Indexing by N-TREOR09

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Indexing by N-TREOR09 in  EXPO2014

       In powder diffraction the first necessary step for solving crystal structure is the indexing, i.e. finding the unit cell parameters and reconstructing the three dimensional lattice from the one-dimensional information of the powder diffraction pattern. The indexing is performed by  EXPO2014 via the program N-TREOR09 (Altomare et al., 2009), the evolution of the N-TREOR software (Altomare et al., 2000).

Preparing input file for indexing in EXPO2014

Indexing by N-TREOR09 in EXPO2014

Output of indexing

The indexing directives

Contact and References

Preparing input file for indexing in EXPO2013

To run  EXPO2014 for indexing you need to create an input file (*.exp). It is possible by graphic interface, creating a new project by the menu "File" > "New".

You must specify the structure name, the profile counts filename and its format, the wavelength and the type of radiation source. Click on button 'Cell Determination by N-TREOR09' and press 'Save'. In addition you can activate the check buttons 'Find Space Group' and 'Structure Solution' if you intend to continue the crystal structure determination process by performing the space group determination and the structure solution steps. The following picture is an example of creation of the input file for crystal structure determination of the cimetidine from the unindexed pattern. All the 2theta range is used even if it is suggested to remove the region at high 2theta values when the noise could be very high and the overlapping of reflections very severe. Alternatively use the button 'Open' to import an existing input exp file.

When you press the button 'Save' an input file cime.exp will be created in the same folder of powder data file and automatically loaded by the program for the indexing. Its content is the following one:

%structure cime
%job structure cime
%init
%data
       pattern cime.pow
       filetype counts
       synchr
       wave 1.52904
%ntreor

%continue


The command that has to be introduced in the input file for coming out the indexing process by N-TREOR09 is %ntreor. It must be added after command %data. Add %continue if you want to continue the crystal structure determination. You can read the meaning of the rest of instructions of the input file in the chapter "command and their use" of this manual.

Alternatively you can edit a new input file or modify an exiting input file with a text editor and save it with the extension '.exp'. Once a time the input file has been created, load the exp input file from the menu 'File' > 'Load & Go'.

More details about preparation of data are reported here.


Main steps for Indexing by N-TREOR09 in  EXPO2014

       First of all, use the button to carry out to the next steps. Firstly an automatic peak-search will be performed. 


Accurate peak search is a fundamental stage for a correct powder pattern indexing; computing and graphical tools are provided to improve it. In order to check the reliability of the automatic peak search results, use the buttons to explore the pattern. If the automatic peak search outcome is not reliable, you can modify the peak search options via different ways:

1) by changing the curve describing the background. This is possible adding or removing background points by clicking on the button and using left mouse click or/and right mouse click to add or/and to delete points, respectively. Background function can be also modified by the button of the 'Pattern' option. When background is changed, the peak positions are automatically updated;

2) by choosing the tool bar button   to add or remove peaks by left click and right click of mouse, respectively;

3) by the menu  'Pattern'>'Modify Peaks'. The button 'Peak search conditions' opens the following window that enables to modify the main search conditions.

4) use 'Pattern' > 'Modify Peaks' > 'Load Peaks' /'Save peaks' to load or save peaks as 2theta or d values.




During the peak search remember that the number of peaks must be not too high and N-TREOR09 can generally solve the indexing problem with the 25 first peaks (even very weak peaks included). Peaks at low angle not clearly resolved and with an appreciable peak width should be not included in case they appear strongly uncertain.
The next step is the automatic refinement of peak positions and profile parameters (a Pearson VII function is used). At the end of the peak search a file named structure_name.pea, containing the refined d values associated to the selected peaks, is automatically created by the program. This file can be used in the future for jumping the peak search procedure (see the directive extefile) if a new indexing process is performed.
At the end of the indexing procedure the cell parameters and the cell volume, the figure of merit FOMnew (Altomare et al., 2009), the classical figure of merit M20 (De Wolff, 1968), the applied zero-shift, the number of unindexed lines and the most probable Extinction group, are supplied by the following window.


Sometimes more plausible cells are suggested by N-TREOR09, ranked according to a new figure of merit (Altomare et al., 2009), FOMnew in figure.


Clicking on each suggested cell of the list, the tick marks at the bottom  of the experimental pattern indicating the calculated positions of the Bragg reflections, will be displayed. The tick marks must correspond to peaks in the pattern. When no experimental peaks are associated to the tick mark, the corresponding reflection is probably systematically absent. On the other side, if a diffraction peak in the pattern is not associated to any tick, the peak can be referred to an impurity phase or the determined cell might be wrong.

Once the cell parameters calculation step has been carried out, you may perform the space group determination step by selecting the cell parameters and by clicking on the OK button. The following dialog window will appear.



Before clicking OK, in this window you must specify the unit cell content. In the case of the cimetidine structure the cell volume suggests that the cell can accommodate 4 molecules (Z=4). During the editing of the cell content, the program calculates and displays a rough estimate of the Content Volume and of the Volume per Atom. Content Volume is an approximate value of the cell volume calculated using the Van der Waals radius and the covalent radius associated to the supplied atoms, Volume per Atom is simply the ratio between the cell volume and number of non-hydrogen atoms. To check the correctness of the cell content consider that the expected Content Volume must be not very different from the cell volume and the Volume per Atom usually has a value between 15-25. Significantly deviation from the expected value, can be observed in the Content Volume or in the Volume per Atom,  due to the presence of H-bonding or large void space (e.g. zeolites) in the crystal structure.

Output of indexing

       The output file contains details about indexing. Use 'Info' > 'View output file' to access to the output file or open the file structure_name.out with a text editor or click on the button   from the main menu.


The indexing directives

Directives in data command

The following directives must be added after the command '%data' in the input file to activate some specific features of the indexing procedure

EXTEFILE file_name

This directive is used to supply an external file containing 'd' or '2theta' values of peak positions. In the latter case the additional '2-THETA' directive has to be used. An example of the use of the directive extefile for the indexing of the pattern of structure cime:

%structure cime
%job structure cime
%init
%data
       pattern cime.pow
       filetype counts
       synchr
       wave 1.52904

    extefile cime.pea
%ntreor
%continue

'cime.pea' is an ASCII file containing the observed 'd' values associated to the selected peaks.

2-THETA

This directive is used combined with the EXTEFILE directive to supply to the indexing program N-TREOR09 an external file containing 2theta values of the peak positions.


Directives in ntreor command

The N-TREOR09 directives must be added after the command '%ntreor' in the input file to enable some specific features of the indexing procedure

All the directives of the indexing program TREOR (Werner, Eriksson & Westdahl, 1985) are still valid for the "%ntreor" command and have to be used with the same syntax (see the N-TREOR manual for the details).

The default choices can be changed via suitable directives.

N-TREOR09 directives:

CEM n

%structure diltia
%initialize
%data
       pattern pd_0029.pow
       wavelength 1.54056
       filetype xy
       extefile diltia.pea
%ntreor
       CEM = 50,


If a set of d (or 2theta) values is already available, the peak search procedure is skipped.

'diltia.pea' is an ASCII file containing the d peak positions.

In a default indexing run, N-TREOR09 searches for cells with a maximum cell volume of 4000 Å3 and a maximum cell axis of 35 Å. Due to this limits the correct cell is not found in a default indexing run for compounds having larger cell axis values. This is the case of Diltiazem hydrochloride for which one of the maximum axis value is 42.190 Å. The directive 'CEM = 50' activates N-TREOR09 for a search for a cell having a maximum axis value of 50 Å.


Contact

For suggestions and bugs contact annagrazia.moliterni@ic.cnr.it.

References

Altomare, A., Campi, G., Cuocci, C., Eriksson, L., Giacovazzo, C., Moliterni, A., Rizzi, R. Werner, P.-E. (2009). Advances in powder diffraction pattern indexing: N-TREOR09. J. Appl. Cryst. 42, 768-775. 

Altomare, A., Giacovazzo, C., Guagliardi, A., Moliterni, A. G. G., Rizzi, R. Werner, P.-E. (2000). New techniques for indexing: N-TREOR in EXPO. J. Appl. Cryst. 33, 1180-1186.

De Wolff, P. M.(1968). A simplified criterion for the reliability of a powder pattern indexing. J. Appl. Cryst. 1, 108-113

Werner, P.-E., Eriksson, L., Westdahl, M. (1985). TREOR, a semi-exhaustive trial-and-error powder indexing program for all symmetries. J. Appl. Cryst. 18, 367-370.

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