Symmetry Toolkit - D3D and D3H Symmetry

Goals: Illustrate building ethane with staggered (D3d ) and eclipsed  (D3h ) symmetries.   Demonstrate Find Symmetry - Find Irreducible Fragment - Assign Symmetry - Generate Ghosts in the Symmetry Toolkit.

Prerequisites: You are familiar with starting the Builder, adding atoms in the work area, applying force field clean, and using the measurement tools.

Setup for Display: Launch the Builder from the Ecce Gateway. To approximate the screen displays in this example, set the general display style as follows:

• Display menu, Style (All) > Ball & Wireframe
  
• Display menu, Render as > Normal
  
• Options menu, Autonormalize Display.
  

For contrast in this example, the display color of carbon was changed from default gray to blue.

1. Create an Ethane Molecule

In the Builder
a.	Create an ethane molecule in the Builder.
b.	Clean the ethane molecule using the force field clean function.
		If the Cartesian axes are not displayed, open the View menu and select Axes.

2. Find Symmetry

a.	From the Toolkits menu, choose Symmetry Toolkit to open the Symmetry Toolkit.
b.	Click on the Find Symmetry button.
		Ecce should determine that symmetry group is D3D and orient the molecule along the Z axis to show the staggered orientation. D3D should be displayed in the Symmetry field of the Builder window.

3. Attach Oxygen to the Carbon

-	Click on the Find Irreducible Fragment button in the Symmetry Toolkit to generate the symmetry unique set of atoms.
		A single carbon atom and a single hydrogen atom should be all that remains.

4. Assign D3H Symmetry and Generate Ghost Atoms

a.	Assign D3H symmetry by typing in the Symmetry Toolkit:
	Remember to move the mouse out of the input field to enter the value. In the Builder window, you should see the grayed-out symmetry specification change to D3H. The three-fold symmetry planes are different for D3D and D3H, so the orientation of the hydrogen atom must be changed. (If you generate the molecule, you will get 6 hydrogen atoms on each carbon).
b.	Click on the Generate Ghosts button in the Symmetry Toolkit.
		This generates a set of ghost atoms: one at the origin (inversion point), one on either side of the Z axis (the three-fold axis), and three showing symmetry planes associated with the three-fold axis.
c.	You may need to reorient the molecule and modify transparency to view all the ghost atoms.
		For example: RotY thumbwheel to rotate the molecule around the Y axis. Display menu, Transparency.

5. Adjust Torsion Angle

a.	Select the torsion angle tool to adjust the torsion angle between the hydrogen atom and one of the equatorial ghost atoms.
b.	First select one of the three symmetry plane ghost atoms followed by the origin, then the carbon atom, then the hydrogen atom.
		Make sure the hydrogen atom is selected last when doing this. Otherwise the ghost atom will be the one to move when the angle is changed
c.	Click on the plane indicators that appear and change the torsion angle to zero (0.0).
d.	Remove the torsion plane by clicking the Clear All Measurements button.

6. Generate the Ethane Molecule (Eclipsed)

a.	Click on the Generate Molecule button to create the full ethane molecule.
		The hydrogen atoms should now be in the eclipsed orientation instead of the staggered orientation.
b.	Remove the ghost atoms by clicking on the Clear All Ghost Atoms button in the Builder.
		The hydrogen atoms should now be in the eclipsed orientation instead of the staggered orientation.