Monthly Archives: November 2018

Creating images of augmented nets

Making beautiful pictures of beautiful nets in augmented version

There is one requisite in order to be able to create and make great looking images of augmented nets: A software package that has the option to make and show customizable coordination polyhedra. Two of the most frequently used (commercial) packages for this purpose are Diamond and CrystalMaker. Although the gorgeous freeware VESTA has also some capabilities in that respect it is, unfortunately, not suitable.

Okey, let’s begin. In this tutorial we want to make an image of the net reo-a.

 

1. In general, you need the structural information of the net-a net, i.e. the space group of the net and the fractional coordinates of the nodes. There are two possible sources:

a) RCSR (please checkmark the “including augmented version” option) – for reo the search is unsuccessfull

b) ToposPro is delivered with a database called “idealnets.cmp” (search with your File Explorer to find this file). Open this database, which contains approx. 3000 nets, within ToposPro and look-up, if you can find the desired net. Again, for reo-a there is no entry. But, if the net from which you want to make a nice-looking figure is present, proceed with step # 15.

2. Even if the coordinates of the augmented version of a net is not in your database “idealnets.cmp”, it is very likely that the coordinates of the basic net are available in the ToposPro database “idealnets.cmp”.

3. Create a new database in ToposPro. Name it “net-a.cmp”.

4. Copy the entry of choice (here reo) from the “idealnets.cmp” into the newly created database. Now we can create the augmented variant within ToposPro.

5. Go to “Compound – Auto Determine – Bond Midpoints”. Repeat this procedure, choose “Compound – Auto Determine – Bond Midpoints” again.

6. Run ADS in the standard simplification mode (Save Simplified Net/Standard), but with the option “Contract Atom” under the tab “Topology” checked.

– select all atoms except carbons
– select all nitrogen atoms
– select all carbon atoms

7. You will get a new database “net-a_c” containing one entry. This entry has to be modified a little bit.

8. Remove all 2-c boron atoms: Choose “Compound – Auto Determine – Simplify Adjacency Matrix” – remove all 0-, 1- and 2-coordinated vertices.

In the case of the reo net the result will look like this:

9. It looks quite okey, but two things are not correct. There are some additional bonds and it is probably not the most symmetrical representation. Remove the additional bonds by modifying the corresponding adjacency matrix. Turn the additional bonds into “No bond”. This looks better:

 

10. Now, try to maximize the symmetry with the help of Systre (which is part of the package Gavrog). Export the file from ToposPro into the Systre format (*.cgd).

11. Run Systre and open the file net-a.cgd. Systre tries to relax the nodes so that a) the average bond length is 1.000 Å and b) that the symmetry of the net is maximized.

12. After a few seconds Systre has finished and you can save the net with the highest possible symmetry by choosing “Save as…” and by specifying the format as “”Embedded nets type (*.cgd)”. Name it for instance “net-a_systre_out.cgd” to distinguish between the input and output file.

13. Import the Systre file into a new database in ToposPro. Run IsoCryst to check your results:

That looks good.

14. Export this net as a CIF. Now, CrystalMaker comes into play…

15. Run CrystalMaker and Import the file net-a.cif. It will look like this:

16. Expand the view so that all polyhedra are clearly visible, remove additional bonds by adjusting the bond length. Then select all atoms of one kind of polyhedron and choose “Selection – Make Polyhedron…”. A new Centroid is created, here coloured in blue:

17. Now, only some slight setting modifications have to be done – choose “Model – Model Inspector…”. In the Atom tab all new centroids (Zz and so on), i.e. the polyhedra have to be rendered as “Rendered solid”, all atoms as “Stick bonds”.

18. In the Bond tab, all bonds in which centroids are involved should be blanked out, and for the bonds between atoms choose an eye-catching colour:

19. A last step is necessary – choose “Model – Polyhedral” (and adjust the stick percentage…).

  1. Done!