Single Crystal X-ray Diffraction (scXRD)

Overview

Growing crystals

Identifying suitable crystals

Mounting a crystal

Data acquisition

Solving a structure

Data acquisition

This page covers the data acquision for a mounted crystal. This includes the screening phase to check if the selected crystal diffracts suitably; the recording of pre-experiment data to calculate a collection strategy; and the data collection. The bottom section of the page covers the data obtained from this process prior to structure solving.

The diffractometer showing the crystal being rotated within the cryostream and the CCD camera repositioning.

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.

A screenshot of the diffraction observed during the crystal screening stage.

During the screening, the crystallographer is looking for a good number of diffraction spots to be observed across a range of angles, especially at high angles. Diffraction spots should have good intensities (appearing as bright spots), with a concise form (not appearing to be elongated or streaked).

The positions of diffraction spots allow the reciprocal lattice to be calculated, and from this, the unit cell parametes are determined (see section below). 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. With a good correlation, this suggests the crystal being analysed has a regular structure with effective diffraction.

Peaks fit -> info

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

Preexperiment

A short pre-experiment data collection is carried out, where a brief set of data collection is carried out, typically taking a couple of minutes. These measurements are performed to calculate how many frames (individual X-ray measurements) are required in order to obtain a complete dataset for the crystal. Each frames is taken at different locations of detector in relation to the X-ray beam, but the crystal itself is not reorientated at this stage.

For many crystals, the symmetry of the crystal may eliminate needing to collect many angles, and therefore reducing the time required to collect data for the sample, as this data can be calculated through symmetry operations. The alternative to this is to carry out 'full sphere' data collection, where diffraction data is collected for a full range of crystal and detector orientations. A common instance when full sphere collection is required is for chiral molecules where the enantiometric configuration is being determined.

Determining the unit cell

A diagram showing the lengths and angles which describe the unit cell of a crystal.

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:

Guide to unit cell parameters

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. A typical rule of thumb used by crystallographers is that...

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.

Computing data collection strategy

Using the pre-experiment data, the crystallographer can review and alter the minimum level of parameters which have been calculated for data collection. The crystallographer would review the following parameters for the data collection:

The time for data collection per frame (0.05 seconds is the fastest, to a maximum of 1 second being generally the upper limit)
Collecting data reflecting the molecule symmetry versus full sphere data collection
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

Changing the measurement parameters will affect the collection time for the crystallography data. The crystallographer will consider the and these need to be balanced.

Inputting some information (metadata) on the expected compound is also provided at this stage. This can be helpful where AutoChemSolve is used to attempt to determine the structure during the data collection stage. The use of realtime analysis can be helpful, especially with longer data collection strategies, to give an indication if the data is worth continuing with the collection.

A screenshot of the experiment strategy screen following initial screening of the crystal.

Collecting frames

Once the data collection is commenced, the detector and crystals will be rotated to the various locations where were determined during the pre-experiment stategy. For each position, a frame of data is collected which provides the diffraction pattern with the spot intensities.

Whilst this is ongoing, a programme called AutoChem will attempt to solve the data in real time, with the structure improving as each additional frame is collected. Autochem has limited information provided to it about the expected structure and is mostly predicting the structure from the diffraction patterns being observed. Despite this, it is common for AutoChem to be displaying the correct structure fairly quickly during the data collection stage.

The screenshots below show the data collection in progress. The blue progress bar in the top right corner gives an indication of the frame collection status, with the AutoChem output further down the right hand side. The first image is about a quarter of the way through the frame collection, with the correct structure depicted. The second screenshot is approaching the end of the data collection. For this crystal just under 3000 frames were collected in around 6 minutes.

Frame collection. The data collection process can be seen on the top right. Despite only being around 1/4 of the way through, the AutoChem structure prediction has correctly identified the structure (middle right).

Approaching the end of the data collection with the structure resolved by AutoChem visible.

Crystal visual recording

Whilst the data collection is taking place, both the crystal and the detector are being rotated. As part of the crystal rotation, the crystal mounting camera records photographs at every angle. These images are used during the structure solving phase to record the physical dimensions of the mounted crystal.

Output

At the end of the crystal data collection the following files will have been obtained:

Photographs of the crystal
Individual diffraction frames
Unit cell parameters
A HKL file
The structure output from AutoChem
Information obtained during the pre-experiment acqusition

These files are then taken through to the structure solving process. More information on each of these files can be found below.

Crystal photographs

Individual frames recorded by the crystal mounting camera showing the crystal as it is rotated. Below is an animation created from these frames. Note the loop holding the crystal and the regularity of the mounted single crystal.

An animated render of the individual photographs of the crystal as it is rotated during data collection.

Individual XRD frames

An image file of the diffraction pattern for each individual frame is created. In the case of the Rigaku XtaLAB Synergy instrument which was used to collect this sample, these frames are output in a proprietary .rodhypix format (Rigaku HyPix detector format).

Can we convert to JPG?

Unit cell parameters

The determined parameters for the unit cell are calculated from the collected data and are provided in the the ??? file. This consists of the three lengths (a, b and c) and the three angles (α, β and γ). The unit cell volume is also reported, which can be calculated from the cell parameters.

One file contains the right data, but not sure this is from the right source? What other info is helpful at this stage?

CELL 1.54184 18.4743 5.3046 29.7915 90 103.781 90

V = 2835.49 F(000) = 624.0 Mu = 0.41 mm-1 Cell Wt = 1189.20 Rho = 0.696

HKL file

How is this file created?

one reflection per line

h, k, l, amplitude, sigma, phase

Part of the hkl file showing the raw data.

AutoChem RES file

During the data collection, AutoChem attempts to solve the data. The results of this automatic data analysis are output as a RES file. This file provides an indication of the structure, but may well be incomplete or incorrect. A crystallographer will be able to carry out a much better analysis during the structure solving process.

The structure as determined by AutoChem during data collection. The yellow blobs show unassigned electron density, which are likely to be hydrogen atoms.

The RES file providing unit cell data and position information for the atoms based on the AutoChem data solving.

Why is the formula wrong? C22 O14...?

Pre-experiment data

The basic data obtained during the pre-experiment data collection is also output at this stage. This is a similar set of files to the full data collection, but with much less data present compared to the full data collection.

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