C638 Problem Set #1
- Search the Cambridge Structural Database (CSD) and find the structure of
FeCl(SANE)2. Create a data file with the information on that structure.
Hint:
- The best way is to perform a Formula search
to get all structures in one search.
- One of the two structures for FeCl(SANE)2 (1974 paper) you will
find in the database is incorrect. The coordinates of some atoms are
faulty. However, this doesn't affect the discussions in
this problem set.
- Now, enter the Mercury program and display the unit cell of
FeCl(SANE)2. Try all the four representation styles: wireframe,
capped sticks, ball and stick, and spacefill. For each representation, rotate the
unit cell and view it from many perspectives.
- In wireframe representation, measure the intramolecular
Fe-Cl and Fe-O distances. As a check, compare these to those reported in the
publications. Now, using "Find Contacts" option to find out the two shortest intermolecular Fe/O
contacts and measure the Fe-O distances. Compare to those in the "loose dimer". In general what is
it about the packing in the C2/c space group which makes the difference?
Hint:
- Hide all the hydrogen atoms for clarity.
- Use the "Find Contacts" feature to examine the intermolecular Fe/O
contacts:
- Read the
section 9.4.5 of the Mercury manual and work through
the
tutorial
1.
- Click Display on the top-level menu and then Contacts... on the
pull-down menu. Then click Add button on the Contacts panel and select
Specific... from the pull-down menu.
- On the resulting Define Specific Contacts panel, set contacts
between O and Fe, and select Actual distance.
Make sure that intermolecular is checked, and then hit Apply. This should find and display
any intermolecular Fe/O contact between 0 ~ 3 Å (default value). If no
contact is found, you should change maximum to a larger value (e.g. 4
or 7 Å) and then hit Apply again.
- Click Build Network tab on the Contacts panel, and hit Expand All
to display all the molecules that undergo the Fe/O contacts to the currently
displayed molecules. You may remove the hanging (red) contacts by clicking Delete
Hanging.
- Now view, using the full screen area, the unit cell with wireframe
representation. Rotate
the unit cell to all angles to fully appreciate the view of the packing. Do
you see any signs of face-to-face P-stacking of
arene rings in the C2/c structure?
Hint:
- Displaying a single unit cell is not always a good choice for examining the
crystal packing and intermolecular interactions. You may need to include more
unit cells in the display in order to check the interactions
between molecules in different cells, or to display just a part
of unit cell for clarity. To do so, click Display on the top-level menu and
then Packing/Slicing... on the pull-down menu, then change the cell
dimensions a, b, or c (not have to be integers) on the Packing and Slicing
panel.
References
- J. A. Bertrand, J. L. Breece, P. G. Eller, Inorg. Chem., 13, 125 (1974)
- C. J. Magurany, C. E. Strouse, Inorg. Chem., 21, 2348 (1982)
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Last updated: 12/6/2002