Exercise 1 (easy):
First build a methane molecule. Then, by using a single structure, change it into a neopentane
in a single step (neopentane is a methane with all hydrogens replaced by methyl groups).
Solution:
1) Using the C-tool, place a carbon atom in the drawing area.
2) Press ctrl-h to add hydrogens to the carbon.
3) Select the ‘t-butyl’ structure from the ‘alkyl chains’ submenu and double-click on one
of the hydrogens.
This could also have been done by selecting all the hydrogens and, via the atom popup menu,
replacing each of them with a methyl group.
Exercise 2 ( easy):
Build an Mn2(CO)10 complex
Solution:
1) In the submenu ‘Metal Complexes’ select the M2L10 Cluster and, with a single click,
place it in the drawing area.
2) Select both the metal centers: left-click the first and shift left-click the second.
3) Right click (or click and hold down) on one of the metals and, from the pop-up menu,
choose ‘Mn’ from the periodic table in the ‘Change atom type(s)’ submenu.
4) Select all the dummy atoms by right clicking one of them and choosing the ‘Select all
Xx atoms’ from the pop-up menu.
5) Right click again on one of the dummy atoms and go the the ‘Add structure(s)’
submenu. Go to the ‘Ligands’ submenu and choose the ‘CO’ structure.
Exercise 3 (part 1, easy/medium):
Build a Fe complex with two ethylenediamine bidentate ligands. Make it a tetrahedral and a
square planar complex, respectively.
Solution:
1) Place an iron atom in the drawing area.
2) Select ‘Ethylenediamine’ from the ‘Ligands/bidentates’ submenu
3) Double click on the Fe atom.
4) Press spacebar and double click again on the metal atom
(You can see that, in this case, the metal atom is not replaced by an atom of the structure,
contrary to previous experience, but that the bidentate ligand is simply attached to the central
metal atom. This works because the bonding atom in all bidentate structures is a dummy
atom, which has the property that it won’t replace an existing atom. The tri- and tetradentates
work in a similar fashion.)
5) Select, in order, the two nitrogen atoms on ligand one, the metal atom, and the
nitrogen atoms on the second ligand.
You can now change the angle between the two planes as defined through the two triangles in
this selection.
6) Change the angle to 90 and 0 degrees, respectively.
Exercise 3 (part 2, easy/medium):
Turn the planar structure build in part 1 into a tridentate ligand as shown (hydrogen atoms
omitted for clarity):
(Hint: Superpose two of the nitrogen atoms and us the ‘Fuse Atoms’ command.)
Solution:
1) Set the angle between two of the nitrogens on opposite ligands to zero (select the
atoms in order N-Fe-N so you can change the angle).
2) Select the ‘Fuse Atoms’ command from the Edit menu.
3) Remove the spurious hydrogens from the fused nitrogen.
If you would now change the metal to a dummy atom and set it as the origin, you have a nice
new tridentate ligand to use!
Exercise 4 (easy/medium)
Define a P(OH)3 ligand and use it to make a Pd(P(OH)3)2 complex.
Solution:
1) Place a bare NH3 ligand in the drawing area. Replace the nitrogen for a phosphorous.
2) Select the three hydrogens and replace them with OH-ligands.
3) It would be wise to optimize the ligand using the preoptimizer. Press the smiley button
located right of the structures menu button.
4) Select the phosphorous and set its coordinates to (0,0,0) by using the Edit/Set Origin
command.
5) Save the structure in your $SCM_STRUCTURES directory. If you have not yet set the
SCM_STRUCTURES environment variable, set it to a directory of your liking.
6) Open a new file (File/New) and place a linear ML2 metal complex in the drawing
area.
7) Replace the dummy atoms with your own new ligands, which should be visible in the
structures menu.
8) Replace the central metal with a Palladium atom.
Exercise 5 (medium/hard)
Build the following structure (hydrogens are omitted for clarity):
(Hint: use the methyleneamine bidentate ligands. Position the first two correctly, then add the
third.)
Solution:
1) Place a metal atom in the center of the molecule window.
2) Add two of the methyleneamine ligands and orient them in a tetrahedral fashion using
the plane angle between them.
As can be seen in the picture, the nitrogens need to be at 90 degrees to each other. The first
nitrogen can be set perpendicular to the plane of the other ligand.
3) Select, in order, a nitrogen, the metal and the carbon atom on the opposite ligand.
Change the angle to 90 degrees.
4) Select, in order, the other nitrogen, the metal, and a nitrogen on the opposite ligand.
Change the angle to 90 degrees.
You should now have the structure as shown above but without the third ligand.
5) Add the third ligand to the metal center.
6) If the third ligand is not positioned correctly, you can correct it by setting the plane
angle relative to the opposite nitrogens to zero.