In trying to understand molecular orbitals you will almost certainly be helped by viewing them in color and in motion using computer graphics (especially if you find the pictures of MOs that we show in class or on handouts confusing). If you happen to have blue/red stereoglasses, you can even see them in 3D.

There are a number of programs that allow you to do this with orbitals, but one that is readily available on the Yale Mac clusters is MacSpartan PLUS. There is a PC version of this program, but we don't have it. Sorry.

With MacSpartan PLUS you can construct molecules and do MO calculations on them at various levels of sophistication up to SCF with reasonably flexible atomic orbital shapes (6-31G(*)). At present we will only be using it to view orbitals that have already been calculated. They are available in the Chem125 MOs folder in the MacSpartan Plus folder.

You'll find the program at the following location: MacHardDisk / Instructional Software / Science/Math

Here's what you need to do once you have launched MacSpartan PLUS by double clicking its icon.

Choose an appropriate background color by clicking the Apple at the top left and selecting Set Colors. Nothing very wrong with white, but black may be more artistic.

Under FILE choose OPEN, click to get the Chem125MOs folder, and choose one of the five subfolders (HF, CH3F, C2H5F, H2C=O, CH3, CF3) within it. I suggest you start with HF. Then click the file with the same name and you're in business. A framework model of the molecule will appear on the screen.

You can adjust the type of model with options under the MODEL menu. Try the following:

Wire
Ball and Wire,
Tube,
Ball and Spoke, and
Space Filling

You can further adjust the view by clicking and moving the mouse with the help of various keys.

Just click and drag to rotate in and out of the plane
Hold clover while you click and drag up and down at the left of the screen to rotate about the axis of view
Hold option clover while you click and drag up (or down) to magnify (or compress) the view
Hold option click and drag to shift the molecule within the frame

For best viewing the orbitals, increase the size of the model and choose Ball and Wire or Tube under MODEL.

Now go to the DISPLAY menu and click SURFACES. Double click one of the orbitals in the box at the top of the new window. A check mark appears at the left to show you want to display this orbital, for example HOMO-1. Several can be checked and shown simultaneously, but this gets confusing. Specify a STYLE of display (Solid is the default, but I prefer Mesh or Transparent). Click OK and you can look at the orbital in "color" (what do the colored surfaces specify?) and space (perceived by rotation with the mouse).

For most molecules only one surface has been calculated, the most interesting one that is characteristic of the functional group. To look at other orbitals go to SETUP / SURFACES and select what you want. For example clicking Surface density and leaving Property as none, as shown below, would generate a contour where the total electron density is 0.002 e/ao3, which corresponds approximately with the van der Waals envelope (the "size") of the molecule. Choosing density (bond) makes the contour at 0.08 e/ao3. (for density you can choose other contours with Value, in fact you can display several contours simultaneously, onion style, by having the largest value, i.e. the smallest contour displayed solid, the intermediate one as a mesh, and the outer one as transparent ). Normally Property will be none, but choosing elpot adds surface coloration coding the energy that an electron would have at different points on the surface. This shows something about how charge is distributed in the molecule. What we're mostly interested in now is the different orbitals, so usually you'll just name a Surface like HOMO-2, and choose none for the property. After you've made your choice click Add, and it will appear in the list with the designation {pending}. After you've chosen all the surfaces you want to look at, click SETUP / SUBMIT and in a few 10s of seconds with a fast Mac the surfaces will be calculated.

You can then examine your new surfaces with DISPLAY / SURFACES, as before.

Have a good time, and remember to quit the program when you're not using it actively.

---

return to Chem125 Homepage