Screening the crystal

Ahead of full data collection, a brief screening process is carried out on the mounted crystal to gain some preliminary information on the crystals and check they are suitably diffracting. Short bursts of X-rays, typically upto 30 seconds are used, with the power steadily being ramped up until a suitable diffraction pattern is observed. The crystal is kept in a single position during this step, unlike the full data collection where the crystal has data collected from many orientations.

The crystallographer is looking for a good number of diffraction spots occurring across a range of angles, especially at high angles. The spots want to have good intensity (bright spots), with a concise form, ie not appearing elongated or streaked.

As part of the screening, the number of spots giving rise to the same unit cell information is indicated. It is rare for this to be 100% from this basic screening stage, but there should be a good percentage showing correlation.

Peaks fit -> info

Once the crystallographer is satisfied that the selected crystal is diffracting suitably, then a pre-experiment data collection is carried out.

Determining the unit cell

The unit cell is the smallest repeating unit which makes up the crystal structure. As part of the initial screening, this will result in the calculation of the unit cell. The unit cell is defined by the lengths (a, b & c) and the angles (α, β & γ). More information on unit cells can be found in the page linked below:

From the unit cell parameters (a, b, c, α, β, γ) the volume of the unit cell can be calculated. The cell volume allows an estimate how many atoms are likely to be in this unit cell. From this information and knowledge about the expected structure, this gives an indication for how many molecules are likely to be found in the unit cell. This could be one or more molecules, or for a compound which shows some symmetry, this could be less than one molecule in the unit cell. Additionally this may give and indication of other atoms or molecules present in the unit cell, for example solvents of crystallisation.

The unit cell data is compared to known compounds which exhibit the same unit cell parameters. This includes information which has been published into the Cambridge Structural Database (CSD) and locally collected data in the department. Any hits for matching cell parameters will be reviewed by the crystallographer to see if any are a compound match. Note that it is perfectly possible for unrelated chemical compounds to share the same unit cell parameters.

Preexperiment

A short pre-experiment data collection is carried out, typically taking a couple of minutes. 

Calculating how many frames (measurements) required in order to obtain a complete dataset.

Frames is each individual location of detector in relation to the X-ray beam.

Symmetry could rule out needing to collect many angles, as this data would already be available from data collected from earlier places.

Computing data collection strategy

The crystallographer can then alter the minimum level of parameters which have been calculated for data collection. The crystallographer could then override:

• Time of data collection per frame (0.05 seconds is the fastest, to a maximum of 1 second being generally the upper limit

• Symmetry v full sphere

• Whether to collect for resolution of chirality (changing hkl and -hkl from being equivalent)

• Setting parameters where a crystal is strongly suspected of being a twinned crystal

• Options to collect additional redundant data

Altering any of the above will affect the data collection time, and these need to be balanced.

Inputting information on the expected compound is also provided at this stage, which allows the programme AutoChemSolve to attempt to determine the structure during the data collection stage. This can be really helpful especially with longer data collection strategies to give an indication if the data is worth continuing with the collection.

Crystal visual recording

The crystal is slowly rotated and photographed at every angle, allowing determination of the physical dimensions of the mounted crystal.

Collecting frames

The detector then rotates to each calculated location and a frame of data is collected for each position. Whilst this is ongoing, AutoChem will attempt to solve the data, with the structure improving as each additional frame is collected. AutoChem knows nothing about the potential structure at this stage?

Output

At the end of all the frames being recroded we have:

• A movie of the crystal

• An image file for each individual frame rodhypix 

• Unit cell data

• HKL file

• The AutoChem RES file 

• Plus the saved preexperiment data