Symmetry Toolkit - C2H Symmetry

Goals: Illustrate building methanol dimer with C2h symmetry.
  Demonstrate Symmetry Toolkit operations: Assign Symmetry - Generate Ghosts - Align to Axis - Align to Plane - Generate Molecule - Find Irreducible Fragment - Translate.

Prerequisites: You have completed previous examples or already know how to

Setup for Display: To approximate the screen displays in this example, set the following options in the Builder:

1. Assign C2H Symmetry & Create a C-O Group

In the Builder
a. Open the Symmetry Toolkit and assign a C2H symmetry.
b. Click on the Generate Ghosts button to create a set of useful ghost atoms.
c. Select View menu, Axes.
d. Change one of the ghost atoms lying along the X axis to an oxygen atom with a valence of two (the default).
 
e. Bond a carbon atom with a single valence to the oxygen atom.
 

2. Align the Carbon Away from the Origin

a. Select the carbon atom in the Builder work area.
b. Select the Align to Axis option in the Symmetry Toolkit.
Select the X button to automatically fill in the parallel axis vector (1,0,0).
c. Be sure the All option is OFF (unmarked).
Select the Align button.
The carbon atom should now lie along the X axis on the side of the oxygen that is pointing away from the origin.
d. IF the carbon atom is lying on the other side of the oxygen:
- Use the Angle Measurement-Adjustment tool of the Builder to rotate it 180 degrees.
- Select the ghost atom at the origin followed by the oxygen and carbon atoms.
- Then adjust the angle to be 180 degrees.

3. Convert the Carbon to Trivalent Pyramidal

a. Convert the carbon atom into a trivalent pyramidal carbon.
b. Select the Add H button in the Builder to add three hydrogen atoms (two to the carbon and one to the oxygen atom).
Now you can use the Symmetry Toolkit's alignment tools to to adjust the position of the hydroxyl group.

4. Align the Hydroxyl Group in the XY Plane

a. Use the Angle Measurement-Adjustment tool to change the C-O-H bond angle to 109 degrees.
Be sure to select the carbon atom first and the hydrogen atom last so that the hydrogen will be moved.
b.

Set the hydroxyl hydrogen atom in the XY-plane:
- Select that hydrogen atom.
- Select Align to Plane in the Symmetry Toolkit.
- Click on the XY plane button.
- Click on the Align button.
 

5. Align the CHH Group

a. Use the Torsion angle Measurement-Adjustment tool to adjust one H-O-C-H angle to 180 and the other to 60 degrees.
Be sure to select the hydrogen on the carbon atom last so that that hydrogen will be adjusted.
b.

Also check to make sure that O-C-H angles are about 109 degrees.
 
c.

Remove the ghost atoms and measurement indicators in the Builder.

6. Generate the Methanol Dimer

a.

Generate the methanol dimer in the Symmetry Toolkit.
The result should be a methanol dimer with the oxygen atoms oriented head-on and the hydrogen atoms oriented away from each other.

7. Adjust the Separation Distance

  You can adjust the separation distance between the two methanol molecules by translating the molecules along the X axis.
a. Start by clicking on Find Irreducible Fragment in the Symmetry Toolkit.
 
b. - Select the oxygen atom.
- Select the Translate option (radio button) in the Symmetry Toolkit.
- Type in a new location on the X axis in the vector input field in the Toolkit.
- Select the All option (next to the Translate button) to specify translation of the entire structure.
- Then click on the Translate button.
  The fragment should move to a new location on the X axis.
c.

Generate the molecule in the Symmetry Toolkit again to get the new dimer configuration.
   
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Revised: August 14, 2003 		Disclaimer