Using PC Spartan 06

By JoAnn Peters, Ph.D.

You can access PC Spartan 06 in the university's computer labs.
You will find PC Spartan 06 under the All Programs menu, or in the Network Applications folder.
I recommend transferring all files to a network drive (the N: drive) before you logout.

Building molecules

  1. Open PC Spartan 06. You will see a blank page with menus displayed at the top.
  2. Open a New file in the File menu. A model kit should appear at the right of your screen.
  3. Use the model kit to construct your molecules.
    Click on the appropriately hybridized atom, move to the middle of the screen and click again.
    If you do not see the hybridization or the atom that you need under the Organic tab, click on the Inorganic tab.
    In the Inorganic model kit you can select the element, valence, and hybridization that you desire.
    You can Make bonds and Break bonds, and Delete atoms, by going to the appropriate selection in the Build menu.
    The Minimize command under the Build menu will adjust bond lengths and angles to normal values.
    Hydrogens will be added automatically to any unfilled valences (yellow stick ends) when you exit the build function.
    Don't worry about drawing single vs double or triple bonds.
    The software will figure out where any multiple bonds belong.
    You can rotate models by depressing the left mouse button and moving the mouse.
    You can move the models about the screen by depressing the right mouse button and moving the mouse.
    You can make the image bigger or smaller by holding down the "shift" key and the right mouse button and moving the mouse.

Calculating structures, vibrational frequencies and surfaces using a semi-empirical electronic structure calculation

The geometry corresponding to the local energy minimum closest to your starting geometry is predicted from equations describing the interactions of electrons with atomic nuclei.
  1. Select Calculation from the Setup menu.
    In the Calculation section select Equilibrium Geometry at Ground state with Semi-Empirical and AM1.
    (You may select Transition State Geometry if you wish to investigate a transition state for a process.)
    Select Initial geometry in the Start from section.
    Deselect Symmetry in the Subject to section.
    Select the desired total Charge .
    The Multiplicity for stable molecules should be 1.
    Click on OK.
  2. Select Submit from the bottom of the Setup menu.
    You'll be asked for a filename if you have not already saved the file.
    A pop-up window will tell when the calculation has been completed.
    You can select different types of representation under the Model menu.
    The Space-filling representation will be especially useful when looking for steric interactions.
    You can measure bond angles and distances by clicking on Angle and Distance under the Geometry menu;
    the numerical values will be displayed at the very bottom of the window.
    Energy, dipole moment, area, and volume may be viewed by selecting Properties from the Display menu.
  3. To calculate surfaces, go to the Surfaces option in the Setup menu, click on Add, and make your selections.
    One of my favorites can be calculated by selecting Density as the Surface option and Potential as the Property option.
    This will result in an electronic potential map of the molecule "surface" with areas of greatest negative charge in red, shading to areas of greatest positive charge in blue.
    You may also calculate the surfaces for the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO).
    To view surfaces, go to the Surfaces option under the Display menu, then click on the surface that you would like to view.
  4. At the AM1 level, you may calculate vibrational frequencies and predict the appearance of IR spectra.
    In the Calculation box under the Setup menu, select Equilibrium Geometry, Ground state, and Semi-empirical AM1 method.
    Then select IR in the Compute section.
    Click on Submit in the bottom right hand corner of the box.
    To view the results, go to Spectra under the Display menu.
    Negative vibrational frequencies are an indication that the geometry optimization did not find a true energy minimum; try the geometry optimization again.

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