Structure analysis from X-ray powder data using real-space methods and pair distribution function analysis
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1 Structure analysis from X-ray powder data using real-space methods and pair distribution function analysis Martin U. Schmidt Institute of Inorganic and Analytical Chemistry Goethe-University, Frankfurt am Main Presentation, Bologna,
2 Content Part I: Crystal structure determination from X-ray powder data by real-space methods Part II: Pair Distribution Function (PDF) analysis of nanocrystalline organic compounds 2
3 Structure analysis from X-ray powder data No single crystals? X-ray powder diagram with (at least) peaks? (Required: Measurement in transmission mode!) Try structure determination from X-ray powder data! Int. Quality sufficient Quality too low / 3
4 Structure analysis from X-ray powder data Standard procedure: Step 1: Indexing Peak positions Lattice parameters Crystal structure prediction (with or without previous indexing) Step 2: Structure solution (e.g. by real-space methods) Peak intensities Approximate crystal structure Step 3: Rietveld refinement Full powder pattern Crystal structure 4
5 Structure analysis from X-ray powder data R Cl N N H S H 3 C N N S. n H 2 (n = 1-3) Ca 2+ R = Cl : Pigment Yellow 183, Phases:,,,, solvates R = CH 3 : Pigment Yellow 191, Phases:,,,,, solvates Both used for plastics colouration M.U. Schmidt et al., European Patent (2001) 5
6 X-Ray Powder Diffraction -P.R.183, lab data, measured in routine manner ( -P.Y.191: isotypic) Diffractometer: STE-Stadi-P - Ge(111) monochr. - Cu-K 1 - linear PSD - transmission a = (3) Å Indexing b = (6) Å (DICVL) c = (1) Å P 1, = (5) Z = 2 = (3) = (3) V = (1) Å 3 1 H 2 6
7 Structure solution by real-space methods Program DASH Ca 2+ Translation ( x, y, z ) Rotation ( x, y, z ) In each step: - calculation of the PD - comparison with exp. PD until calc. PD fits exp. PD Intramol. torsions Structure solved Ca 2+ (H atoms neglected) 7
8 Rietveld refinements Program TPAS Restraints on: - bond lengths - bond angles - planarity of aromatic ring systems Anisotropic peak broadening No preferred orientation 8
9 Rietveld refinement of -P.Y. 183 Lab data (STE) R wp = 4.6 % R p = 3.4 % 2 =
10 X-Ray Powder Diffraction of -P.Y P.Y. 191, lab data a = (1) Å Indexing b = (2) Å (DICVL) c = (3) Å P 1, = (1) Z = 2 = (1) = (1) V = (3) Å 3 2 H 2? 10
11 Structure solution by real-space methods 1 st attempt Translation ( x, y, z ) Rotation ( x, y, z ) Intramol. torsions Ca 2+ (H atoms neglected) (H atoms neglected) 11
12 Structure solution by real-space methods Result: - rganic anion: located - Molecular geometry: sensible - Ca 2+ and H 2 : questionable - Ca 2+ coordination: strange 12
13 Structure solution by real-space methods 2 nd attempt: 2 Ca 2+, both on 1 (cc. ½) Translation ( x, y, z ) Ca 2+ Rotation ( x, y, z ) Intramol. torsions Ca 2+ (H atoms neglected) (H atoms neglected) 13
14 Structure solution by real-space methods Result: - rganic anion: reproduced - Molecular geometry: sensible - Both Ca 2+ moved off from 1 - Ca 2+ coordinations: strange Where is Ca 2+? Where is H 2? 14
15 Structure solution by real-space methods Ca 2+ with occupancy ½: 18/2 = 9 electrons : 8 electrons (H 2 : 10 electrons) Both Ca 2+ and both H 2 substituted by F (9 electrons) Structure solution by Rietveld refinement (program TPAS): - Positions and occupancies of F refined - Restraints for the organic anion (bond lengths, bond angles, planar groups) 15
16 Structure solution by real-space methods Results: Atom cc. No. of e - F F F F Assignment Ca 2+ H 2 H 2 H 2 Ca 2+ on general position Trihydrate! 16
17 Crystal structures -P.Y. 183, -P.Y. 191 Monohydrates -P.Y. 191 Trihydrate 17
18 Advertisement break Further structures solved from X-ray powder data by real space methods: - organic pigments, e.g. H N H 3 C N N H H N H N N H - metal complexes H 2 N Pigment Yellow pharmaceutical API, including - hydrates of salts - solvates Cooperations and inquiries welcome! 18
19 Part II: Pair Distribution Function (PDF) analysis of nanocrystalline organic compounds 19
20 Pair Distribution Function (PDF) PDF, G(r): Probability to find two atoms with a distance r - weighted with the atomic number (for X-rays) - normalised to a homogeneous atom density - similar to a sphere-averadged Patterson, but for amorphous compounds, too G(r) PDF: G(r) = 4 r [ (r) 0 ] 0 r r 20
21 How to get the PDF Powder diagram - total scattering - measured to high 2 - background measured Int Carefull background correction 2 / Normalisation F(Q) Fourier transformation Q / Å -1 21
22 How to get the PDF Probability G(r) / Å -2 1 Pair distribution function Interatomic distance r / Å 22
23 Pair Distribution Function (PDF) Applications of PDF: Local structures of - quasicrystals - disordered crystals - nanocrystalline inorganic compounds - amorphous compounds - glasses New: nanocrystalline and amorphous organic compounds 23
24 PDF on a nanocrystalline pigment H 3 C H 3 C N N H H N CH 3 NH Pigment Yellow 213 (for car coatings) CH3 HN Int. -Phase (yellow) -Phase (brown) -Phase: - indexing failed - electron diffraction - powder diffraction: real-space methods - Rietveld refinement => Crystal structure / M. U. Schmidt, S. Brühne, A. K. Wolf, A. Rech, J. Brüning, E. Alig, L. Fink, C. Buchsbaum, J. Glinnemann, J. van de Streek, F. Gozzo, M. Brunelli, F. Stowasser, T. Gorelik, E. Mugnaioli, U. Kolb, Acta Cryst. B 2009, 65,
25 PDF on a nanocrystalline pigment a = (3) Å b = (6) Å c = (7) Å = (4) = (9) = (10) V _ = (1) Å 3 P 1, Z = 2 View direction [100] Layer structure 3.3 Å View direction [011] 25
26 PDF on a nanocrystalline pigment -Phase: Best sample ever obtained Synchrotron data (ESRF, ID31) / (for = 1.54 Å) H 3 C H CH 3 N N H 3 C N H NH CH3 HN 26
27 PDF on a nanocrystalline pigment -Phase: Best sample ever obtained Synchrotron data (ESRF, ID31) / (for = 1.54 Å) Does this diagram contain any usefull information? Yes! Use Pair Distribution Function Analysis (PDF)! 27
28 PDF on a nanocrystalline pigment Synchrotron data (ESRF, ID31): - = 0.40 Å -2 (max) = longer counting time at high 2 Int -Phase -Phase / 28
29 PDF on a nanocrystalline pigment Synchrotron data (ESRF, ID31): - = 0.40 Å -2 (max) = longer counting time at high 2 Int -Phase -Phase Carefull background correction / F (Q) Normalisation 5 Q / Å Q max = 15 Å -1 29
30 PDF on a nanocrystalline pigment -Phase 3.3 Å G(r) / Å Å Layer distance Domain size > 100Å r / Å 30
31 PDF on a nanocrystalline pigment -Phase G(r) / Å Å Distances => Molecular stacking Domain size < 40Å (in stacking direction) r / Å 31
32 PDF on a nanocrystalline pigment -Phase and -phases G(r) / Å -2 -Phase r / Å 32
33 PDF on a nanocrystalline pigment - and -phases G(r) / Å -2 -Phase -Phase r / Å Molecule Neighbouring molecules (packing) => Local structures of - and -phases similar 33
34 PDF of a pharmaceutical formulation Formulation: - Felodipine (well crystalline API) - in two different types of "Eudragit" polymers (polyacrylates) - Melt extrusion Experimental observation: 10 % API 90 % polymer 1 Poor dissolution behaviour 10 % API 90 % polymer 2 Poor dissolution behaviour 10 % API 85 % polymer 1 5 % polymer 2 Why? Much better dissolution behaviour 34
35 PDF of a pharmaceutical formulation 10 % API in polymer 1 In t Polymer 1 10 % API in polymer 1 2 / G(r) PDF => API is dissolved No structural changes of polymer 1 r / Å 35
36 PDF of a pharmaceutical formulation 10 % API in polymer 2 In t Polymer 2 10 % API in polymer 2 2 / G(r) PDF => API is dissolved No structural changes of polymer 2 r / Å 36
37 PDF of a pharmaceutical formulation 10 % API 85 % polymer 1 5 % polymer 2 G(r) PDF 10 % API 85 % polymer 1 5 % polymer 2 10 % API in polymer 1 Structure of the mixture changes considerably. 10 % API in polymer 2 r / Å This explains the observed differences in the dissolution behaviour. 37
38 Pair Distribution Function (PDF) Further applications of PDF: - Pharmaceutical cocrystals: Prove that a micronized cocrystal remains to be a cocrystal, even if it is amorphous. (Done) - Similarly: hydrates, solvates, polymorphs - Investigation of local structures in disordered organic compounds. (Done) - Investigation of packing motifs for semi-amorphous organic compounds. (Done) - Local structures of nanocrystalline and amorphous organic compounds 38
39 Acknowledgements Crystallization attempts: Melt extrusion: Labor. powder diffraction: Thermal analyses: Synchrotron data: Structure solution and Rietveld refinement: PDF analysis: Financial support: J. Brüning, A. Rech, J. Djanhan and many others... J. Dressman & coworkers (Univ. Frankfurt) E. Alig, L. Fink, J. Glinnemann, M. Ermrich (Reinheim) E. Alig F. Gozzo (SLS) M. Brunelli (ESRF) R.E. Dinnebier (NSLS) J. van de Streek, S. Ivashevskaya, C. Buchsbaum F. Stowasser (Basel) S. Brühne, N. Rademacher DFG (SFB 625), DAAD, Univ. Frankfurt Clariant GmbH and other companies 39
40 For Part I: References 1. S. N. Ivashevskaya, J. van de Streek, J. E. Djanhan, J. Brüning, E. Alig, M. Bolte, M. U. Schmidt, P. Blaschka, H. W. Höffken, P. Erk: "Structure determination of seven phases and solvates of Pigment Yellow 183 and Pigment Yellow 191 from X-ray powder and single-crystal data", Acta Cryst B 2009, 65, M. U. Schmidt, J. van de Streek, S. N. Ivashevskaya: "The First Crystal Structures of Industrial Laked Yellow Pigments Determined by X-ray Powder Diffraction ", Chem. Eur. J. 2009, 15, For Part II: 1. M. U. Schmidt, S. Brühne, A. K. Wolf, A. Rech, J. Brüning, E. Alig, L. Fink, C. Buchsbaum, J. Glinnemann, J. van de Streek, F. Gozzo, M. Brunelli, F. Stowasser, T. Gorelik, E. Mugnaioli, U. Kolb: "Electron diffraction, X-ray powder diffraction and pair-distribution-function analyses to determine the crystal structures of Pigment Yellow 213, C 23 H 21 N 5 9 ", Acta Cryst. B 2009, 65, K. Nollenberger, A. Gryczke, Ch. Meier, J. Dressman, M. U. Schmidt, S. Brühne: "Pair distribution function X-ray analysis explains dissolution characteristics of felodipine melt extrusion products ", J. Pharm. Sci. 2009, 98, This presentation is available from: 40
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