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. 278-280

Section 3.4.4.6. Examples of applications of indexing programs

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. Examples of applications of indexing programs

| top | pdf |

3.4.4.6.1. Indexing using DICVOL06

| top | pdf |

The program DICVOL06, as implemented in the WinPLOTR/FULLPROF suite (Roisnel & Rodríquez-Carvajal, 2001[link]) and recently introduced into EXPO, was applied to two experimental diffraction patterns.

Example 1

Norbornene (Brunelli et al., 2001[link]). Published information: C7H10, monoclinic, a = 7.6063 (9), b = 8.6220 (1), c = 8.749 (1) Å, β = 97.24 (1)°, P21/c, experimental range 5–60° 2θ, λ = 0.85041 Å, RES = 1.0 Å (where RES is the data resolution), synchrotron data, indexed by Fzon (Visser, 1969[link]).

The 2θ values of the first 25 peaks, in the range 5–25°, were determined by WinPLOTR and supplied to DICVOL06. The first 20 peaks were used for searching for the solution. No plausible cell was found when assuming that no impurity was present and exploring all the systems (from cubic to triclinic). DICVOL06 was also unsuccessful when the non-default strategies of extended search and data correction for zero-point error were considered (by setting some flags to 1 in the input file). If it was supposed that two impurity lines might be present among the peaks (by setting the flag corresponding to the maximum number of accepted impurity/spurious lines to 2), DICVOL06 was able to find the following monoclinic cell: a = 8.7480 (36), b = 8.6313 (32), c = 7.6077 (26) Å, β = 97.201 (33)°, with two unindexed lines, M18 = 41.5, F18 = 125(0.0041, 35). The refinement of the cell by considering all the 25 lines gave a = 7.6087 (26), b = 8.6295 (30), c = 8.7459 (34) Å, β = 97.201 (34)°, which is very similar to the published one; 23 indexed lines, M20 = 30.1, F20 = 102.6(0.0048, 41). The presence of the two impurity lines has been ascribed by the authors to a small amount of hexagonal plastic phase.

Example 2

Cu(II)–Schiff base complex (Banerjee et al., 2002[link]). Published information: Cu(C15H12NO2)2, triclinic, a = 11.928 (4), b = 12.210 (5), c = 9.330 (5) Å, α = 102.54 (4), β = 111.16 (5), γ = 86.16 (4)°, [P \bar 1], experimental range 6–100° 2θ, λ = 1.54056 Å, RES = 1.22 Å, high-quality X-ray laboratory data, indexed by DICVOL91. The 2θ values of the first 30 peaks, in the range 6–25°, were determined by WinPLOTR and supplied to DICVOL06. The first 20 peaks were used for searching for the solution. If it was assumed that no impurity was present, no plausible cell was found down to the monoclinic system. When the triclinic system was explored, DICVOL06 suggested only one plausible solution: a = 12.2157 (73), b = 12.2031 (77), c = 9.3071 (41) Å, α = 65.798 (46), β = 102.572 (59), γ = 95.711 (61)°, with no unindexed lines, M20 = 27.0, F20 = 77.0(0.010, 26). The refinement of the cell considering all the 30 lines gave a = 12.2125 (65), b = 12.1989 (61), c = 9.3016 (32) Å, α = 65.826 (33), β = 102.569 (40), γ = 97.755 (44)°, no unindexed lines, M20 = 27.9, F20 = 72.8(0.0106, 26). For this,the corresponding conventional cell is a = 11.93313 (61), b = 12.2125 (65), c = 9.3016 (32) Å, α = 102.569 (40), β = 111.152 (33), γ = 86.151 (44)°, similar to the published one.

3.4.4.6.2. Indexing using N-TREOR09

| top | pdf |

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]

Figure 3.4.1 | top | pdf |

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

Banerjee, S., Mukherjee, A., Neumann, M. A. & Louër, D. (2002). Ab-initio structure determination of a Cu(II)-Schiff base complex from X-ray powder diffraction data. Acta Cryst. A58, c264.Google Scholar
Brunelli, M., Fitch, A. N., Jouanneaux, A. & Mora, A. J. (2001). Crystal and molecular structures of norbornene. Z. Kristallogr. 216, 51–55.Google Scholar
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
Roisnel, T. & Rodríquez-Carvajal, J. (2001). WinPLOTR: a windows tool for powder diffraction pattern analysis. Mater. Sci. Forum, 378–381, 118–123.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
Visser, J. W. (1969). A fully automatic program for finding the unit cell from powder data. J. Appl. Cryst. 2, 89–95.Google Scholar








































to end of page
to top of page