Solving Centrosymmetric Crystal Structures in Non-Centrosymmetric Space Groups

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# Solving Centrosymmetric Crystal Structures in Non-Centrosymmetric Space Groups - PowerPoint PPT Presentation

Solving Centrosymmetric Crystal Structures in Non-Centrosymmetric Space Groups. Michael Shatruk September 12, 2011. Steps in X-ray single crystal experiment. Crystal selection (including unit cell determination). Data collection. Data processing:

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### Solving Centrosymmetric Crystal Structures in Non-Centrosymmetric Space Groups

Michael Shatruk

September 12, 2011

Steps in X-ray single crystal experiment
• Crystal selection (including unit cell determination).
• Data collection.
• Data processing:
• Absorption correction (to match intensities of equivalent reflections)
• Space group determination (XPREP)
• Structure solution (SHELXS)
• Structure refinement (SHELXL)
• Structure validation (Platon, IUCR checkcif)
Step 3 – Data Processing

After integration and absorption correction, the space group is determined with XPREP, which also writes SHELXS input files.

• # reflections total
• # reflections (strong)
• Step a.
• Determine the lattice type
• The options in square brackets are default ones.

Step b.

• Search for higher metric symmetry
• The table of possible higher symmetries
• Desired R(sym) < 0.10

Step c.

• Determine the space group
• Space group determination options
• In most cases, we use option [S].
• Sometimes, we will choose to input the space group.

Step c.

• Determine the space group
• XPREP determines the space group
• Lattice type
• Centrosymmetric?
• Systematically absent reflections allow locating specific symmetry elements
• All the information gathered above is used to derive the possible space groups
• Desired CFOM < 5 (the lower, the better)

In most cases, the option D can be skipped, and we can proceed directly to option C

• Step d.
• Molecular formula
• This is painful!
• Do this ahead of time in your experimental description in APEX, and you won’t have to enter the formula here!
• Again, we skipD and proceed directly to F
• Option F sets up the input file for structure solution in SHELXS.

Step e.

• SHELXS input
• Choose an appropriate filename (e.g., I prefer to use the corresponding space group symbol)
• This is the SHELXS input file
• Usually we overwrite the hkl file (intensity data)
• Now we can quit, although it is possible to go back, if necessary

Step c.

• Determine the space group
• Now we choose to input the space group
• The symbol is not case-sensitive
• The systematic absences statistics calculated for the input space group
• After this, choose option F again to set up the SHELXS input file with the newly defined symmetry
Important Points Regarding XPREP
• In most cases, use defaults commands, but always beware of what they are. Don’t just hit “Enter” without thinking.
• Sometimes XPREP might now show you the correct space group, and you might need to change the space group later on, as you move on with the structure refinement.
• It is better to set up all the possible space groups right away, to save time and don’t need to use XPREP again.