Edge-net simplification of the crystal structure of SAYNAI, 3-(chloroacetamido)pyrazole.
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1. Open the database SAYNAI and compute the adjacency matrices for the crystal structure of 3-(chloroacetamido)pyrazole (AutoCN Method: Domains; hydrogen bonds have to be found).
2. Simplify the crystal structure to its underlying net in standard representation using the method Whole molecule. What is the coordination number of the molecule?
3. Turn to the initial SAYNAI database. Run IsoCryst and find the three molecules connected with a given one. For this purpose, toggle off Take Hydrogen bonds, select a molecule and grow it. Then toggle on Take Hydrogen bonds and grow the structure one time. Toggle off Take Hydrogen bonds again and grow surrounding molecules. Show atom names.
Pay attention that the molecules form dimers with pairs of molecules connected by H-bonds.
4. Get a simplified net were the nodes are the centroids of the dimers (synthon simplification, see e.g. Baburin, I. A.; Blatov, V. A.; Carlucci, L.; Ciani, G.; Proserpio, D. M. Cryst. Growth Des.; 2008; 8; 519-539). For this purpose we will change the type of the hydrogen bonds N2…H2 (in valence, specific or Wan der Waals bond type) to distinguish it from other hydrogen bonds. Duplicate the entry so you can make any changes and save the original structure: right-click and choose Duplicate command (or also form the top menu bar: Compound/Duplicate). Open a Crystal Data window for the duplicate entry. Go to Adjacency Matrix tab and change the type of the bonds to valence. Add also some comments on the General/Formula field separated by a slash, for example write: " / dimers ". This allows keeping track of all the changes made.
Save the changes and simplify the structure again using the Whole Molecule approach, now the "isolated" molecules are dimers (related by the synthon). What is the coordination number of the dimer?
5. We can obtain the net of dimers starting from the simplified net in the standard representation. We need to find the "dimers", here represented by the shortest connection. Also the other two long connections are related by symmetry, so the set of "bonds" is divided in 1+2. The single independent "bond" must be the dimer. Now we can do a simplification, changing the two equivalent bonds into H-bonds, making the "dimer" isolated, hence the standard representation can be done. Turn to the SAYNAI_c database and open a Crystal Data window for the first record. Change the type of two equivalent bonds to H bond.
Save the changes and simplify the net (Choose Whole Molecule while simplification procedure). The resulting net is a partial edge net with dia topology with respect to the initial net since its nodes correspond to some edges of the initial net. And in this case is equal to the "dimer" net. See Appendix 2 for details and definitions.