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Tutorials and Examples

Automated Crystal Structure Solution from Powder Diffraction Data Using EXPO

Basic run Through of Sirware EXPO - Constant Wavelength Neutron Powder Diffraction Data Example

The CCP14 Homepage is at http://www.ccp14.ac.uk
[Tutorials page] | [EXPO Tutorial Index]

This example uses calculated Neutron data from a Fullprof Rietveld example file (urea.dat) which consists of deuterated urea.

Also refer to Armel LeBail's Tutorial on solving structures from powder data

Starting Information

The starting information that is normally known before starting EXPO is:
  • Wavelength of Neutron radiation used.
    • 1.0791 Angstrom
  • Space group
    • P -4 21 M

    • (It should be noted that if you have not determined the space group, manual interpretion of the HKLs could be possible. Of via WinGX you can try using ABSEN authored by P McArdle to try and determine the spacegroup).

      In the case of overlap problems, Le Bail fitting on various spacegroups and using the overall profile fit as a guide is another possible method.

      A quick method of narrowing down possible spacegroups is to use the celref software as described in Using Celref to help Assign a Spacegroup after Powder Indexing

  • Chemical Composition/Formula:
    • C 1, O 1, N 2, H(D) 4
  • Number of Formula Units per Unit Cell
    • Z = 2
  • Thus the Unit Cell contents are:
    • C 2 O 2 N 4 H 8
  • Unit Cell Dimensions:
    • a=5.5840 , b=5.584, c=4.689, Alpha=90, Beta=90, Gamma=90
From either an Icon in MS-Windows (or typing expo on UNIX command line), run expo.

This brings up the following screen

Click on OK and you are then prompted to open up a EXPO control file. If relevant, type in the correct working directory. (in this case c:\expo\neutron)
The file we are going to look at here is described above, urea. Following is the information inside the file that you would be expect to edit manually and is described in the EXPO manual [Home Site] | [CCP14 Mirror].

One thing to note is the Deuterium scattering factor is defined for H. 

%struct urea
%job Urea from Fullprof example
%init
%data
neutron
format  (f9.0)
isotope H 0.67
range  5.0000  100.0000  0.0200
pattern urea2.pow
cont  C    2  O    2  N    4  H 8
wave 1.0791
cell     5.5840  5.584   4.689  90  90  90
space P -4 21 M
%extraction
%continue

Note that you may have to reformat your neutron data to make EXPO happy. A column format seems to be the easiest to make it EXPO happy with the minimum of fuss.

      492.000
      507.000
      461.000
      525.000
      514.000
      467.000
      531.000
      500.000
      532.000
Click on the Browse to view what input files are available and click on the urea.exp file.

Click on OK to confirm your selection.

If the range of the data is incorrect. It could be the format statement in the EXP file is not correct.

Then click OK again to let EXPO go through its stuff (like Sir97 this is the fun to watch bit). At various points, the program stops to give you the choice of changing the defaults. In this example, all you have to do is keep pressing the CONTINUE button.

At this point, you can redefine the range of the data on which the structure factor extraction is performed. In this case, we may as well just go up to the full range but in some cases, this is a variable to play with as above a certain angle, the overlap can be so excessive as to be useless.
Click continue and EXPO will select what it considers to be the best intervals for the analysis. You can over-ride this if you which. For this example, we don't wish to over-ride anything, so just press CONTINUE

EXPO determines the background. You can zoom and inspect this, but we will just accept this and CONTINUE.
EXPO tries to determine the best peak profile to use, the goes about extracting intensities in the "regions" it selected.

Now it is continuing onto "Interval 2".

Now EXPO does an extraction cycle on the full pattern.
EXPO is now finished the extracting of intensities and now we can proceed for the direct methods by pressing CONTINUE. In this case, if EXPO queries if you want to use pseudo-translational effects, just say no - but normally you would be checking these options out.
EXPO now is Phasing.
EXPO is now attempting to place Atoms.
EXPO now is assigning elements to the atoms.
EXPO now presents a structure to us. Note that due to the nature of neutron diffraction, it may be difficult for both EXPO and you as the user to define atoms and interpret the connectivity. Thus, while ESPO may have solved the structure, the user may have to delve into this and see what can be gleaned from the resulting co-ordinates.

As with Sir97, we have the option to add Atom labels by using the PlotStyle Menu Option.
On quitting EXPO produces a *.xyz file with the co-ordinates that can be input into any other refinement/structure checking program for seeing if this is a reasonable solution. Bond angles and lengths, as well as Fourier maps can be examined from within the EXPO menu system.

Urea from Fullprof example                                                      
 number of atoms =     7 for set no.     1

   type          x       y       z       Int.     occ.   B

     o         0.348   0.152   0.820     1859.   0.500      2.043
     o         0.500   0.000   0.668     1680.   0.250      2.043
     o         0.500   0.000   0.395     1143.   0.250      2.043
     o         0.448   0.052   0.995      671.   0.500      2.043
     o         0.159   0.341   0.895      380.   0.500      2.043
     o        -0.006   0.127   0.772      366.   1.000      2.043
     o         0.590   0.257   0.938      346.   1.000      2.043
One suggestion it so use Louis Farrugia's WinGX and Ortep-3 to look and examine the structure. Especially with organics, this may help resolve connectivity and atom assignment issues. Following is the EXPO resulting structure less some of the lower peaks. This is followed by the structure as original defined in Fullprof.

Processed structure from EXPO .. Original structure from Fullprof, less hydrogens .. Original structure from Fullprof

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