Computing Molecular Orbitals

Task: Compute (and display) the MO surfaces of Ammonia

The first step in generating MO surfaces for a molecule requires that we optimize the geometry. Review the tutorial on Geometry Optimization before getting started.

1. Open the file with ammonia molecule you built earlier.
2. If you have not already done so, optimize it using MOPAC (PM5 Geometry which uses MOPAC and PM5 parameters to optimize the molecule)
3. Save the file.

Now that we have the electronic information from the MOPAC calculations, we can generate the molecular orbital surfaces.

1.  Open the file with the optimized ammonia molecule.
2. Select Experiment|New. The experiment box opens
3. Select:
1. Property of: Chemical Sample
2. Property: all molecular orbitals
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 after the calculations are complete.

The last step is visualization.  Since we computed all of the MO surfaces, we can visualize them all at one once (gets confusing if there are lots of MOs) or one at a time.

1. Open the file if necessary (File|Open ammonia)
2. Select Analyze|Show Surfaces.  A Show Show Surfaces dialog box opens containing a list of Displayed surfaces.
3. Locate the surface ending in .MO4.  Click Open.  Your molecule displays the highest occupied molecular orbital (HOMO).
4. To view other MO surfaces, select Analyze|Show Surfaces, deselect the HOMO surface and select another (.MO5 will be the lowest unoccupied molecular orbital or LUMO). As a general rule, when you deselect a surface, it disappears from the window.

In the next section you will learn to generate other molecular surfaces that allow you to predict the reactivity of a molecule: