Welcome to the CAChe Molecular Modeling Tutorials

Department of Chemistry

University of Pittsburgh at Johnstown

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Ferrocene

Electrostatic Interactions -- Nucleophilic Susceptibility

Task: Generate and visualize the Nucleophilic Susceptibility surface of nitrocyclopentadiene (). 

Time: 3 minutes

The nucleophilic frontier density surface shows which regions of the molecule are most susceptible to nucleophilic attack.

  1. Open the file: File|Open "nitrocyclo-PM5".
  2. Select Experiment|New. The experiment box opens
  3. Select:
    1. Property of: Chemical Sample
    2. Property: nucleophilic susceptibility
    3. Using: PM5 geometry with PM5 wavefunction
    4. Click Start.
  4. The calculation window opens.  Information about the progress of the experiment scrolls in the window.  When the calculation is done, it will say "Tabulation complete".
  5. Save the molecule: File|Save "nitrocyclo-PM5". 
  6. Visualize the surface
    1. Select Analyze|Show Surfaces.   A Show Surfaces dialog box opens containing a list of Displayed surfaces.
    2. Locate the surface with the name nitrocyclo-PM5.csf.NFonD. The file names for other surfaces may be listed as well.  A check mark will appear when you click on the name nitrocyclo-PM5.csf.NFonD.
    3. Click OK. Your molecule displays a surface colored to show areas of maximum nucleophilic reactivity. 
  7. 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.
  8. To see what the different colors mean, select Analyze|Surface Legend.  A color legend appears.  The smaller the number, the higher the reactivity toward nucleophiles (OH-, CH3O-, Br-).
This is the last lesson in the tutorial module on Chemical Reactivity. 

To learn more about Visualizing Chemical Reactivity, check the Reaction Modeling Lab Exercises from the CAChe Training Workshops.

The next series of tutorial modules discuss Conformational Searching and Energy Maps.