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Solving Centrosymmetric Crystal Structures in Non-Centrosymmetric Space GroupsPowerPoint Presentation

Solving Centrosymmetric Crystal Structures in Non-Centrosymmetric Space Groups

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Solving Centrosymmetric Crystal Structures in Non-Centrosymmetric Space Groups

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Solving Centrosymmetric Crystal Structures in Non-Centrosymmetric Space Groups

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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 Non-Centrosymmetric Space Groups

- Crystal selection (including unit cell determination).
- Data collection.
- Data processing:
- Integration (to assign intensity to each observed hkl spot)
- Absorption correction (to match intensities of equivalent reflections)
- Space group determination (XPREP)
- Structure solution (SHELXS)
- Structure refinement (SHELXL)
- Structure validation (Platon, IUCR checkcif)

Step Non-Centrosymmetric Space Groups3 – 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. Non-Centrosymmetric Space Groups
- Search for higher metric symmetry

- The table of possible higher symmetries

- Desired R(sym) < 0.10

- Step c. Non-Centrosymmetric Space Groups
- 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. Non-Centrosymmetric Space Groups
- 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. proceed directly to option C
- 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. proceed directly to option 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 proceed directly to option C

- 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.