Home / FAQ / Simplification of the H2S crystal structure.
1. Open the database H2S and compute the adjacency matrix taking into account S–H…S hydrogen bonds. For this purpose, include sulfur atoms into the lists of A and B atoms in the AutoCN options.
2. Simplify the crystal structure of H2S to its standard representation (centroids of molecular groups are the nodes of the simplified net). For this purpose, set the ADS options: Topology/Bond Types/Valence = At.; H bonds = Mol. This means that any group of atoms connected by valence bonds is considered as a molecule, and the isolated molecules are linked by hydrogen bonds.
Run ADS and press the Whole Molecule button to choose no central atoms and to consider all atoms equally composing molecules.
To simplify the molecular structures in one step select the records pressing Insert key or Shift+↓ or Ctrl mouse click, open ADS window and leave empty the line Central Atoms in ADS Options/Continuous tab.
Check the coordination number of nodes in the simplified net and molecular coordination number for H2S in initial structure. What numbers of molecules are H-bonded with an H2S molecule? Find that there are two interpenetrated 3D nets in the simplified structure using IsoCryst, and find the two nets also in the not simplified representation. One single net is shown here:
Try to change the colors of the atoms with the Magic wand (selected in the figure above) and the thickness of the H-bonds in the IsoCryst Option / Bonds window clicking on the left column (Thick)
Exercise: simplify the structures of H2O polymorphs from the H2O database. Set Resonance bonds for
disordered AutoCN option to take into account resonance O–H↔H–O hydrogen bonds. To simplify the molecular structures at one step remember to leave empty the line for Central Atoms in ADS Options/Continuous tab.
Answer: The polymorphs I, II, III, IV, and VII for H2O have 4-coordinated underlying nets with topological types lon, ict, kea, icf, and 2-fold interpenetrated dia respectively.