Builder Example - Ferrocene (D5H and D5D Symmetry)

Goals:		Illustrate building ferrocene Fe(C₅H₅)₂ with D_5h and D_5d symmetry.
		Demonstrate Symmetry Toolkit operations: Assign Symmetry - Generate Ghosts - Generate Molecule - Find Irreducible Fragment.

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:

In the Builder
a.	Add Fe to the atom palette and place an iron atom into the Builder work area. Turn on the axis display (View menu, Axes command).
		The atom will be automatically located at the origin.
b.	Open the Symmetry Toolkit and assign a D5H symmetry.
c.	Click on Generate Ghosts button to create a set of useful ghost atoms.
		Note the five-fold symmetry axis is the Z axis containing two ghost atoms, one at +1 and one at -1.

Move one of the ghost atoms on the Z axis 1.65 angstroms from the iron atom using the Distance Measurement-Adjustment Tool.

This adjusted ghost atom will serve as an anchor for positioning carbons.

The image shown here is rotated around the Y axis with the Display menu's Transparency option turned on.

a.	Add a carbon atom (no bonds) to the system near the adjusted ghost atom.
b.	Use the Angle Measurement-Adjustment Tool to adjust the angle between the carbon atom, the adjusted ghost atom along the Z axis, and the iron atom to 90 degrees.
		For these adjustments, be sure to select the carbon atom last so that it is the atom that moves.
c.	Clear the measures.
d.	Use the Distance Measurement-Adjustment Tool to adjust the distance between the carbon atom and the adjusted ghost atom on the Z axis to 1.2 angstroms.
		Be sure to select the carbon atom last.
e.	Use the Torsion Angle Measurement-Adjustment Tool to adjust the torsion angle between the carbon atom, adjusted ghost atom on the Z axis, iron atom, and one of the five equatorial ghost atoms to 0 degrees. Make sure the carbon atom is selected last so that it is the atom that actually moves.

f.	Clear the measures.

a.	Change the carbon to make it monovalent.
b.	Select the Add H button to add a hydrogen atom to the carbon.
c.	Use the Angle Measurement-Adjustment Tool to adjust the angle between the adjusted ghost atom on the Z axis, the carbon atom, and the hydrogen atom to 180 degrees.
d.	Clear the measures.
		This completes the irreducible fragment that will be the basis for generating the completed ferrocene molecule.

a.	Remove the ghost atoms.
b.	Select the Generate Molecule button in the Symmetry Toolkit.
		The result should be a complete ferrocene molecule with eclipsed hydrogen atoms.

	To generate ferrocene with staggered hydrogen atoms as in the crystal structure, you need to regenerate the molecule based on D5D symmetry.
a.	Select Find Irreducible Fragment in the Symmetry Toolkit.
b.	Assign a D5D symmetry in the Symmetry Toolkit.
c.	Select the Generate Molecule button in the Symmetry Toolkit.

	The result should be a complete ferrocene molecule with staggered hydrogen atoms.

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Revised: August 14, 2003