Searching for all structures containing/not containing ligands with sulfur atoms 


Algorithm:

1. Open the database ligands and compute the adjacency matrices for all structures using the AutoCN method Domains (the options concerning non-valence contacts can be unchecked since we are interested only in coordination bonds).
   
   
   
   
2. Select all structures again, open the ADS program and specify the options Cont.Calc., Dimen.Calc., Save CCF & Ligands and Central atoms = Me (other options should be unchecked for speed).
   
   
   
   
3. Show the column of RefCodes in the database window and open a Crystal Data window for the second record (BAYDIO). Be sure that according to the name of the compound it contains polymeric complex groups with cadmium atoms, succinato and aqua ligands as well as not coordinated water molecules.
   
   
   
   
4. Open the Comment tab the Crystal Data window. You see the information on the central atoms and ligands after the keywords CENTAT and LIGAND:
   
   
   
   This informs you that there are two inequivalent complexing cadmium atoms (Cd1 and Cd2), two inequivalent bridge µ₃ ligands C4O4 (succinato), four inequivalent terminal ligands O (aqua) and one not coordinated molecule O (water). Pay attention that hydrogens are not allocated in the structure. The coordination types of ligands are given in square brackets; the following rules are used:
   
   • the ligand denticity (number of donor atoms used to connect to metal atoms) is designated by capital letters M, B, T, K, P, G, H, O, N, D for mono-, bi-, tri-, tetra-, penta-, hexa-, hepta-, octa-, nona-, decadentate ligands, respectively; if the number of donor atoms >10 the letter X is used;
   • the integers mbtkpghond… following after the letter show the numbers of metal atoms coordinated by one (m), two (b), three (t), … donor atoms of the ligand. The sum of these integers is equal to the total number n of metal atoms coordinated by the µ_n ligand.
   (The keyword ATOMLIG contains information about atoms that compose the ligand).
   For example, the coordination type M1 (M¹) means that the ligand is monodentate and is connected to one metal atoms by its (one) donor atom. It is the terminal aqua ligand in our example. The coordination type K12 means that the ligand has four donor atoms and is connected to three metal atoms (µ₃); for the connections with one of them it uses one donor atom and two metal atoms are coordinated by two ligand atoms each. Be sure of this using IsoCryst:
   
   
   
   If the molecule is not connected to a metal atom, its dimensionality (0D) is given instead of coordination type.
   
   
5. Close the Crystal Data window and open the filter Filter/Topology/Ligands. Specify the options as shown below to find all compounds with any complexing atoms and any ligand containing sulfur atoms. Click Ok. How many hits have you got?
   (answer: 4)
   
   
   
   
6. Use Filter/Composition/Element to find all structures with sulfur atoms (there are 6):
   
   
   
   Why the number of the found compounds is not equal to the number of hits at the previous step?
   
   
7. Find all structures with sulfur-containing molecules not connected to metal atoms:
   
   

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