Moleuclar Orbitals

  • If you are a chemist you will have already met Atomic Orbitals AOs they are s, p and d. Electrons fill atomic orbitals in pairs. In molecules, we have Molecular Orbitals, which are filled by electron pairs. MOs are built up from the AOs of individual atoms, because the orbitals overlap they become smeared out and so MOs can look a bit strange if you haven't seen them before. MOs are the basis of modern bonding theories and understanding. MOs are something you will study at in your 2nd year of a chemistry degree.
  • Use your open the *.chk file (not the *.log file!) for final optimised NH3
  • Then from the "Tools" pulldown menu, choose "MOs"
  • A MO window should open. In the new window select the Visualize tab and then in the box Add List type a list of 10 MOs, typically the orbitals closest and under the highest occupied MO (HOMO) are the most interesting (although you can look at them all!), this is
    • for BF3(CF3) this is "23a-33a"
    • for SO3(CF3) this is "27a-37a"
  • then click on Update. What will happen next is that gaussview will read information off the checkpoint file and covert this into the molecular orbitals for you to visualise. Be patient, this requires quite a bit of number-crunching and may take up to 5min. The larger the list of MOs to compute the longer this will take, hence it is best to do 10 at a time.

    vlab_wiki_nh3_compute_mos

  • While you wait, we want to set the surfaces to appear as transparent, this makes the MOs easier to interpret as you can see the atomic nuclei. Click on the Gaussview tab (top-right) select "Preferences" a new window will open. In the new window select "Display Format" click on the "Surface" button and then select "Transparent" from the pulldown menu. Once done click the "OK" button.

    vlab_wiki_display_format

  • Once the MOs are computed you can step through each of the MOs you have calculated (and do another 10 if you like).
    • the deep MOs determine the bonds that form in a molecule
    • the highest occupied MO and lowest unoccupied MO determine the reactivity
    • these two aspects mean that MOs are a central part of modern chemical understanding

    vlab_wiki_mos

  • You could also look at the higher energy MOs above the LUMO, however their shapes are not as reliable as those of the bonding MOs particularly the higher energy ones. If you take a quantum mechanics course you will learn that the mathematics of the way we arrive at the un-occupied MOs is not as robust.

  • Congratulations you are now finished, with NH3!

  • Return to the outline to see what you could do next if you have a bit more time
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