Open the database BEQXEB and compute the adjacency matrix using the AutoCN method Domains.
Make a duplicate of the record, add comment /simplified to the formula (use Crystal Data window) and run the Compound/Auto Determine/Modify Adjacency matrix procedure with parameters: Atom A = Nm; Atom B = Nm; Bonds to Change = Valence; Change To = None; Apply Parameters To = Change Bonds. As a result all bonds between non-metals (X) will be broken and the cluster skeleton containing only Mn–Mn or Mn–X–Mn bonds will be separated.
Run Compound/Auto Determine/Simplify ADM with parameters: Atoms = Nm; Remove = 0coordinated + 1-coordinated; Type = Valence. As a result all non-metal atoms except bridges between metal atoms will be removed.
Run Compound/Generate Representations with parameters: A = Me; Duplicate checked; all other parameters are default.
You generate a database with all possible representations of the clusters. In this case two representations created: the first one (Set #2) is the initial structure (all bonds have Ω ≥ 11.00%); the second one (Set #1) does not contain weaker Mn–O bonds (all bonds with Ω < 16.50 % were broken). Open the Crystal Data window for the last record, go to the Adjacency matrix tab, right click and show the Information window. Be sure that the distances of the broken bonds (No bond) vary in the range 2.24-2.39Å, i.e. there is no chemical reason to ignore these bonds. So we will use the first representation (Set #2).
Run ADS in the Simplification mode; Simplification Method = Standard; Topology Flags = Contract Atom.
After running select all Mn atoms as Central Atoms, all Mn atoms as Atoms to Contract to and all oxygen atoms as Atoms to Contract. As a result you get the cluster skeleton in a new database BEQXEB_c. Draw these wheel-lite skeletons in IsoCryst.
Run ADS in the Classification mode and be sure that the skeleton has the 3,5,6M84-1 topology (see Appendix 5 for details of the NMk-n nomenclature).
Go back the initial record in the database BEQXEB. Look at the Adjacency Matrix tab, Information window and be sure that there are “valence” contacts C–C of length more than 3Å and O–O of length about 2.8Å. Such contacts can appear the structure is not completely solved (in this case, chloroform solvent molecules are not allocated). Break all these bonds with the Compound/Auto Determine/Modify Adjacency matrix procedure keeping the same options as before, but specifying Bond AB Length = 2:100.
Run ADS with the same options as at step (5). As a result you get the cluster skeleton with additional polyatomic Mn–Xn–Mn bridges. Be sure that this topology is novel. Compare the coordination numbers of Mn atoms in the two skeletons. What are the differences? With IsoCryst find the Mn atoms that are linked by only polyatomic bridges.
In IsoCryst, select the skeleton and save it in the BEQXEB.gph file (Select/Save Selection, file type: *.gph). You may then use this file to identify skeletons (or parts of more complex skeletons) of this topology in other compounds using the SubGraph filter (see Module 3, task 2).
For further details on the analysis of polynuclear coordination clusters see “A method for topological analysis of high nuclearity coordination clusters and its application to Mn coordination compounds” G.E. Kostakis, V.A. Blatov and D.M. Proserpio, Dalton Trans., 2012, 41, 4634.