In Oscail clink File/ptest/moilin/scratch
and then start Moilin. Click Bu on the toolbar to start build and
then Purge on the menu.
Click the blank screen and change the atom type to Fe select 2 connections and
click OK
This should give
Click one of the H atoms and select eta-5-Cp ring and OK. Do the same for the second H attached to Fe
You should now have
Remove centroids as shown
Click the left toolbar button to exit build and Use
File/Save Current Job As to save the job in a new folder. Click the Orca
toolbar button. On the Orca menu select NewInput
and Run.
Orca should start.
When Orca has finished the structure should look like..
Notice that the geometry is eclipsed (point group D5h).
When first built the structure was staggered (point group D5d).
It is good to see that Orca has given the correct structure. Click the Start
MultiWFN button.
There are two options Start MultiWFN to use any of its
functions or use MultiWFN to plot only specific MOs
Use the first option and click OK. When the MultiWFN DOS window opens press 0 and return to plot MOs.
Click inside the orbitals box on the bottom right. You can
see the orbital energies and Occ. of 2 electrons in the DOS window. Go to the
HOMO (the highest energy containing 2 electrons. It is orbital number 48.
Moving down from 48 46 looks like the Fe dz2 and it is non bonding
(no overlap with ligand orbitals). The strongest
bonds are MOs 42 and 43. They are orthogonal (90° about the five fold axis) and
have almost the same energy. They should be exactly the same in energy but Orca
is not imposing strict D5h symmetry.
Close the MultiWFN orbital window using its Return button and close the DOS window with lower case q and return.
Click the MultiWFN button again and select the second
option and enter 42,43,46 into the dialog
Click OK and when the calculation is finished start Chimera. In Chimera select File Open and find the file ferrocene_orca.pdb. This file was written by Moilin after the structure was optimized.
Use File Open to open orb000046.cub.
On the Volume Viewer pull the level bars out from the centre one at a time (each by the same amount).
To change the colors click a limit bar and notice that the color button has the
same color as the limit bar. Click the color button move green and blue to the
left and the light colored lobes are now red. Select the dark limit bar and set
its color to blue. It may be faster to select the color name and set it to "red"
or "blue" and hit return.
Use Actions Surface Transparency on the main window to set the surface transparency to 30% for
example and File Save image (also on the main window) to save a png or other file
type.
On the volume viewer use File Close map and File open map to get pictures of MOs
42 and 43
.
A basic MO composition analysis
for orbitals 42, 43 and 46 are also generated by MultiWFN
The analyses are written to the files
042.lst, 043.lst and 046.lst. With some text removed the files
contain
Orbital 42 | ||
Atom | 1(Fe): | 23.29120% |
Atom | 2(C): | 12.42053% |
Atom | 3(C): | 5.97581% |
Atom | 4(C): | 4.87492% |
Atom | 5(C): | 13.12665% |
Atom | 6(C): | 0.88199% |
Atom | 7(H): | 0.37839% |
Atom | 8(H): | 0.16792% |
Atom | 9(H): | 0.13015% |
Atom | 10(H): | 0.39605% |
Atom | 11(H): | 0.00184% |
Atom | 12(C): | 12.42068% |
Atom | 13(C): | 0.88199% |
Atom | 14(C): | 13.12671% |
Atom | 15(C): | 4.87496% |
Atom | 16(C): | 5.97587% |
Atom | 17(H): | 0.37839% |
Atom | 18(H): | 0.00184% |
Atom | 19(H): | 0.39605% |
Atom | 20(H): | 0.13015% |
Atom | 21(H): | 0.16792% |
Orbital 43 | ||
Atom | 1(Fe): | 23.27069% |
Atom | 2(C): | 2.47457% |
Atom | 3(C): | 8.93935% |
Atom | 4(C): | 10.04421% |
Atom | 5(C): | 1.79941% |
Atom | 6(C): | 14.03319% |
Atom | 7(H): | 0.05378% |
Atom | 8(H): | 0.26131% |
Atom | 9(H): | 0.29997% |
Atom | 10(H): | 0.03176% |
Atom | 11(H): | 0.42704% |
Atom | 12(C): | 2.47458% |
Atom | 13(C): | 14.03323% |
Atom | 14(C): | 1.79942% |
Atom | 15(C): | 10.04420% |
Atom | 16(C): | 8.93942% |
Atom | 17(H): | 0.05378% |
Atom | 18(H): | 0.42704% |
Atom | 19(H): | 0.03176% |
Atom | 20(H): | 0.29997% |
Atom | 21(H): | 0.26131% |
Orbital 46 | ||
Atom | 1(Fe): | 92.81119% |
Atom | 2(C): | 0.23856% |
Atom | 3(C): | 0.24473% |
Atom | 4(C): | 0.2436% |
Atom | 5(C): | 0.24248% |
Atom | 6(C): | 0.24451% |
Atom | 7(H): | 0.47091% |
Atom | 8(H): | 0.47475% |
Atom | 9(H): | 0.48026% |
Atom | 10(H): | 0.47996% |
Atom | 11(H): | 0.47464% |
Atom | 12(C): | 0.23857% |
Atom | 13(C): | 0.2445% |
Atom | 14(C): | 0.24246% |
Atom | 15(C): | 0.24359% |
Atom | 16(C): | 0.24476% |
Atom | 17(H): | 0.47091% |
Atom | 18(H): | 0.47463% |
Atom | 19(H): | 0.47995% |
Atom | 20(H): | 0.48027% |
Atom | 21(H): | 0.47476% |
The overlap between Fe and the ring atoms is clear in 42 and 43 and 46 is almost 100% Fe as expected.