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Single Crystal XRD

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This is a guide for conducting Single Crystal XRD using Bruker D8 Venture Duo with APEX4.

On APEX4:

Left Side Bar and Right Side Window

Create new project New sample (top left) (always save other people’s old projects), fill in crystal information.

On diffractometer:

  • Mount crystal
  • Close the door when detector is moving
  • Physically center with goniometer
    • Up/down movement is higher one
    • Left right is lower one
  • Turn on the light bottom at right side of the diffractometer

On APEX4:

Left Side Bar and Right Side Window

Set UP -> Center Crystal: Click Center once mounted

On diffractometer:

  • Open doors on diffractometer (always close the door when detector is moving)
  • Align once, rotate 90
  • Align again, rotate 90
  • Align again, rotate 180
  • Rotate around to check if it is centered
  • Once it can rotate without misalignment use the camara to take measurement of crystal. size (each tick is 20 micron (0.02mm), radius is 100 micron (0.1mm))

On APEX4:

  1. Put the size in Set UP -> Describe

  2. Evaluate -> Determine unit cell
    • Run (it will go through each step automatically to find a unit cell), if the unit cell is not right, you can manually adjust the threshold (MIn.I/sigma to 3), and manually go through the process.
  3. Collect -> Calculate Strategy
    • Anode: Mo, Resolution: 0.4A for solid state
    • Symmetry: lower than your space group, check the HKL range at top window, make sure cover both positive and negative HKL.
  4. Parameters for the strategy determination:
    • Crystal to detector: 40mm standard (50mm if long axis), click ok
    • Shortest normalized exposure time: 0.5
    • Select Scan Parameter:
      • Frame angle: 0.5 degree
      • Frame time: depending on crystal can change time per step, <5s. we use 2 sec for iridates
  5. Collect -> Run Experiment
    • Add Crystal video into 2
    • Append strategy
    • Validate to make sure it’ll run
    • Execute
  6. After collection, find a unit cell with better data: Evaluate -> Determine unit cell
    • Select image (folder at top), don’t use fast scans use actual scans (samplename_001)
    • when you go to last scan should be _0180
    • Harvest spots
      • Min I/signal = 3, harvest
      • Once harvested, index, index
      • Pick group, accept, set
      • Bravais, select one you want
      • Refine, use more peak, refine until it converge, now have new unit cell
  • With the new unit cell, start processing:
  1. Reduce data -> integrated images:
    • Select unit cell you just made
    • Import runs from experiment (make sure you don’t use the fast scans or use fast scans when missing low angle data)
    • Resolution limit: 0.4
    • Refinement options:
    • XYZ box size to 0.8, 0.8, 1.2 or 1,1,2 depends on your crystal - Integration options:
    • More options -> Algorithm -> Monte Carlo simulation: 32, start integration
  2. Reduce data -> Scale
    • Symmetries: (Laue and Point Group)
    • Mu*r : 0.1 or 0.2, probably not need to change
    • Start
    • Refine

  3. Examine data -> Analyze data (x-prep) This will export required files for refinement, follow the step by x-prep.

  4. Start refinement.

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