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Simplification of CaCO3 polymorphs.
Algorithm:
1. Open the database CaCO3 and compute the adjacency matrices for all the CaCO3 polymorphs with the Domains method.
2. Analyze successively the crystal structure of each polymorph with IsoCryst. Determine the number of carbonate ions connected to Ca atoms. For this purpose, select a Ca atom, leave it only in the picture and perform Growth command until carbon atoms emerge. Then select carbons by clicking on the carbon atom in the legend and grow the structure one time again. Select all oxygens and leave selected atoms (central Ca, all carbons and oxygens) in the picture. Calculate the number of carbonate ions (it is equal to the number of selected carbons in the status line).
Determine in the same manner the number of Ca atoms connected to carbonate ions.
3. Simplify the crystal structure of aragonite to get its underlying net in standard representation (metal atoms and centroids of ligands are the nodes of the “simplified underlying net”; see Appendix 2 for details and definitions). For this purpose, open a window of the program ADS, click Options, clear all checkboxes on Common and Topology tabs, set Topology/Coord. Seq. = 1 (this is just to make it faster), check the option Common/Save Simplified Net and Simplification Method = Standard.
Press Ok and run the program.
4. Answer Yes to the request to create the database CaCO3_c that will contain the simplified structure. Then enter your user code 1.
5. Select Ca atoms as central and press Ok.
After the program finishes look at the coordination numbers of the nodes in the simplified structure, open a Crystal Data window and compare with the numbers determined at step (2). Go to Comment tab and draw attention that the nodes 'ZA' designate centroids of carbonate ions (the line entitled SIMPLIG contains the description of which ligands were simplified).
6. Turn to the window of the database CaCO3 and simplify the crystal structures of calcite and vaterite by one step. For this purpose, select the records pressing Insert key or Shift+↓ or Ctrl-mouse click. Open one more ADS window and go to Options/Continuous tab. Press El button at Central Atoms line.
In the Periodic Table window click All Up button and then Me button to select all metals. (To make it faster , you can just type "Me" in the Central Atom window)
Press Ok and then Ok in the ADS Options window. Then run the program and answer Yes to reload the database with simplified structures.
Check the resulting simplified structures.
You will notice that the three derived underlying nets are 6-coordinated but (after classification) of only two distinct topological type pcu and nia, however aragonite and vaterite, belonging to the same topological type (nia), are antitypes (cations and anions are topologically exchanged).
Exercise: simplify the structures of MgCO3 and SrCO3 from the Mg_SrCO3 database.
Answer: MgCO3 and SrCO3 can be simplified to 6-coordinated underlying nets with topological type pcu and nia respectively.
Algorithm:
1. Open the database CaCO3 and compute the adjacency matrices for all the CaCO3 polymorphs with the Domains method.
2. Analyze successively the crystal structure of each polymorph with IsoCryst. Determine the number of carbonate ions connected to Ca atoms. For this purpose, select a Ca atom, leave it only in the picture and perform Growth command until carbon atoms emerge. Then select carbons by clicking on the carbon atom in the legend and grow the structure one time again. Select all oxygens and leave selected atoms (central Ca, all carbons and oxygens) in the picture. Calculate the number of carbonate ions (it is equal to the number of selected carbons in the status line).
Determine in the same manner the number of Ca atoms connected to carbonate ions.
3. Simplify the crystal structure of aragonite to get its underlying net in standard representation (metal atoms and centroids of ligands are the nodes of the “simplified underlying net”; see Appendix 2 for details and definitions). For this purpose, open a window of the program ADS, click Options, clear all checkboxes on Common and Topology tabs, set Topology/Coord. Seq. = 1 (this is just to make it faster), check the option Common/Save Simplified Net and Simplification Method = Standard.
Press Ok and run the program.
4. Answer Yes to the request to create the database CaCO3_c that will contain the simplified structure. Then enter your user code 1.
5. Select Ca atoms as central and press Ok.
After the program finishes look at the coordination numbers of the nodes in the simplified structure, open a Crystal Data window and compare with the numbers determined at step (2). Go to Comment tab and draw attention that the nodes 'ZA' designate centroids of carbonate ions (the line entitled SIMPLIG contains the description of which ligands were simplified).
6. Turn to the window of the database CaCO3 and simplify the crystal structures of calcite and vaterite by one step. For this purpose, select the records pressing Insert key or Shift+↓ or Ctrl-mouse click. Open one more ADS window and go to Options/Continuous tab. Press El button at Central Atoms line.
In the Periodic Table window click All Up button and then Me button to select all metals. (To make it faster , you can just type "Me" in the Central Atom window)
Press Ok and then Ok in the ADS Options window. Then run the program and answer Yes to reload the database with simplified structures.
Check the resulting simplified structures.
You will notice that the three derived underlying nets are 6-coordinated but (after classification) of only two distinct topological type pcu and nia, however aragonite and vaterite, belonging to the same topological type (nia), are antitypes (cations and anions are topologically exchanged).
Exercise: simplify the structures of MgCO3 and SrCO3 from the Mg_SrCO3 database.
Answer: MgCO3 and SrCO3 can be simplified to 6-coordinated underlying nets with topological type pcu and nia respectively.
