International
Tables for
Crystallography
Volume H
Powder diffraction
Edited by C. J. Gilmore, J. A. Kaduk and H. Schenk

International Tables for Crystallography (2018). Vol. H, ch. 3.4, pp. 279-280

Section 3.4.4.6.2. Indexing using N-TREOR09

A. Altomare,a* C. Cuocci,a A. Moliternia and R. Rizzia

aInstitute of Crystallography – CNR, Via Amendola 122/o, Bari, I-70126, Italy
Correspondence e-mail:  angela.altomare@ic.cnr.it

3.4.4.6.2. Indexing using N-TREOR09

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Two examples of powder diffraction pattern indexing by using N-TREOR09, as implemented in the EXPO program, will be described. To activate the procedure some specific instructions must be given to EXPO via the input file or the graphical interface. As a first step, the peak-search procedure is automatically performed on the experimental powder pattern and the list of corresponding d values are supplied to N-TREOR09. During the indexing process a correction for zero-point error is automatically carried out (positive and negative shifts are taken into account). Both the examples below were successfully indexed by a default run of EXPO.

Example 3

Decafluoroquarterphenyl (Smrčok et al., 2001[link]). Published information: C24H8F10, monoclinic, a = 24.0519 (9), b = 6.1529 (3), c = 12.4207 (5) Å, β = 102.755 (2)°, I2/a, experimental range 7–80° 2θ, λ = 1.79 Å, RES = 1.39 Å, medium-quality X-ray laboratory data. The first 43 peaks (in the range 7–67°) with intensities greater than a default threshold were selected (an intensity-based criterion is automatically adopted). The first 25 lines were used to find a possible cell that was then refined by considering all the 43 peaks. At the end of the automatic indexing procedure, N-TREOR09 suggested two possible cells ranked according to WRIP20 [equation (3.4.5)[link]], as shown in Fig. 3.4.1[link] (WRIP20 is denoted as FOMnew in N-TREOR09). The first one in the list is the correct cell. It is worth mentioning that the classical M20 figure of merit was not able to pick up the solution. The best cell parameters, found according to FOMnew, were a = 24.0951 (50), b = 6.1697 (21), c = 12.4578 (37) Å, β = 102.724 (18)°, similar to those reported in the literature, with FOMnew = 0.61, M20 = 12; all the lines in the pattern were indexed. The program provided the solution thanks to its automatic check for a zero-point correction (2θ zero shift = 0.04°) and was able to correctly identify the extinction group (I_a_). For the second suggested cell (the wrong solution) FOMnew = 0.41, M20 = 15, and two lines were unindexed.

[Figure 3.4.1]

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The list of possible cells for the decafluoroquarterphenyl structure automatically found using N-TREOR09.

Example 4

Hexagonal turkey egg-white lysozyme (Margiolaki et al., 2005[link]). Published information: hexagonal, a = 71.0862 (3), c = 85.0276 (5) Å, P6122, experimental range 0.4–12° 2θ, RES = 3.35 Å, synchrotron data. The first 94 peaks (in the range 0.4–6°, λ = 0.700667 Å) with intensities greater than a default threshold were selected. An intensity-based criterion was automatically adopted. The first 25 lines were used to find possible cells that were then refined by considering all 94 peaks. Five possible unit cells were automatically suggested by the program in the following systems: hexagonal (1), ortho­rhombic (1) and monoclinic (3). The highest value for WRIP20 was 0.99, and was for the correct hexagonal cell parameters: a = 71.0922 (4), c = 85.0269 (7) Å, which are similar to those reported in the literature; all the 94 selected lines in the pattern were indexed. For this cell, the program detected a geometrical ambiguity (see Section 3.4.2.2[link]) between hexagonal and orthorhombic lattices and automatically selected the higher-symmetry one.

References

Margiolaki, I., Wright, J. P., Fitch, A. N., Fox, G. C. & Von Dreele, R. B. (2005). Synchrotron X-ray powder diffraction study of hexagonal turkey egg-white lysozyme. Acta Cryst. D61, 423–432.Google Scholar
Smrčok, L., Koppelhuber-Bitschau, B., Shankland, K., David, W. I. F., Tunega, D. & Resel, R. (2001). Decafluoroquarterphenyl – crystal and molecular structure solved from X-ray powder data. Z. Kristallogr. 216, 63–66.Google Scholar








































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