Ring-net simplification of the crystal structure of XEHKIE, 2,3,5,6-tetrachloro-trans-1,4-diethynylcyclohexa-2,5-diene-1,4-diol 


  1. Open the database XEHKIE and compute the adjacency matrices for the crystal structure of it (AutoCN Method: Domains; hydrogen bonds have to be found).
  2. Simplify the crystal structure to its standard representation using the method Whole molecule. What is the coordination number of the molecule?
  3. Turn to the initial XEHKIE database. Run IsoCryst and look for H-bonded tetrameric synthons (O–H)4.

    Close IsoCryst and separate the synthons in the structure. For this purpose, change the type of hydrogen bonds to valence, and the type of C4–O1 bonds to H bond. Save the changes and run IsoCryst again to be sure that the synthons are really separated.

  4. Simplify the crystal structure and pay attention that there are 2-coordinated nodes corresponding to the residues of the molecules connecting the synthons. Contract the 2-coordinated nodes transforming them into edges. For this purpose duplicate the record, go to the duplicate and run Compound/Auto Determine/Simplify Adjacency Matrix procedure.

In the column Remove is possible to select the nodes/atoms to be removed

  • Selecting 0–connected the atoms/nodes isolated are removed;
  • Selecting 1–connected all atoms/nodes connected only with one link (terminal) are removed (e.g. all the hydrogens of benzene rings, all "dangling" atoms).
  • Selecting 2 – connected all bridge atoms/nodes will be transformed into edges.
All the procedures are cyclic, i.e. if new 0-, 1- or 2-connected nodes emerge during the simplification, they will be removed in turn.

In the column Type is possible to select on which kind of interaction the simplification above applies. All the interaction left unselected will not be considered, and will be discarded in the final picture. For example if we want to simplify a network built by H-bonds (we want to keep all the H-bonds in the final simplified net) we must select both Valence and H bonds.

WARNING: it is better to make a duplicate of the structure in use before doing any simplification; the process is irreversible.

Press Ok and be sure that the 2-coordinated nodes are contracted. The resulting net is a partial ring net with respect to the simplified net in the standard representation since its nodes correspond to some rings of the initial net. Pay attention that both standard representation and the partial ring net are 4- coordinated, but have different topologies that will be proved in Module 5. See Appendix 2 for details and definitions.

Tips: The Compound/Auto Determine/Simplify Adjacency Matrix procedure is a very useful procedure to be used quite often, even at the beginning. It is always easy to look at a molecule if all the dangling atoms (1-connected) are removed. So, after all the bonds/contacts/H-bonds are found via AutoCN , it may be useful to duplicate your structure and simplify it. The IsoCryst representation will be more legible. See for example the simplified picture for XEHKIE (with some bond/color changed... try!), the complex 2,3,5,6-tetrachloro-trans-1,4-diethynylcyclohexa-2,5-diene-1,4-diol C10H4Cl4O2 is represented by a much simpler C6(OH)2.

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