C637 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.
- The hit structures should be saved in FDAT format so that they can be read
properly by Cerius2 (version 3.5).
- One of the two structures for FeCl(SANE)2 (1974 paper) you will
find in the database is incorrect. The positional parameters of some atoms are
faulty. However, this doesn't affect the discussions in
this problem set.
Most of the following exercises can be done with the 3D
Visualiser in the ConQuest program. However, Cerius2 is a more powerful
program and has more features that you may want to utilize for this
problem set (e.g., stereo view, viewing more unit cells, measuring distances
for more than one pair of atoms simultaneously, etc.).
- Now, enter the Cerius2 program and display the unit cell of
FeCl(SANE)2, first as a stick figure, then with cylinder bonds,
then in a space-filling representation. For each representation, rotate the
unit cell and view it from many perspectives.
- Using the "evaluate" option and stick bonds, obtain the intramolecular
Fe-Cl and Fe-O distances. As a check, compare these to those reported in the
publications. Now calculate the two shortest intermolecular Fe/O
contacts. 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.
- More unit cells should be included in the display to measure distances
between the atoms in the molecules in different cells.
- The Geometry/Close Contacts feature can be utilized to implement
multiple distance measurements simultaneously. To measure intermolecular
Fe/O distances:
- Set the Selection Target popup to Atom and the Selection
Criterion popup to EI on the
toolbar.
- Click an O atom then <Shift>-click a Fe atom to select
all O and Fe atoms.
- Click Geometry/Close Contacts to open the Close Contacts control panel. On
this panel, choose between SELECTED atoms; choose
DISTANCE for Contact Criteria and set Cut-off to 7 (for PESALF01, or 4 for
PESALF10); choose FRAGMENT for Contact Exclusions and ensure
Annotate close-contacts is checked.
- Hit the Monitor close-contacts button.
- Now view, using the full screen area, the unit cell with stick bonds. 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:
- Hit F2 key on the keyboard to turn the full screen display on or off.
- More unit cells should be included in the display to check the interactions
between molecules in different cells.
- The stereo view feature can be utilized for this purpose (note: Splatter
is the only computer in room A701 which is equipped with the stereo view accessory):
- Wear the stereo eyewear (please be careful, it is fragile and expensive) and
turn it on by pushing the button on it.
- Hit F4 key on the keyboard to turn the stereo view on.
- Move and view the structure in usual way.
- When you are done, turn the eyewear off by pushing the button again -- be
sure that you don't see the structure in 3D any more, then hit F4 key to turn
the stereo view off.
- Put the stereo eyewear back to the box !!
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: 03/21/2001