Getting Cell Parameters from Powder Diffraction Data
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Getting Cell Parameters from Powder Diffraction Data Armel Le Bail Université du Maine, Laboratoire des Oxydes et Fluorures, CNRS UMR 6010, Avenue O. Messiaen, 72085 Le Mans, France Email : alb@cristal.org. Outline The Indexing Problem(s) Indexing Software Indexing Benchmarks

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Getting Cell Parameters from Powder Diffraction Data Armel Le Bail

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Getting Cell Parameters from Powder Diffraction Data

Armel Le Bail

Université du Maine, Laboratoire des Oxydes et Fluorures, CNRS UMR 6010, Avenue O. Messiaen, 72085 Le Mans, FranceEmail : alb@cristal.org


Outline

The Indexing Problem(s)

Indexing Software

Indexing Benchmarks

Demonstrations (screen shots)

Live Demonstrations


The Indexing Problem(s)

1 to 6 unknownsmaximum :a, b, c, , , 

Data :20 first peak positions

Problem overdetermined,looks simple…


Difficulties come from :

- inaccuracy in peak positions (due to zeropoint error, sample misplacement, low resolution, bad crystallinity),

- the presence of impurities providing spurious additional peaks,

- the possibility to miss some large high-symmetry cells which can also be described in smaller sub-cells of lower symmetry,

- the fact that one of the a, b, c parameters can be very short if compared to the two others (dominant zone) so that the first diffraction peak involving it through the hkl Miller indices may not be included among the first 20 which will be exclusively h0l lines for instance (if b is small),

- etc.


INDEXING SOFTWARE

The best description is in this 2003 Robin Shirley paper :


From Robin Shirley


From Robin Shirley

Underlined are inside the CRYSFIRE package


The Indexing Benchmarks


Bergmann, J., Le Bail, A., Shirley, R. & Zlokazov, V. Zeitschrift für Kristallographie219 (2004) 783-790.


Demonstrations - Screenshots

WinPLOTR, PowderX(peak position hunting, and more)

McMaille, TREOR, DICVOL(indexing)

CHEKCELL(visualization, and more)

FULLPROF(cell-constrained whole pattern fitting, and more)


ACADEMIC SOFTWARE WITH TRADITIONAL OPEN ACCESS


WinPLOTR saving the Y2O3 peak positions for an indexing program


Typical data for indexing in automated mode with McMaille

Y2O3! Wavelength, zeropoint and NGRID (NGRID=3: black box mode) 1.54056 0.000 3! List of 2theta positions, intensity (min.=20) 20.504 1411. 29.157 11198. 33.791 2632. 35.910 531. 37.921 135. 39.848 606. 41.700 118. 43.488 881. 46.889 271. 48.528 4213. 50.120 230. 51.685 66. 53.207 506. 54.697 117. 56.169 404. 57.614 2603. 59.035 563. 60.433 471. 61.811 194. 63.178 149.


McMaille displaying its best results for Y2O3


McM20 = [100./(RP*N20)] * Br * Sy,

N20 is the number of possibly existing lines up to the 20th observed line (for a primitive P lattice). Br is a factor arbitrarily set to 6 for F and R Bravais lattices, 4 for I, 2 for A, B, C and 1 for P. Sy is a factor equal to 6 for a cubic or a rhombohedral cell, 4 for a trigonal/hexagonal/tetragonal cell, 2 for an orthorhombic cell, and 1 for a monoclinic or triclinic cell.


WinPLOTR displaying the McMaille best cell for Y2O3


Background estimation with PowderX for -AlF3


K2 stripping with PowderX for -AlF3


Peak positions hunting with PowderX for -AlF3


McMaille displaying its best results for -AlF3


F.o.M. for -AlF3


Examining with Chekcell the list of most probable -AlF3 cells from McMaille


Pawley or Le Bail methods are used for a penultimate proof of the cell quality(the ultimate being the structure solution and refinement)


The Le Bail fit of the -AlF3 conventional laboratory powder pattern by using FULLPROF and the P4/mmm space group, showing the possible (hk0, h+k = 2n) extinction rule


WinPLOTR saving the C28H24O8 data for TREOR


TREOR running inside of WinPLOTR for C28H24O8


The Le Bail fit of the C28H24O8 synchrotron powder pattern by using FULLPROF selecting the P21/c space group

Another plague of SDPD : anisotropic line broadening


WinPLOTR saving the tetracycline hydrochloride data for DICVOL


Selection of the indexing conditions for DICVOL04


DICVOL04 cell Proposition for the tetracycline hydrochloride


Live Demonstrations

Once a (good) powder pattern is recorded,and if the compound(s) remain unidentified, the time needed for a successful indexing is somewhere between 15 minutes and never…


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