Pittsburgh at Johnstown

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What's the difference between MM3 and PM5?

Different computational methods provide different levels of accuracy for different properties.  There are several different ways to compare the levels of accuracy. In this module on geometry optimization you have optimized the geometry of cyclohexanol using molecular mechanics  (MM3) and a semi-empirical quantum mechanical method (MOPAC, PM5). Now we will compare the two by superimposing the images of the two molecules. 

Task: Superimpose cyclohexanol optimized using MM3 and cyclohexanol optimized using MOPAC and compare the structural differences.

Time: 8 minutes

The images in this section of the tutorial use the  cyclohexanol optimized with MM3 and the  cyclohexanol optimized with PM5.

  1. Open the cyclohexanol molecule you optimized using molecular mechanics, by selecting File|Open "cyclohexanol-ax-MM3".
  2. Open the cyclohexanol molecule you optimized using MOPAC by selecting File|Open "cyclohexanol-ax-PM5".
  3. In the cyclohexanol-ax-PM5 workspace, select the Select Molecule tool, , from the tool palette and click on the molecule.
  4. Copy the molecule and paste it into the workspace of the cyclohexanol molecule optimized with Mechanics.
    1. Choose Edit|Copy
    2. Select the cyclohexanol-ax-MM3 workspace by choosing it from the Window menu.
    3. Choose Edit|Paste.
  5. The two molecules are superimposed one directly on the other; it looks a little fuzzy.  We want to move them apart to see both structures more clearly.
    1. Choose Edit|Move Selected. The rotate tool, ,is enabled by default.
    2. Select the Translate tool, , click and drag to move the selected molecule.
  6. With the two molecules separated, we'll select three (or four) atoms on each molecule and superimpose them.
    1. Choose the Select tool . Select an atom from the molecule that you moved aside.
    2. Hold down the shift key and select two more atoms in the same molecule.
    3. Hold down the shift key and select the same three atoms in the other molecule, in exactly the same order as in the first molecule.
    4. Select Analyze|Superimpose from the menu bar.
  7. Now you see the differences in structural geometry between the two superimposed molecules.  Any differences in structural geometry are indicated by an RMS label. There are a couple of ways you can compare the molecules visually:
    1. Select the Rotate tool . Click and drag to rotate the molecules around the x, y and z axes.
    2. Select the Scale tool .  Click and drag the Scale tool to zoom in or out.
    3. Select View|Lines to display the superimposed molecules as line drawings.
    4. Select View|Ball & Cylinder to redisplay the molecules as ball and stick.
  8. To separate the molecules again
    1. Choose the Select Molecule tool, and click on one of the superimposed molecules.
    2. Select Edit|Move Selected.
    3. Choose the Translate tool, , and move the selected molecule away from the other one.
    4. You may rotate or zoom this molecule more.
    5. Use the Select Molecule tool,   to select the other molecule and rotate or zoom it.
  9. To close the windows:
    1. Select File|Close. Respond No to the alert dialog box asking if you would like to save changes made to cyclohexanol-MM3.
    2. Select File|Close. Respond No to the alert dialog box asking if you would like to save changes made to cyclohexanol-PM5.

Go back to the discussion of Which Theoretical Method to Use.