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 : [email protected] 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

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 : [email protected]


Getting cell parameters from powder diffraction data armel le bail

Outline

The Indexing Problem(s)

Indexing Software

Indexing Benchmarks

Demonstrations (screen shots)

Live Demonstrations


Getting cell parameters from powder diffraction data armel le bail

The Indexing Problem(s)

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

Data :20 first peak positions

Problem overdetermined,looks simple…


Getting cell parameters from powder diffraction data armel le bail

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.


Getting cell parameters from powder diffraction data armel le bail

INDEXING SOFTWARE

The best description is in this 2003 Robin Shirley paper :


Getting cell parameters from powder diffraction data armel le bail

From Robin Shirley


Getting cell parameters from powder diffraction data armel le bail

From Robin Shirley

Underlined are inside the CRYSFIRE package


Getting cell parameters from powder diffraction data armel le bail

The Indexing Benchmarks


Getting cell parameters from powder diffraction data armel le bail

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


Getting cell parameters from powder diffraction data armel le bail

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)


Getting cell parameters from powder diffraction data armel le bail

ACADEMIC SOFTWARE WITH TRADITIONAL OPEN ACCESS


Getting cell parameters from powder diffraction data armel le bail

WinPLOTR saving the Y2O3 peak positions for an indexing program


Getting cell parameters from powder diffraction data armel le bail

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.


Getting cell parameters from powder diffraction data armel le bail

McMaille displaying its best results for Y2O3


Getting cell parameters from powder diffraction data armel le bail

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.


Getting cell parameters from powder diffraction data armel le bail

WinPLOTR displaying the McMaille best cell for Y2O3


Getting cell parameters from powder diffraction data armel le bail

Background estimation with PowderX for -AlF3


Getting cell parameters from powder diffraction data armel le bail

K2 stripping with PowderX for -AlF3


Getting cell parameters from powder diffraction data armel le bail

Peak positions hunting with PowderX for -AlF3


Getting cell parameters from powder diffraction data armel le bail

McMaille displaying its best results for -AlF3


Getting cell parameters from powder diffraction data armel le bail

F.o.M. for -AlF3


Getting cell parameters from powder diffraction data armel le bail

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


Getting cell parameters from powder diffraction data armel le bail

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


Getting cell parameters from powder diffraction data armel le bail

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


Getting cell parameters from powder diffraction data armel le bail

WinPLOTR saving the C28H24O8 data for TREOR


Getting cell parameters from powder diffraction data armel le bail

TREOR running inside of WinPLOTR for C28H24O8


Getting cell parameters from powder diffraction data armel le bail

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


Getting cell parameters from powder diffraction data armel le bail

WinPLOTR saving the tetracycline hydrochloride data for DICVOL


Getting cell parameters from powder diffraction data armel le bail

Selection of the indexing conditions for DICVOL04


Getting cell parameters from powder diffraction data armel le bail

DICVOL04 cell Proposition for the tetracycline hydrochloride


Getting cell parameters from powder diffraction data armel le bail

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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