Viewing and editing crystallographic information. 


Algorithm:

1. Open the database Examples and double click on the first record to open a Crystal Data window with four main tabs collecting all the crystallographic information on this compound the database contains:
  • General information on the compound: name, chemical composition, crystallographic data (unit cell and space group), possible bibliographic data.
  • Atoms, a window with the complete list of the independent atoms present in the unit cell (asymmetric unit) with name, list number, oxidation state (if available), site symmetry, crystallographic coordinates x-y-z, site occupation (important in disordered structures), coordination number of the atom.
Adjacency Matrix. Lists all the atoms with all the other atoms connected/interacting with them, ordered by type of interaction. From this window is possible to modify the kind of connection type: we scroll the list of possible interaction (clicking on +); with the mouse right button we open the local menu and we can change or delete a specific interaction. Changing the type the display of the atom interacting will change too: Valence // Hydrogen bonded // Specific (secondary interactions) // Van der Waals // No bond //; different types of bonds are marked in different colours by V, H, S or W symbols, respectively.

Pay attention to the field in the Adjacent Matrix tree:

Root (all inequivalent atoms A in the unit cell):
CN – coordination numbers for valence (V, first number) and non-valence (second number H, S or W) contacts;
Rsd – radius of spherical domain value (Å) (see Appendix 1);
BVS – sum of bond valences according to Brese, N.E. & O’Keeffe, M. (1991) Acta Cryst. B47, 192- 197.

Branch (all atoms B connected to a particular atom from the root):
SA – solid angle in percentage of the total solid angle of 4π steradian (see Appendix 1);
R – interatomic distance A–B (Å);
BV – bond valence for A–B;
Mult – multiplicity of the bond.

Comment. All the notes may be written here.

2. Press Symmetry button to look at the lists of symmetry operations, minimal supergroups and maximal subgroups of the space group of the structure. Pay attention that you may easily transform any nonconventional setting (e.g. F1 → P1 or PbnmPnma) of a space group into the conventional one by clicking the Change Setting button. The button is active only in the case when the current setting is nonconventional. To transform the space-group symmetry into the symmetry of a subgroup you have to select the subgroup in a bottom list and click the Change Group button.
Close the Symmetry window.

3. Now let’s perform the Compound/Add command. Fill the window fields with the data for NaCl given below. To enter the authors’ names press Enter key after typing every name in the line Authors. The journal name should be chosen from the Journal dropping list. After entering the whole information, determine the composition of the unit cell by going to the General tab and pressing Calculate button. Be sure that VolCell =177.50 Å3. Press Save button.

Data NaCl CsCl
Space group Fm 3 m Pm 3 m
а, Å 5.620 4.120
Atoms Na: (0,0,0)
Cl: (0.5,0.5,0.5) or (1/2,1/2,1/2)
Cs: (0,0,0)
Cl: (0.5,0.5,0.5) or (1/2,1/2,1/2)
Bibliography Abrahams S. C., Bernstein J. L. // Acta Crystallographica, 1965, V. 18, P. 926-932 Posnjak E.,Wyckoff R.W.G. // J. Am. Chem. Soc., 1924, V.46, P. 2368-2374

4. Duplicate the record by right-clicking and choosing Duplicate command.

5. Change the information in the duplicated record using the data for CsCl. For this purpose use the Compound/Edit (or double left-click on entry) command and change the content of the fields. To remove the authors’ name select it by left-click, then right-click on the name and choose Delete Author. Save the changes.

Exercise:

Create a database with your own structures from CIF or SHELX formats. Copy them into another database. Create a new record in the database manually using crystallographic data from a journal paper.

Questions/Hints:

Why the "Composition" field in the Crystal Data Window shows Fe0 Cl0 N0 H0 C0 ? Click on the Calculate button and see/explain what happens.


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