Step 1 - Import the CIF
Our first task is to import the CIF file - Dissolve has a wizard to help you do this, and which also allows some tidying of the imported coordinates, replication of the unit cell to create a supercell etc.
Species ⇨ Import ⇨ From CIF…
Select the relevant CIF file (7108574.cif) and then click
Dissolve will parse the CIF and display some basic information from it such as the authors (Peikert, Hoffmann, and Froba), publication reference, and space group (Fm-3m). Click when you’re ready
If the space group can’t be detected from the file, or Dissolve isn’t sure which one to use, the wizard will show an additional page asking for clarification.
The wizard will now be showing you the unit cell and its contents as determined from the CIF (you might need to zoom out or rotate the view a bit to see something meaningful). On this page you have some broad choices on the tolerance for removing overlapping atoms (which arise from defined symmetry generators creating symmetry-identical copies), for how connectivity between atoms is calculated (either by Dissolve or from defined bond distances in the CIF) and which structural assemblies / groups (typically arising from disordered moieties in the determined crystal structure) are used.
Basic Cu-BTC unit cell
The default options get us most of the way there, but it’s instructive to take a look at the Assemblies that were detected in the CIF. An assembly is a set of symmetry-unique atoms that have one or more configurational states (i.e. they have different positions) and can represent disorder, different conformers of molecules, or even completely different molecules within the same unit cell. If you look at Peikert, Hoffman, and Froba’s original paper you’ll see that the focus is on an amino derivative of the BTC linkers, and both the original Cu-BTC and the amino-substituted structure are represented in the CIF. The default assembly/group combination of Global/Default, B/Default and A/1 gives the normal Cu-BTC structure, while disabling A/1 and enabling B/2 and C/2 gives you the amino-substituted version.
Before we proceed, make sure that the default Cu-BTC groups (Global/Default, B/Default, and A/1) are the only ones enabled.
Now, if you look closely at the crystal structure you’ll see “extra” oxygen atoms attached to the copper sites:
Dangling oxygens on Cu sites
These are in fact from coordinated water molecules present when the crystal structure was determined - the water hydrogen atoms are not present in the CIF data. We will remove these oxygen atoms since we want a perfectly “dry” unit cell.
Click in the wizard to move to the Clean Structure page
The Clean Structure page has several options for cleaning up various aspects of the structure we currently have, for example removing free atoms/ions. We want to use the option to remove water molecules, which will also remove terminal oxygen atoms based on the assumption that hydrogen positions were not available in the CIF. So:
Enable the Water and coordinated oxygen option
You should see those terminal oxygen atoms disappear from the structure, leaving us with a “pure” Cu-BTC framework. There are a couple of pages left in the wizard which allow us to create a supercell from the unit cell,
Click in the wizard to move to the Create Supercell page. For production simulations you will probably want to work on something bigger than the unit cell, but here we’ll keep things limited in size
Click to move to the final page of the wizard, the Species Partitioning page. We have a couple of options here of what to actually generate in terms of the species. The default option Periodic Framework creates a species encompassing the entire periodic (super) cell, which is what we want
Click to complete the wizard and generate the Cu-BTC species
Our new species not only contains the atoms of the framework, but also the unit cell (or supercell) definition - later on we can use this as our configuration’s box rather than defining it ourselves.