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Solving Centrosymmetric Crystal Structures in Non-Centrosymmetric Space Groups

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

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  1. Solving Centrosymmetric Crystal Structures in Non-Centrosymmetric Space Groups Michael Shatruk September 12, 2011

  2. Steps in X-ray single crystal experiment • 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)

  3. 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.

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

  5. 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.

  6. 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)

  7. 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.

  8. 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

  9. 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

  10. 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.

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