Indexing
-
Correct indexing of the powder pattern (i.e. determination of the unit cell dimensions) is crucial: you cannot solve the structure if the pattern is not indexed properly. DASH can help you with indexing by allowing you to determine peak positions with great accuracy. However, DASH does not do the actual indexing itself. For this, you must use one of the many, freely available cell-indexing programs. DASH does provide an interface for DICVOL (see How to create a DICVOL91 input file), which is convenient for many users.
-
However, it is strongly recommended that one should use at least two indexing programs. The freely available CRYSFIRE suite of Shirley provides a rudimentary interface to most of the popular indexing programs, e.g. DICVOL and ITO and is currently available for download from
http://www.ccp14.ac.uk.
The steps involved in indexing are:
-
Selecting the first 20 or so low-angle peaks and measuring their positions for input to the indexing program. Of course, only the positions of the lines are important for indexing, not their intensities. It therefore follows that weak peaks carry just as much weight as strong ones in the indexing process (see Selecting Peaks for Indexing).
-
Indexing the pattern to find a plausible set of cell dimensions (see Running the Indexing Program).
-
Checking for possible cells of higher symmetry (see Searching for Cells of Higher Symmetry).
-
Checking the cell in DASH by comparing observed and calculated peak positions (see Checking the Cell in DASH).
-
You should select the lowest-angle peaks available, regardless of their intensity, to ensure that the indexing program has a chance to find the correct cell.
-
In general, you should pick the first 20 peaks or so (including shoulders), trying not to miss any.
-
As long as a peak is clearly present, you should pick it, even if it is weak; but if you are not sure the peak is significantly above the background, you can leave it. On balance, if you are at all uncertain about a peak or shoulder, it is probably better to include it in the first instance. You can easily edit it out of the peak list later if the pattern fails to index.
-
As successive peaks are selected, DASH will refine the peak shape parameters.
-
Submit these peaks to a cell-indexing program such as DICVOL or McMaille in order to obtain a preliminary unit cell and crystal system.
-
Zoom in to well-resolved single peaks, working from lowest 2θ upwards.
-
Pick the peak using the right mouse button as described in (see How to use the Interface to Select Peaks).
-
Continue picking peaks (the peak count appears beside the blue peak position line).
-
Finish peak picking when you have between 20-25 peaks.
- Switch to viewing peak positions by selecting Peak Positions from the View menu:
Note that if you want to copy the set of peak positions into the notepad for feeding to other programs, you can easily get the peak positions out of DASH and into a file as follows:
-
Select View from the Peak Positions menu and then click on the word Position at the top of the peak position column. This selects the entire column.
-
Use Ctrl-C to copy the entire column to the clipboard.
-
Once inside an appropriate editor such as Notepad or Wordpad, use Ctrl-V to paste the column into a file.
-
Switch to viewing peak positions by selecting Peak Positions from the View menu.
-
Create an input file for DICVOL using the DICVOL... button (see below).
-
Fill in the information required on maximum values allowed for cell axes and volume.
-
Click Save DICVOL File... button. Give a file name e.g. hctpeak21.dat.
-
Run the DICVOL program with this file as input.
-
The menu for creating a DICVOL91 file is shown here. In the example below, values have been entered such that: minimum cell volume = 0 Å3, maximum cell volume = 3000 Å3. The maximum cell axial length is set to 30 Å, and the maximum monoclinic cell angle is 125o. All crystal systems except triclinic will be searched, and the wavelength has been set as 1.1294 Å. As it is synchrotron data, DASH has set the peak position error to 0.02 by default (0.03 for laboratory data). The other values have been left at their default setting, and will not affect the DICVOL result.
Alternatively, indexing may be performed using the Wizard (see View Data / Determine Peak Positions).
-
DASH provides an automated interface to DICVOL91, just click Run DICVOL.
-
DASH also provides an interface to DICVOL04 (and later) and McMaille. The interfaces to these programs can be accessed through the Peak Picking wizard window (see View Data / Determine Peak Positions).
-
There is no automated interface between DASH and indexing programs other than DICVOL91, DICVOL04 and McMaille, i.e. it is necessary to set up the input files for the programs by hand. However, this task is facilitated by copying the peaks from the DASH Peak Positions listing into the notepad (see How to Cut and Paste Peak Positions to External Programs).
-
Each indexing program has its own strengths and weaknesses. We have found DICVOL, TREOR and ITO to be useful when indexing organic crystal structures, but this is not to say that other programs will not be equally successful.
-
Frequently, one program will successfully index a pattern where another has failed. It is therefore always worth trying at least two indexing programs on each problem.
-
Before running an indexing program, it is useful to get some idea of the size of cell you might expect, given the molecular formula. For example, a molecule comprising 20 non-hydrogen and 25 hydrogen atoms will occupy about 450 Å3 (allowing 20 Å3 for each of the non-H atoms and 2 Å3 for each of the H atoms). Therefore, a good starting point would be to search for cells of up to ~2000 Å3 in volume, as a cell of this size will accommodate four molecules i.e. Z=4, a likely number when dealing with organic structures. You can always increase this size limit later if you do not get any reasonable cells from the initial runs.
-
The majority of indexing programs were designed for use with relatively small unit cells. Advances in structure solution mean that people are tackling larger and larger crystal structures, thus stretching indexing programs to their limits and beyond. For example, it is not unheard of for TREOR to suggest that a unit cell is too large and that the data should be checked, even when the cell is correct. A useful trick here is to simply divide all the line positions by two and try again. The cell that results will be 8 times too small, but you simply double the axial lengths to recover the correct cell. DASH offers this option through the use of a scale factor.
-
By default, DASH creates a DICVOL input file in which the axis lengths is limited to 30 Å or less. Since organic structures may contain a cell axis of length >30, you may need to alter this default if initial indexing fails. Similarly, you may need to increase the volume limit beyond 3000 Å if you are dealing with a large structure or a centred cell.
-
The majority of organic crystal structures crystallise in monoclinic, orthorhombic and triclinic space groups and you should check these symmetries first. Within DICVOL and McMaille, the crystal symmetries are searched in order, from highest to lowest symmetry. As the symmetry falls, the cell searches take longer to execute. It can take quite a while (possibly 2-3 hours, even on a fast processor) to find triclinic cells using DICVOL or McMaille. This is the main reason why triclinic cells are not searched by default, so don’t forget to try triclinic if your initial indexing attempts fail.
-
Some indexing programs (e.g. TREOR) will report if they have located a non-primitive unit cell whereas other simply report the equivalent primitive cell.
-
Like most indexing programs, DICVOL gives two figures of merit, M(#lines) and F(#lines), for identifying the best solution. For synchrotron data, M(20) values of 50 or more and F(20) values of 100 or more are encouraging. Values for laboratory data will be generally lower – an M(20) of, say, 20 or more might be considered reasonable and worthy of pursuit. McMaille reports a number of figures of merit for its solutions and even suggests cells that it judges to be worth investigation.
-
Multiple solutions (i.e. several possible unit cells) are a common occurrence, especially when the input data are not especially good. However, even when the data are good, a program may report two or more unit cells that apparently match the data. In such circumstances, the solutions should be closely examined. If all the cells have almost identical cell volumes, then they are likely to be alternative settings of the same cell, and any one of them could be used. This can be checked by cell reduction. If, however, the cells are markedly different in volume, then they are likely to be unrelated and each one needs to be examined more closely.
-
If you find several cells, all with good figures of merit, the correct cell is likely to be the one of highest symmetry.
-
A large number of low figure-of-merit solutions are normally a bad sign – it indicates that the input positions are sufficiently vague that a number of cells match to within experimental error.
-
If you have trouble finding a cell, it is sometimes worth deleting the last 3 or 4 peaks from the input, e.g. try with the first 16 rather than the first 20 peaks. Or try deleting very weak peaks or dubious shoulders. It is important to realise that DICVOL is more tolerant of missing lines than it is of spurious lines. Most importantly, try another program.
-
Once a plausible cell has been obtained from an indexing program, it is worth performing cell reduction, using a program such as TRACER, to check whether it corresponds to a cell of higher symmetry.
-
Searching for cells of higher symmetry is particularly important when the cell from the indexing program is triclinic. This is especially true when the indexing program lists a lot more calculated than observed peaks, since this suggests systematic absences.
-
Cell reduction is also useful for identifying equivalent solutions, i.e. cells from the indexing program that appear to be different but actually correspond to the same reduced cell.
- Once a pattern has been indexed and a preliminary cell identified, you can return to DASH and input the profile and the cell. You will need to specify a space group: start with the space group of the crystal system that has no systematic absence (e.g. P2 for monoclinic). The pattern is displayed with tick marks indicating the reflection positions predicted from the input cell and space group:
- The first thing to do is to check that the tick marks actually correspond to the pattern, i.e. that the unit cell is correct. The correspondence shown below is very good, indicating that the cell is probably correct. The excess tick marks are probably systematic absences, indicating that the correct space group has a higher symmetry than the one currently being assumed.
