Filtering different modifications of lithium sulfate including hydrates, computing and saving adjacency matrices for them. 


Algorithm:

1. Open the database Li_S_Se (66 entries). Using the filter Filter/Fragment/Name find all compounds with the substring “lithium sulfate” in the compound name. Type the name to be searched and click on Add, then click Ok (or simply click Ok; if the list of filters is empty the current filter will be added automatically). 58 compounds are found. Selected them all and copy into the database Li2SO4. (see Example 2 in the previous Module 1) (If you want to see again all the 66 entries in Li_S_Se right-click in the window of the selected database and go on Show Main in the local menu.)

2. Open the database Li2SO4 and filter the structures containing the atoms other than Li, S, O or H. For this purpose, use the filter Filter/Composition/Element, clear from previous filters by click on “Clear” button and now set the filter fields: Elements: ‘Li S O H’; Only; One Filter Operator: Without. Click on Add, then Ok. Select all the 35 records found and remove them (use Del key, or F8, or (Un)Delete in the local menu)

Go to the main list of the database Li2SO4 (use Show Main command of the database local menu). 23 compounds are left.

3. Filter and remove the records containing no coordinates of atoms. For this purpose use the filter Filter/Composition/CompFlags and check the No Coordinates flag (after clear from previous filters check that One Filter Operator is set to With).

Select them all, remove, Show Main. How many structures are left? 23–4=19 How many hydrates does lithium sulfate form? (use filter to look for “hydrate”, you will find 11)

4. Using Crystal Data window find a hydrate in the list in whose structure the hydrogen atoms are allocated. (For example, Ref. Code 22347)

5. Open the window of the program AutoCN (Programs/AutoCN) or click on .

6. Specify the following AutoCN options (Options/Matrix):

Method: Domains; Save: Atoms (to store coordination numbers in the Li2SO4.cd file and adjacency matrix in the Li2SO4.adm file);

Matrix Data: Spec. Cont., vdW Cont., Dist. + Rsds to store the information on specific and van der Waals bonding as well as interatomic distances.

Check the options for computing hydrogen bonds (H bonds tab). Consider also the possibility to search for hydrogen bonding also when the hydrogen atoms are disordered or allocated too close to each other (use the option Resonance bonds for disordered).

Leave the Default selections in Common and VDP Calculations.

Press Ok button. 7. Run the program by the command Run to get the output like follows.

At the bottom part of the output the computed connectivity is resumed in columns, pay attention to three of them:
  • CN contains the number of covalent bonds connecting the listed Atom;
  • Hb contains the number of hydrogen bonds connecting the listed Atom;
  • Sp and vdW contain information on non-valence specific and van der Waals interactions.
For example atom O2 is connected to 2 atoms (Li and S) and is involved into one hydrogen bond. ATTENTION: Sometimes you may get the message Inconsistent contacts: A-B which means that AutoCN has found wrong A…B contact that will not be included into the adjacency matrix. The point is that two AutoCN algorithms, Domains and Solid Angles, use some parameters of Dirichlet domains to determine type of interatomic bonds. These parameters are computed with some errors and it may occur that for a contact A-B the method gives the bond type, say, valence, if the Dirichlet domain of atom A is considered, but if we rest upon the Dirichlet domain of atom B, the contact will be classified as, say, van der Waals. It occurs when parameters of the contact are very close to accepted limits separating bond types, ordinarily for non-valence types (specific or van der Waals) and most frequently for H atoms as they are often wrongly allocated. In other words AutoCN requires that the 'semi'-bonds A- and -B must obey the 'self-consistency' principle: they must be of the same type. Otherwise an error message is output and such 'bond' is broken. It is not crucial in most cases but rarely (especially if one of such 'semi'- contacts is valence) can indicate some inconsistency in the structural data (e.g. disordering, wrong atomic coordinates, etc.).

The main AutoCN algorithm, Domains, is universal and be applied to both inorganic and organic (including metal-organic) compounds. The method Solid Angles is useful in the case of compounds with undirected interactions, such as intermetallides, noble gases, ionic compounds. The method Ranges is designed for artificial nets like sphere packings, RCSR nets or epinets. For more details of the methods see Appendix 1.

8. Close the program window with the Quit command. 9. Open the Crystal Data window and be sure that the adjacency matrix was saved (see the Adjacency matrix tab).

10. Select all records and run AutoCN again (options should not be changed, but you may uncheck Data/Show Data flag to toggle off the output and speed up the calculation). As a result, adjacency matrices will be stored for all the structures.

Exercises:

(a) perform the algorithm to find all structures of lithium selenate in the Li_S_Se database and to compute adjacency matrices for them. Do lithium sulfate and selenate have similar hydrates?

(b) compute adjacency matrices for organic and metal-organic compounds contained in the Org_MOF database. Use the method Domains (Options/Matrix).

(c) compute adjacency matrices for your own structures converted in Module 1.


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