It may help to better understand the process of defining a rigid body by following an exercise, where I define two residue rigid bodies. Later in this chapter I will then place these rigid bodies into a metal-organic framework (MOF) material where the two rigid bodies each coordinate a transition-metal atom. The two moieties to be used here are a pyrazine-2,3-dicarboxylic acid ion and a 4,4’-bipyridine (bipy) molecule.
A chemical diagram for the pyrazine-2,3-dicarboxylic acid ion is shown in Fig. 26.6. From this we need to obtain a set of three dimensional set of coordinates, which can be done by locating where this molecule has been used in a crystal structure, but my preference is to generate an idealized version of the ion. The two free options for this mentioned earlier in §26.3.2 are the Avogadro program or the MolDraw website. In either of these programs, we can “draw” the chemical diagram to generate the chemical representation for this, but an easier way to do this is to use the SMILES/indexPSMILES—textbf (simplified molecular-input line-entry system) name, which encodes the chemical connectivity. The SMILES notation for the pyrazine-2,3-dicarboxylic acid molecule is readily available from a web search, but the SMILES notation for the deprotonated ion, C1N=C(C([O-])=O)C(C([O-])=O)=NC=1, is likely a bit harder to find. I generated this from the SMILES for the molecule and then deleted the two H atoms.
If this SMILES string is entered into Avogadro using the Build/Insert/SMILES... the ion will be created. It can then have the geometry optimized using the Extensions/“Optimize Geometry” menu command, and then the coordinates can be written for GSAS-II using the File/“Save As...” command (be sure to select the XYZ format).
While I prefer Avogadro as giving more accurate bond distances and angles, with MolDraw, use their SMILES to 3D Structure Converter (https://www.moldraw.com/tools/free-chem-tools/smiles-to-3d-structure-converter.html) where you can paste the SMILES entry on the left, click on the “Render 3D” button in the middle of the browser window and see the molecule generated in 3D to the right. Click on the “XYZ” button in the downloads section under the 3D visual and an .xyz file is downloaded.
Then we want to create a rigid body with these coordinates in GSAS-II, but there is a minor problem if we want to do this with a new project, because an empty project file does not have any of the overall data tree entries. One must either add a phase or a histogram to the project, and when that is done, the Rigid Body data tree entry will be present. The simplest way to address this is to use the Data/“Add new phase” menu command to create a phase and then use the Data/“Delete phase entries” menu command to immediately delete it. However, since you likely have diffraction data to use with the rigid body, you can import that and this will also create the Rigid Body data tree entry.
To create this rigid body, click on the Rigid Body data tree entry and click on the “Residue rigid bodies” tab. Then use the “Edit Residue Body”/“Import XYZ” menu command and select the file that was created with Avogadro or MolDraw. The data window will appear as in Fig. 26.7. Note that this rigid body is not likely to occur in a high-symmetry location in a lattice, as this group of atoms can only have any internal symmetry (one or two mirror planes) when the torsional rotations for the four carboxylate O atoms are matched. Since there is no symmetry present, we do not need to worry about the axes orientations. Nonetheless, to show how the controls on this data window are used and because I just prefer to have nicely oriented axes, we will select the C1 to C3 vector as the x axis and the C1, C3 and C12 atoms to define the x-y plane, with the y-axis to be in the approximate direction of C1 to C12 by selecting the A-B-C orientation reference atoms to be C1, C3 and C12, as seen in Fig. 26.8. Press the “Plot” button and the ion will be displayed as in Fig. 26.9.
There are still more things that need to be done in this data window. The torsions need to be added to the carboxylate groups, since they depending on the material, they will have very different orientations that optimize bonding. This is done by invoking “Edit Residue Body”/“Define torsion” menu command. For one torsion angle, use C3 as the origin and C4 as the pivot in the successive input windows. (Note that in the second window the choices are the three atoms bonded to C3.) For the other torsion, use C7 as origin and C8 as pivot. You should change the name of the rigid body to something else using the text entry box in the upper left. While not required, pressing the “Center RB?” button will place the origin at a location close to the center of mass. This is useful, as this will simplify TLS fitting (see §26.9), should we choose to do that later. After these actions, the ion will be displayed as in Fig. 26.10 in the graphics window, where the view point has been moved. The data window appears as seen in Fig. 26.11. If you will use this rigid body in other GSAS-II projects, you are recommended to save it into a file. This is done with the “Edit Residue Body”/“Save rigid body” menu command, which writes a file with extension .resbody. That file can be read in to a different project using the “Edit Residue Body”/“Read rigid body” menu command.
A chemical diagram for the 4,4’-bipyridine (bipy) molecule is shown in Fig. 26.12. As before, we need to obtain a set of three dimensional set of coordinates, and again this can be done using the Avogadro program or the MolDraw website. The SMILES notation for the 4,4’-bipyridine molecule is readily available from a web search, C1=CN=CC=C1C2=CC=NC=C2. The same process is used as before in either Avogadro or MolDraw, or any other forcefield or quantum-mechanical modeling program. Interestingly, the Avogadro program creates a planar molecule, while MolDraw provides a molecule with a significant torsion rotation on the bond between the two pyridine groups. Either is fine for our purposes.
Unlike the pyrazinedicarboxylic acid ion in the previous section, the bipy molecule will always have an internal center of symmetry, regardless of the torsion angle setting. In fact, we will need to place this internal center of symmetry at a specific location in a structure later in this chapter. For this example, we will create two slightly different versions of the bipy molecule that will be used later in the chapter to demonstrate aspects of how GSAS-II handles internal symmetry when rigid bodies are incorporated into the structure. In one case, the rigid body will contain only one-half of the molecule. e.g. the unique atoms, and in the other case, we will include both C atoms on either side to the center of symmetry so that the rigid body contains a redundant atom. There is a third option, where we include all the C and N atoms in both rings, but then we would need to delete the H atoms from the torsional riding atom C and that gets a bit more complex than is needed.
Since we will want to place the origin in a location between two atoms, the “Import XYZ” menu command that was used prior will not work for us here. We will instead use the “Edit Residue Body”/“Extract from file” menu command which offers more control over the origin and axes location.
When the “Edit Residue Body”/“Extract from file” menu command is used, the first window that is opened asks for the format of the file to be read. In this case, we will read an XYZ file created above, so XYZ is selected. In the next window, select the .xyz file written previously. The contents of the data window will display the atoms read from the file, as seen in Fig. 26.13 and the graphics window contents are seen in Fig. 26.14. This visualization will be very useful as we now need to select only the atoms we need for the next step. Unselect atoms 7 through 11 (C7-C10, N2) and 16-19 (H5-H8), leaving only one phenyl ring and the first carbon of the second ring, as seen in Fig. 26.14. Once the atoms are selected, press the “Continue” button at the bottom of the data window.
The data window is then updated, as seen in Fig. 26.16 and the graphics window contents are seen in Fig. 26.17. This where we have the ability to determine the origin and axes, as was discussed in §26.3.1.0.
Here we want to place the origin midway between atoms 5 and 6 (C5 and C6), so press the “Toggle” button, so that no atoms are selected, and then select C5 and C6, and finally press the “Set origin” button. Note that the coordinates for these two atoms now add to zero. While for this use, setting the axes is optional, the body will be easier to understand if we place the atoms in one ring into the x-y plane. Select all atoms using the “Set All” button and then press the “Place in plane” button with “xy” selected. Note that z is very close to 0. for all of the selected atoms, confirming that they all do lie in a plane. Finally, we will want to place the x-axis along the C5-C6 bond, so now select either one of those two atoms (but not both as their average position is the same as the origin). Press “Set All”, then “Toggle” and select C5, and finally press the “Set origin” button. Note that C5, C6 and N1 now lie on the x-axis as both y and z are now approximately 0.
Finally, to create the rigid body, we want to remove the one duplicate atom (C6) from the body, so we will want to select all the atoms but that to create the rigid body. Again press “Set All” and then unselect the C6 atom. The graphics window will now show the molecule as shown in Fig. 26.18. To create the body press the [... create] “a Residue Body” button and the second residue body is created. The data window then appears as was seen in Fig. 26.5, except a new control at the top of the window allows you to select between the two rigid bodies that have now been entered. The body will be initially named for the XYZ file, but rename this to “half-bipy”.
To illustrate how GSAS-II handles “duplicate” atoms, lets create a rigid body that has both C5 and C6, even though the two atoms will be related by symmetry once the body is inserted into the structure. For this follow the instructions from the previous Half-molecule Bipy section (§26.4.2.0), except that in the final paragraph when we create the rigid body, we want to retain all atoms in the body, including C6) , so we will want to select all the atoms. Again press “Set All.” The graphics window will now be similar to Fig. 26.18, but all atoms will be selected. To create the body press the [... create] “a Residue Body” button and the third residue body is created. Again the data window then appears as was seen in Fig. 26.5, except a new control at the top of the window allows you to select between the three rigid bodies that have now been created. The body will be initially named for the XYZ file, but rename this to “half-bipy+1”.
