For this, we will approximately duplicate the structure model used in the MOF structure from Silvana Urcia-Romero et al. (2022), Crystal Growth & Design, 2382–2391.1. The CIFs from this paper can be downloaded for free from the CCDC 2. Any of the CIFs from that paper will do. After the coordinates are read, and the “Draw Atoms” or “Draw Options” phase tab is selected, the structure will appear as shown in 26.22.
To insert the pyrazinedicarboxylic acid ion rigid body that was previously created, select the “RB Models” phase tab. If for some reason the structure is not plotted, select the “Draw Atoms” or “Draw Options” phase tab and then return to the ‘RB Models” tab. The ‘RB Models” tab posts the menu labeled “Edit Body” and from that menu select the “Locate & Insert Rigid Body” menu command. This will open a window where one can select from the three rigid bodies that were previously defined. The body we want was called “pzdc”; select this and press OK. The data window will appear, as seen in Fig. 26.19 and the structure visualization will appear as shown in 26.23, where now the rigid body is also displayed.
Our next task will be to orient the pyrazinedicarboxylic acid rigid body on the approximate positions of the atoms that are in that group. This will be very hard to see with these atoms shown as space-filling. Press the “Ball & Sticks” or “Sticks” button to change the display according to your preference. As noted before (in §26.5) we can identify atoms to be paired by highlighting them. The most easily identified atoms to me are the ring nitrogens and the carboxyilic carbons. In Table 26.1 I have provided a list of atoms to be paired.
| rigid body | structure |
| N2 | N13 |
| N11 | N14 |
| C4 | C6 |
| C8 | C7 |
Assign these four atoms, as seen in Fig. 26.24. Then press the “Set both” button and note that the rigid body is now largely superimposed, as seen in Fig. 26.25 and the assignments table (Fig. 26.26) now shows the C and N paired atoms are all within a few tenths of an Ångstrom. The O atoms can be brought into better agreement by adjusting the torsion angles with the sliders.
Finally, complete the rigid body insertion process by pressing the “Add” button. The two sets of superimposed atoms are replaced by a single set, where the bonds are now colored in orange, to indicate that this is a rigid body, as seen in 26.27. The positions of the rigid body atoms are updated in the Atoms tab and the coordinates and \(\rm U_{iso}\) values are shaded to indicate that these values are generated from the rigid body, as seen in Fig. 26.28.
Before beginning this example, you should save the GSAS-II project so that we can return to this point, where only the first rigid body has been inserted. This rigid body is a bit different from the previous because it has internal symmetry. It is duplicated by a center of symmetry. This \(\overline {1}\) located at (0,\(\frac {1}{2}\),0), so this is where the origin of this rigid body needs to be placed.
Again, select the “RB Models” phase tab, if needed. To insert the bipyridine molecule rigid body from the “half-bipy” rigid body that was previously created; again use the “Edit Body”/“Locate & Insert Rigid Body” menu command. This will open a window where one can select from the three rigid bodies that were previously defined. The body we want was called “half-bipy”; select this and press OK. The data window will appear similar to what was seen before (Fig. 26.19) and the half-molecule bipyridine rigid body is also displayed.
To set the origin location, change the “Origin” y value to 0.5 at the top of the data window and select the “Lock” selection so this does not get changed accidentally. At this point, given that the origin is fixed, it is not that hard to use the Alt+Left mouse and Alt+Middle mouse drag motions to align the rigid body to the atoms in the structure. This will not be easy to explain in writing how to do this, but let me try. Note that the following paragraph is optional as the following one duplicates the alignment process.
The initial plot appears with the rigid body approximately opposite where we want it, as seen in Fig. 26.29. Holding the Alt key down, drag the middle mouse button (Alt+middle mouse) vertically until the two rings are approximately aligned, as seen in Fig. 26.30. While this looks to be fairly reasonable alignment, rotating the view by approximately \(90^\circ \), by dragging with the left mouse button (no Alt key) produces a view that shows the rings are not in the same plane, as seen in Fig. 26.31. Rotation of the rigid body using Alt+left mouse, will bring the rings to be closely overlapped.
The other way to align the rigid bodies is to assign atoms, as was done before. Note that the rigid body N1 atom must be paired to the N15 atom in the structure. The two rigid body atoms bonded to N1 are C2 and C3, which can be seen from the atom labels in the plot. In the structure, it can be determined that C8 and C12 are bonded to N15 using the “Crystal Highlight” option. As before, assign these atoms. Assign rigid body atoms C2, N1, and C3, respectively, to structure atoms C8, N15, and C12, respectively, and press the “Set Orientation” button. (Note that it does not matter if C8 is assigned to C2 or to C3, so the two C atoms assignments could be reversed.)
Finally, press “Add” to complete the insertion of this rigid body. The half of the bipyridine molecule will now appear with orange bonds, as was seen before for the pyrazinedicarboxylic acid.
The last example will be to repeat the previous rigid body insertion, but to use a version of the rigid body that includes atoms that are duplicated by symmetry. The rigid body insertion in previous step needs to be reversed before this step can be performed. Either reload the GSAS-II project (.gpx) file that was saved in the last step or delete the rigid body insertion by selecting the half-bipy:0 body on the “RB Models” tab and then press the “Delete” button.
Follow approximately the same process as before to insert the bipyridine molecule rigid body. Again use the “Edit Body”/“Locate & Insert Rigid Body” menu command, but this time use the “half-bipy+1” rigid body that was previously created, . This will open a window where one can select from the three rigid bodies that were previously defined. Again, set the origin location by changing the “Origin” y value to 0.5 at the top of the data window and select the “Lock” selection. Assign rigid body atoms C2, N1, and C3, respectively, to structure atoms C8, N15, and C12, respectively, and press the “Set Orientation” button.
One important extra step is needed relative to the previous example. While atoms C1-C5, N1, and H1-H4 match atoms in the structure, there is no matching atom for C6. The default action would be to pair this atom with one of the \(\rm CO_2\) C atoms, but here we need is for GSAS-II to add this atom to the structure when the rigid body is inserted. From the pull-down menu in the “Assign as atom” for C6, select the “Create new” option. Then press the “Update Assignments” button and the assignments table should appear, as in seen in Fig. 26.32.
After the “Add” button has been pressed, the rigid body information is updated in the Atoms tab, which appears as in seen in Fig. 26.33. Note that the C6 atom in the rigid body has been added to the atoms list as atom #29 (the second atom labeled as RbC29.) Note that since this atom is a symmetry duplicate, the occupancy has been set as zero during the insertion process.
