Creating a Molecule of NH₃

The following are detailed instructions on how to set up a calculation, it is important you take the time to read the instructions and follow them precisely.

• you will have two windows, one grey window with buttons, which has all the controls, do NOT build your molecule in this window.
• the second window is blue/purple by default and has nothing in it currently, this is where you build your molecule
• on the controls palette click on the button that has a grey periodic table with a large ⁶C for carbon on it:

  

• when the periodic table comes up choose N for nitrogen (1.), then when the nitrogen options appear along the bottom of this window choose the pyramidal fragment (2.):

  

• now move the mouse to the blue molecule builder window and click once inside this window, a molecule of NH₃ will appear:

  

• on the controls palette click on the button with a question-mark in front of a ruler. This is the inquiry button and we will use it later, however once in inquiry mode the other buttons deactivate and this will stop you accidentally making changes to your molecule.

  

• options for labelling and manipulating your molecule
  • now put the mouse on one of the atoms and move it across the screen, the molecule will rotate. Spend a few minutes getting comfortable with manipulating your molecule. Make sure you can
    • rotate the molecule
    • magnify and shrink the molecule
    • translate the molecule

    I took this image from the gaussview help menu. If at any point you want to find out more about manipulating molecules in gaussview the help section should be your first port of call.

    

• you should also look at the options in the view menu, for example you can put the letters for each atom on the ball-and-stick diagram

  

• controlling bond distance parameters
  • along the top of the controls palette the next three buttons allow you to change the bond distances, angles and torsion angles of a molecule

    

  • click on the bond distance "button"
  • then click on the N-atom and one H-atom, they should now be highlighted and a new window will appear
  • when we set the new bond distance, we don't want the N to move, only the H, so set the N atom to be "Fixed" (1.), this will be either atom 1 or atom 2 depending on whether you clicked on the N atom first (atom 1) or second (atom 2)
  • then we want to make the bond longer, enter 1.3 in the text box (2.), you will see the chosen bond elongate (3.) Then press the "OK" button, if you don't press ok the change will not be actioned.
  • set all three N-H bonds to 1.3 angstrom.

    

• the angle and torsion angle controls work similarly, if you want to try them out make a new molecule and explore how these controls work, leave this NH₃ molecule alone as it has been set up for the next part of the exercise
• now we will check the symmetry of your molecule
  • the model builder does not always get the symmetry right, and so for each molecule we need to manually check it.
  • In the edit menu choose "Point group"

    

  • a new window will open, as shown in the image below
  • first select the enable point group option (1.)
  • then select C_3v (2.) and click OK

    

  • if you didn't know that NH₃ belongs to the C_3v point group or you can't remember how to get to C_3v, now is a good time to set yourself some revision homework!
  • the point group "names" a structure according to a set of rules which define how a molecule transforms onto itself. For example if you look "down" on the molecule (with the N in the center and the 3 H-atoms spread out away from you) you can see that if the molecule is rotated 120 degrees it maps back onto itself. We say that the molecule has 3-fold rotational symmetry and a C₃ axis. This is where the "3" in the point group name comes from.

• you have now created and manipulated your first molecule!

• when you are ready move onto the next step