Creating a rigid body
TOPAS includes a 'rigid-body editor' which can be used to create and test rigid bodies. There are some examples of rigid bodies in the 'C:\TOPAS-6\rigid' folder; if at any point you get stuck while editing the z_matrix for this section, it may help to look at some of the examples in this folder.
In TOPAS, select 'Tools' > 'New Rigid-body editor Window'.
Click 'Load / Hide' to bring up the file load dialogue, navigate to the file 'para_partial.rgd' and double click on it to open it in the editor. This is a partially completed
z_matrixdescription of an idealised paracetamol molecule. Notice how bond lengths (prm !rCC 1.30,prm !rCO 1.20etc.) and dihedral angles (prm !dCOH 90,prm !dCNC 90etc.) are defined as parameters at the top of the rigid body. These parameters also have sensibleminandmaxvalues applied to them. Try changing a few of these parameters and click Updateto see the effect on the rigid body.
Edit the
z_matrixto add the C=O and CH3 groups on the end of the molecule. Use the naming scheme shown below (i.e. add O2, C8, H8, H9 and H10). It is best to add one site at a time, then click Update to see the effect on the rigid body. This will allow you to fix problems as you go. The completed structure should look like this:
If you are having problems adding atoms to the rigid body, there are some hints here at the bottom of this page.
Click 'Save As' and save your new .rgd file of the completed paracetamol rigid body on your computer.
Matching a rigid body to a known structure
Although we now have a rigid body description of the paracetamol molecule, we don't yet know the translations / rotations needed to get the molecule where it should be within the unit cell. We can use TOPAS to optimise the position of the paracetamol rigid body to that of the known atomic positions from a .cif file; thanks to Prof Simon Parsons, University of Edinburgh, for this tip! In order for us to do this, it is easiest if the naming conventions in our rigid body are the same as those from our .cif. The site names in the rigid body described above already match those of the .cif file, so in this case we can carry out.
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You now have the translate and rotate values needed for a good starting point for your PDF refinement in the next part of this tutorial.
Hints
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First we need to add the O2 atom, which is connected to C7 by a bond distance with a parameter name of Next we need to add the C8 atom, which is connected to C7 by a bond distance with a parameter name of Finally we need to add three H atoms (H8, H9 and H10), all connected to C8 by a distance of parameter |
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