Symmetry Toolkit - D5 Symmetry

Goals: Illustrate building protactinyl pentahydrate with D5 symmetry.   Demonstrate Symmetry Toolkit operations: Assign Symmetry - Align to Axis - Generate Ghosts - Translate - Generate Molecule - Find Irreducible Fragment.

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

• start the Builder from the Ecce Gateway
• add atoms in the work area
• add elements and bond geometries to the Builder palettes by using the Periodic Table tool.

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

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

1. Build a Protactinyl Structure

In the Builder
a.	Open the Periodic Table by selecting the more… button in the Builder's element palette.
b.	Select protactinium (Pa) and a linear bond geometry.
c.	Select View menu, Axes to display the Cartesian axes.
d.	Select Options menu, Auto Normalize Display.
e.	Add a divalent Pa atom (linear sp valence) to the window.
		The atom will be located at the origin. With the axes displayed, you must click the mouse away from the origin. Otherwise the atom will not be added.
f.	Bond two oxygen atoms to the protactinium using a single valence.
		You should now have protactinyl (PaO2) in the Builder window.

2. Assign D5 Symmetry & Align to Z Axis

a.	From the Toolkits menu, choose Symmetry Toolkit to open the Symmetry Toolkit.
b.	Assign D5 symmetry by changing the specification in the Symmetry Toolkit (not the Builder window).
c.	Generate ghost atoms by selecting the Generate Ghosts button in the Symmetry Toolkit.
		The 5-fold symmetry axis is the Z axis by definition. The next step is to line up the O-Pa-O bonds along this axis.
d.	Select the Align to Axis option in the Symmetry Toolkit. Select the Z button to automatically fill in the parallel axis vector (0,0,1).
e.	Be sure the Builder is in "Select" mode and select one oxygen atom in the Builder work area.
f.	Turn ON the All option near the bottom of the Symmetry Toolkit. Select the Align button.
		The chemical system should realign itself to the Z axis.

3. Add Water Molecules in D5 Symmetry

a.	Change one of the ghost atoms in the XY-plane to be an sp3 divalent (bent) oxygen atom. (This is the default valence.)
		The new oxygen atom should be moved so it is 2.6 angstroms from the protactinium atom. We want to put the atom on the positive Y axis so that the bonding nubs are facing away from the origin. To do this, you will use the Translate capability of the Symmetry Toolkit to move the new oxygen to (0, 2.6, 0).
b.	Select the Translate option (radio button) in the Symmetry Toolkit.
c.	Select the Origin button to reset the origin to (0, 0, 0).
d.	Edit the "n-y:" input box to be 2.6.
e.	Select the divalent oxygen atom. Turn OFF the All option in the Symmetry Toolkit. Then select the Translate button.
		The divalent oxygen atom is moved into position on the Y axis.
f.	In the Builder, click on Add H to complete the valence on the divalent oxygen atom.
g.	Select the Generate Molecule button in the Symmetry Toolkit to generate the whole molecular system.
h.	Remove the ghost atoms by clicking on the Clear All Ghost Atoms button in the Builder.
		You should have five water molecules around the protactinyl group.

4. Adjust Water Molecule Orientation

	Adjusting the orientation of the water molecules can be done by a series of steps using the Symmetry Toolkit. The initial conformation in this procedure has the H-O-H bond in the XY-plane. Let’s rotate all five water molecules by 90 degrees.
a.	Select the Find Irreducible Fragment button in the Symmetry Toolkit to reduce the molecular system to the unique atoms.
		You can then use the Torsion Angle Measure/Adjust Tool to adjust the torsion angle between the O-Pa-O-H atoms. The fragment shown here was rotated around the Y axis to show all atoms clearly.
b.	Select the torsion "T" button.
c.	While holding the Shift key down on your keyboard, select the four atoms in order, O-Pa-O-H, being sure to select the hydrogen atom last.
		Gray planes display to indicate the torsion angle.
d.	Click on the plane displayed in the Builder window to pop open the Torsion window.
e.	Change the torsion angle to 0.0 degrees [[and press the Enter key on the keyboard.]]
		The torsion angle changes to 0.0.
f.	Now generate the whole molecular system by selecting the Generate Molecule button in the Symmetry Toolkit.
		The molecular system is reoriented here to show its symmetry.

5. Adjust Bond Lengths & Regenerate Molecule

	The default bond lengths for the protactinyl group are too long. These could be adjusted for each bond by using the Geometry Text Table, the Distance Measure/Adjust tool, or the "Translate" option in the Symmetry Toolkit. It is quickest to use the Symmetry Toolkit to reduce the system to unique atoms before making the adjustment. Then only one bond length needs to be modified.
a.	Select the Find Irreducible Fragment button in the Symmetry Toolkit to reduce the molecular system to the unique atoms.
		You may need to adjust the view so that you can see the Pa-O bond clearly.
b.	Select the distance measure/adjust button.
c.	While holding the Shift key down, select the protactinium atom followed by the bonded oxygen atom.
		The bond length will be displayed. Adjusting this length will now move the oxygen atom.
d.	Click on the Pa-O bond to pop open the Length entry window.
e.	Change the distance to 1.78 angstroms [[and press the "Enter" key on the keyboard.]]
f.	Finally regenerate the whole molecular system by selecting the Generate Molecule button in the Symmetry Toolkit.