Simplification of the crystal structure of ACOKIM, 4-iodo-2,3,5,6-fluoro-benzonitrile.
Home / FAQ / Simplification of the crystal structure of ACOKIM, 4-iodo-2,3,5,6-fluoro-benzonitrile.
1. Open the database ACOKIM and compute the adjacency matrix using the AutoCN method Domains. Check the options to determine specific bonds A-X…B with participation of iodine atoms.
2. Open IsoCryst and find the 4-iodo-2,3,5,6-fluoro-benzonitrile connected by specific C-I…N bonds. Check the IsoCryst option Bonds/Show/Specific to see the specific bonds. Compute the C-I…N angle that is equal to 167.28°.
3. Simplify the crystal structure to its underlying net in standard representation. Check the ADS option Topology/Bond Types/Specific = Mol. Run ADS and press the Whole Molecule button.
4. Look at the simplified net and be sure that it contains inclined chains of molecular centroids. Come back to the initial structure and find the chains in it.
Exercise: simplify the structures from the database CYANAM_TISRAO. Which structures contain hydrogen or specific bonds? Which of them is interpenetrating?
Answer: Structure of CYANAM01 contain two interpenetrated H-bonded frameworks (hydrogen bonds H1-N2, H2-N2) with topology of 4-coordinated net dia. Structure of TISRAO contain a Halogen bonded framework (Halogen bonds = Specific bonds I1-I2, I1-I3) with topology of 4-coordinated net cds (to obtain cds topology you should remove 2-c nodes using the simplify adjacency matrix, see Task 2, Example 2).