ACA 2005, Workshop WK.01
Structure Solution and Refinement
of Difficult Structures
Using Powder Diffraction
Peter Y. Zaval...
 What is Reflex
 Restrains & Constraints
 Constraints in Reflex
 Examples of Restrained Refinement:
- Motion group (ri...
Materials Studio / Relex
Materials Studio
provides wide range of computational methods on the desktop
in structural and co...
Constraints
Constraints
• specify exact relationship between atomic or geometric parameters
• reduce number of variable pa...
Restrains
Restrains
• specify approximate (desirable) relationship between geometric parameters
• increase number of varia...
Constraints in Reflex
- Constraints on fractional atom positions and other geometric constraints are ignored
- Atoms that ...
Constraints in Reflex 2
From Reflex help:
Tip. Although Reflex allows you to define only translations, rotations, and intr...
0
1000
2000
3000
4000
5000
6000
7000
8000
9000
10000
11000
12000
10 20 30
Intensity
2-theta
Rietveld Refinement: Rwp = 8.0...
0
1000
2000
3000
4000
5000
6000
7000
8000
9000
10000
11000
12000
13000
14000
10 20 30 40 50 60
Libob2.pro
2-theta
Bis-Oxal...
0
1000
2000
3000
4000
5000
6000
7000
8000
9000
10000
11000
10 20 30 40 50 60
Intensity
2-theta
Rietveld Refinement: Rwp = ...
0
10000
20000
30000
40000
50000
60000
70000
10 20 30 40 50 60 70 80
Intensity
2-theta
Rietveld Refinement: Rwp = 13.84% Rw...
0
1000
2000
3000
4000
5000
6000
7000
8000
9000
10000
11000
12000
13000
10 20 30 40 50 60
Title =
2-theta
Motion group & To...
0
1000
2000
3000
4000
5000
6000
7000
8000
9000
10000
11000
12000
10 20 30 40 50 60
Intensity
2-theta
Rietveld Refinement: ...
Azithromycin – Degrees of Freedom
• Orthorhombic, P212121
• 3 motion groups:
- Azithromycin molecule – 6 parameters
- 2 Wa...
Azithromycin – Groups & Torsions
• Orthorhombic, P212121
• 3 motion groups:
- Azithromycin molecule – 6 parameters
- 2 Wat...
Demonstration
1. Motion group in FePO4
2. Motion group in .m. site, Li[B(C2O4)2]
3. Motion group in mm2 site, Na[B(C2O4)2]...
Instead of Conclusions
Special thanks to Accelrys
for providing full version
of the Materials Studio
Rigid-Body in Torsion
Reflex References
1. Alexander, L.E. X-ray Diffraction Methods in Polymer Science, Robert E. Kreiger Publishing Company (1...
Upcoming SlideShare
Loading in …5
×

Restrained refinement using Reflex

708 views
624 views

Published on

Workshop: "Structure Solution and Refinement of Difficult Structures Using Powder Diffraction".
ACA 2005 Orlando, FL

0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total views
708
On SlideShare
0
From Embeds
0
Number of Embeds
13
Actions
Shares
0
Downloads
3
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide

Restrained refinement using Reflex

  1. 1. ACA 2005, Workshop WK.01 Structure Solution and Refinement of Difficult Structures Using Powder Diffraction Peter Y. Zavalij Department of Chemistry and Biochemistry University of Maryland, College Park, MD Restrained refinement using Reflex
  2. 2.  What is Reflex  Restrains & Constraints  Constraints in Reflex  Examples of Restrained Refinement: - Motion group (rigid-body) in FePO4 - Motion groups in special positions, Li & Na [B(C2O4)2] - Motion group & torsion angle in VO(C6H5PO3) - Restrains in large molecules  Demonstration - Reflex restrained refinement Outlines
  3. 3. Materials Studio / Relex Materials Studio provides wide range of computational methods on the desktop in structural and computational chemistry and materials science offering expert-level modeling and simulation still in an easy-to-learn environment. Accelrys Inc. (www.accelrys.com) Materials Visualizer - construction & manipulation of models/structures Reflex - powder pattern simulation - ab initio indexing (ITO, TREOR, DICVOL & X-Cell1 ) - full pattern decomposition - automatic space group determination - structure refinement (the Rietveld method) - determination of crystal structures (Reflex +) Reflex works with any radiation and medium- to high-quality powder diffraction data. 1. Neumann, M. X-Cell - A Novel Indexing Algorithm for Routine Tasks and Difficult Cases, J. Appl. Cryst., 36, 356
  4. 4. Constraints Constraints • specify exact relationship between atomic or geometric parameters • reduce number of variable parameters For example: - special relationship between atomic coordinate and displacement parameters for atoms in special position, e.g. atom on diagonal mirror plane (1 1 0 ) has x=y - relationship between occupation factors, e.g. 2 different atoms (or group) occupying the same position (space) - H atoms in the fixed groups, e.g. CH group in aromatic rings, -CH3 group, etc. - rigid-body groups or molecules, e.g. fixed geometry benzene rind
  5. 5. Restrains Restrains • specify approximate (desirable) relationship between geometric parameters • increase number of variable parameters For example: - restrained composition (content of specific element in the unit cell) - approximately equal distances or angles of the same type - approximately flat groups - approximately isotropic displacement parameters - others
  6. 6. Constraints in Reflex - Constraints on fractional atom positions and other geometric constraints are ignored - Atoms that not included in a motion group or a torsion object are considered to be fixed - Limits on the variation of a degree of freedom cannot be specified. All degrees of freedom are either completely flexible or fixed 1 Relex automatically imposes symmetry constraints on: • Lattice parameters • Parameters of atoms in special positions • Motion groups or torsion angles Reflex allows only two type of constraints : • Motion groups (rigid-body) - a whole molecule, a molecular fragment or a single atom • Torsion angles - torsions of the molecular fragments within a motion group • Individual atoms can be refined when defined as motion groups
  7. 7. Constraints in Reflex 2 From Reflex help: Tip. Although Reflex allows you to define only translations, rotations, and intra-molecular torsions as degrees of freedom, these types of degrees of freedom are sufficient to refine any desired degree of freedom, including bond lengths and angles. Degrees of Freedom of Motion Groups in special positions: 1 This column also shows degree of freedom of individual atoms Symmetry Translation1 Rotation Total 1 3 3 6 -1 0 3 3 m 2 1 3 2 1 1 2 2/m 0 1 1 mm2 1 0 1 mmm, 222 0 0 0
  8. 8. 0 1000 2000 3000 4000 5000 6000 7000 8000 9000 10000 11000 12000 10 20 30 Intensity 2-theta Rietveld Refinement: Rwp = 8.03% Rwp(w/o bck) = 8.63% Rp = 6.33% Motion group in FePO4 • Monoclinic, P21/n 2 motion groups: - PO4 3- ion, general site – 6 parameters - Fe atom, general site – 3 parameters w/o constraints: 6 atoms – 24 parameters
  9. 9. 0 1000 2000 3000 4000 5000 6000 7000 8000 9000 10000 11000 12000 13000 14000 10 20 30 40 50 60 Libob2.pro 2-theta Bis-Oxalato-Borate (BOB) BOB- Ion Max. symmetry4m2 Li Salt - Li[B(C2O4)2] • Orthorhombic, Pnma Pseudo-hexagonal lattice parameters
  10. 10. 0 1000 2000 3000 4000 5000 6000 7000 8000 9000 10000 11000 10 20 30 40 50 60 Intensity 2-theta Rietveld Refinement: Rwp = 12.59% Rwp(w/o bck) = 15.78% Rp = 10.00% Li[B(C2O4)2] m • Orthorhombic, Pnma 2 motion groups: - BOB ion, symmetry .m. – 3 parameters - Li atom, same symmetry – 2 parameters • w/o constraints (8×2+3×3) – 33 parameters
  11. 11. 0 10000 20000 30000 40000 50000 60000 70000 10 20 30 40 50 60 70 80 Intensity 2-theta Rietveld Refinement: Rwp = 13.84% Rwp(w/o bck) = 18.43% Rp = 10.41% NaBOB & KBOB • Orthorhombic, Cmcm 2 motion groups: - BOB ion, symmetry m2m – 1 parameter - Metal atom, same symmetry – 1 parameter • w/o constraints (2×1+12×2) – 26 parameters
  12. 12. 0 1000 2000 3000 4000 5000 6000 7000 8000 9000 10000 11000 12000 13000 10 20 30 40 50 60 Title = 2-theta Motion group & Torsion angle in VO(PhPO3) • Monoclinic, C2 • 2 motion groups: - PhPO3 2- , general site – 6 parameters and - O atom, general site – 3 parameters - V atom, general site – 2 parameters or - vanadyl V=O motion group (if V-O distance is known) • w/o constraints – 36 parameters
  13. 13. 0 1000 2000 3000 4000 5000 6000 7000 8000 9000 10000 11000 12000 10 20 30 40 50 60 Intensity 2-theta Rietveld Refinement: Rwp = 15.94% Rwp(w/o bck) = 22.62% Rp = 11.77% Motion group & Torsion angle in VO(PhPO3) • Monoclinic, C2 • 2 motion groups: - PhPO3 2- , general site – 6 parameters - O atom, general site – 3 parameters - V atom, general site – 2 parameters • Torsion: – 1 parameter - – Ph –– PO3 – torsion angle defining orientation of PO3 group • w/o constraints – 36 parameters
  14. 14. Azithromycin – Degrees of Freedom • Orthorhombic, P212121 • 3 motion groups: - Azithromycin molecule – 6 parameters - 2 Water molecules (2×6) – 12 parameters • Torsions: – 7 parameters • w/o constraints (3×54) – 162 parameters Courtesy Dr. Srebri Petrov, U. of Toronto
  15. 15. Azithromycin – Groups & Torsions • Orthorhombic, P212121 • 3 motion groups: - Azithromycin molecule – 6 parameters - 2 Water molecules (2×6) – 12 parameters • Torsions: – 7 parameters • w/o constraints (3×54) – 162 parameters
  16. 16. Demonstration 1. Motion group in FePO4 2. Motion group in .m. site, Li[B(C2O4)2] 3. Motion group in mm2 site, Na[B(C2O4)2] 4. Motion group & torsion angle in VO(C6H5PO3) 5. Restrains in large molecules
  17. 17. Instead of Conclusions Special thanks to Accelrys for providing full version of the Materials Studio Rigid-Body in Torsion
  18. 18. Reflex References 1. Alexander, L.E. X-ray Diffraction Methods in Polymer Science, Robert E. Kreiger Publishing Company (1985). 2. Baur, W.H.; Kassner, D., Acta Cryst. B 48, 356-369 (1992). 3. Baldinozzi, J.; Berar, J.F. "Modeling of line-shape asymmetry in powder diffraction", J.Appl.Cryst., 26, 128, (1993). 4. Boultif, A.; Louër,D. "Indexing of Powder Diffraction Patterns for Low-Symmetry Lattices by the Successive Dichotomy Method", J. Appl. Cryst. 24, 987-993 (1991) 5. Caglioti, G.; Paoletti, A.B.; Ricci, F.P. "Choice of collimators for a crystal spectrometer for neutron diffraction", Nucl. Instrum. Meth., 3, 223-228 (1958). 6. Cromer, D.T.; Weber, J.T. International Tables for X-ray Crystallography, Vol. IV, Ibers, J.A.; Hamilton, W.C., Eds., The Kynoch Press: Birmingham, 99-101 (1974). 7. David, W.I.F. "Powder diffraction peak shapes. Parameterization of the pseudo-Voigt as a Voigt function", J.Appl.Cryst., 19, 63-64, (1986). 8. Debye, P. Ann. Physik., 46, 809 (1915). 9. Dollase, W.A. "Correction of intensities for preferred orientation in powder diffractometry: application of the March model", J. Appl. Cryst., 19, 267-272 (1986). 10. Doyle, P.A.; Turner, P.S. "Relativistic Hartree-Fock X-ray and electron scattering factors", Acta Cryst., A24, 390 (1968). 11. Engel, G.E.; Wilke, S.; Harris, K.D.M.; Leusen, F.J.J, J. Appl. Cryst. 32, 1169 (1999). 12. Hermann, C. Z.Kristallogr., 68, 257-287 (1928). 13. Howard, C.J. "The Approximation of Asymmetric Neutron Powder Diffraction Peaks by Sums of Gaussians", J.Appl.Cryst. 15, 615 (1982). 14. Finger, L.W.; Cox, D.E.; Jephcoat, A.P. "A Correction for Powder Diffraction Peak Asymmetry due to Axial Divergence" J. Appl. Cryst. 27, 892 (1994). 15. Klug, H.P.; Alexander, L.E. X-ray Diffraction Procedures, 2nd Ed., John Wiley: New York (1974). 16. Le Bail, A.; Duroy, H.; Forquet, J.L. Matter. Res. Bull. 23, 447-452 (1988). 17. Neumann, M. "X-Cell - A Novel Indexing Algorithm for Routine Tasks and Difficult Cases", J. Appl. Cryst., 36, 356 (2003). 18. Pawley, G.S. J. Appl. Cryst. 14, 357 (1981). 19. Press, W.H.; Flannery, B.P.; Tuekolsky, S.A.; Vetterlin, W.T. Numerical Recipes , Cambridge University Press (1986). 20. Rietveld, H.M. "A Profile Refinement Method for Nuclear and Magnetic Structures", J. Appl. Cryst., 2, 65-71 (1969). 21. Scherrer, P. Gött. Nachr., 2, 98 (1918). 22. Smith, G.S.; Snyder, R.L. J. Appl. Cryst. 12, 60-65 (1979). 23. Thompson, P.; Cox, D.E.; Hastings, J.B. "Rietveld Refinement of Debye-Scherrer Synchrotron X-ray Data from Al2O3", J.Appl.Cryst., 20, 79-83, (1987). 24. Tomandl, R.L. Univ. Erlangen, Private Communication (1987). 25. Toraya, H.; Marumo, F. Mineral. J., 10, 211 (1981). 26. Visser, J.W. "A Fully Automatic Program for Finding the Unit Cell from Powder Data", J. Appl. Cryst., 2, 89 (1969). 27. Warren, B.E. X-ray Diffraction, Addison-Wesley: Reading (1969). 28. Werner, P.E.; Eriksson, L.; Westdahl, M. "TREOR, a semiexhaustive trial-and-error powder indexing program for all symmetries", J. Appl. Cryst., 18, 367-370 (1985). 29. Wilson, A.J.C. Mathematical theory of X-ray powder diffraction, Philips Technical Library: Eindhoven (1963). 30. Yakimanski, A. V.; Kolb, U.; Matveeva, G. N.; Voigt-Martin, I. G.; Tenkovtsev, A. V. "The Use of Structure Analysis Methods in Combination with Semi-empirical Quantum-Chemical Calculations for the Estimation of Quadratic Nonlinear Optical Coefficients of Organic Crystals", Acta. Cryst., A53, 603-614 (1997). 31. Young, R.A. The Rietveld Method , IUCr Monographies of Crystallography 5, Oxford University Press, Oxford (1993).

×