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Example 1: Zn

Example 1: Zn Application of Jana2006 to simple organometallic structure. Creating jobname, reading input files, determination of symmetry, solving structure with charge flipping, editing of atomic parameters, refinement, hydrogen assignment. Chemical formula: (NH 3 CH 2 CH 2 NH 3 ) 2 ZnCl 6

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Example 1: Zn

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  1. Example 1: Zn Application of Jana2006 to simple organometallic structure. Creating jobname, reading input files, determination of symmetry, solving structure with charge flipping, editing of atomic parameters, refinement, hydrogen assignment. Chemical formula: (NH3CH2CH2NH3)2ZnCl6 Single crystal data measured with Oxford Diffraction four-circle diffractometer Input files: Zn.hkl, Zn.sum Frame scaling, absorption correction: done with software of diffractometer

  2. Data import Determination of symmetry Charge flipping Anisotropic ADP Hydrogens to carbon Hydrogens to nitrogen

  3. Weighting scheme, minimized function, R factors, goodness of fit 1. Refinement on F 2. Refinement on F2 R value in both cases: Good data should provide the same results for F and F2. Screen output of refinement: 1857 independent reflections, 1257 observed, 600 unobserved. 74 refined parameters. The maximal change during the refinement in terms of s.u. occurred for U13 coordinate of atom N1.

  4. Details about refinement listing In the Fo-Fc list the most important column is sq(wdFq) (weighted difference). Numbers below ~6 mean there is nothing left for refinement. R-statistics splits the data set to groups according to sinθ/λ or intensity.

  5. Zn compound after introducing isotropic Gaussian extinction There are still oscillations on “av. wd F” (numerator of GOF)and weighted diference “sqr(wdFq)” still shows some large numbers

  6. The found peaks projected along a*: admixture of another component may influence data reduction

  7. Details about M40 19 0 0 0 1.236363 0.000000 0.000000 0.000000 0.000000 0.000000 100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 000000 0.320509 0.000000 0.000000 0.000000 0.000000 0.000000 100000 Zn1 1 2 0.500000 0.294759 0.250000 0.116071 0.026192 0.022592 0.028442 0.000000-0.000292 0.000000 0101111010 Cl1 5 2 1.000000 0.100183 0.010873 0.207773 0.025679 0.036781 0.024603-0.000476-0.001518-0.000649 0111111111 Cl2 5 2 0.500000 0.322197 0.250000-0.255838 0.037633 0.030616 0.026326 0.000000 0.004409 0.000000 0101111010 Cl3 5 2 0.500000 0.119932 0.250000 0.171782 0.024537 0.047383 0.041946 0.000000 0.003058 0.000000 0101111010 . . . . Zn1 0.000000 0.000032 0.000000 0.000065 0.000239 0.000229 0.000245 0.000000 0.000188 0.000000 Cl1 0.000000 0.000048 0.000033 0.000095 0.000332 0.000370 0.000325 0.000291 0.000263 0.000277

  8. Refinement keys Before start of refinement: Automatic refinement keys: all refinement keys (except twin fractions and individual occupations are set to “1” Automatic symmetry restrictions: refinement keys of structure parameters forbidden by symmetry are set to “0” and the program derives also equation between parameters following from symmetry User commands: keep commands, fixed commands, equations, restrictions. They must not be in contradiction, otherwise: unpredictable results. The checkboxes are ignored when automatic keys and restrictions are applied, except scales and individual occupations. For powder profile parameters only background is automatic.

  9. List of constraints/restraints for Example 1 (Zn) printed in refinement listing

  10. Example 2.1: PbSO4 Application of Jana2006 to simple structure from powder data. Ideal case where determination of symmetry and structure solution are simple. Powder data measured with laboratory diffractometer Input files: PbSO4.mac (powder profile data) PbSO4.txt (additional information)

  11. Trap: For wavelength type first select Kalpha1/Kalpha2 doublet and then select X-ray CuWarning: selecting X-ray Cu first and Kalpha1/Kalpha2 doublet in the second step would give slightly different wavelengths because the doublet would be calculated from the current wavelength, i.e. the average value. correct incorrect

  12. Step 1: profile fitting Wizard for profile fitting connects tools, which can be also started separately from the main Jana window

  13. Step 2: symmetry determination Each line contains ratio of extinct and all reflections and Rp corresponding to a profile with discarded extinct reflections. Thus we are looking for case where number of extinct reflections is large without serious impact on Rp .

  14. Data import Refinement of profile parameters (with symmetry P1) Determination of symmetry Charge flipping (based on Bragg intensities calculated from the profile) Rietveld refinement

  15. Step 3: structure solution Superflip uses intensities from profile decomposition Step 4: Rietveld refinement Instead of Le Bail fit the intensities are calculated from the structure.

  16. Step 4: Completing the structure from difference Fourier map

  17. Example 3.1: AD3 Simple structure with pseudo-merohedric twinning. Finding twinning matrix from group-subgroup transformation. Creating publication CIF. Bis[N-(2-benzylidenepropylidene)phenyl]ether Single crystal data measured with Oxford Diffraction four-circle diffractometer Input files: AD3.hkl, AD3.sum Frame scaling, absorption correction: done with software of diffractometer

  18. Charge flipping Correcting chemical types Anisotropic ADP Hydrogens R=20%

  19. Cell parameters: 7.4728 55.89 6.0235 90 90.0418 90 Rint for mmm: 17.9% Rint for 2/m: 1.6% (setting b) Lost symmetry mmm -> 2/m: x -y -z can be used like twinning operation Refined twin fractions: 0.72, 0.28 R factor after twinning: 3.66%

  20. Example 3.2: PyNinit Simple structure with non-merohedric twinning. Handling twin overlaps in Jana2006 Single crystal data measured with Oxford Diffraction four-circle diffractometer Input files: 1st twin domain: pyNinit_twin1.hkl, pyNinit_twin1.sum 2nd twin domain pyNinit_twin2.hkl, pyNinit_twin2.sum hklf5: pyNinit_twin1_hklf5.hkl Twinning matrix: (-1 0 -0.733| 0 -1 0| 0 0 1) Frame scaling, absorption correction: done with software of diffractometer J. Černák, M. Dušek, K. Fejfarová, Acta Cryst. (2009). C65, m260-m262.

  21. LATTICE Current cell 14.5940(15) 9.8526(5) 16.0519(11) 90.005(5) 113.739(8) 90.016(6) 2112.8(3) Constrained current cell 14.6005(13) 9.8578(7) 16.0454(17) 90.0 113.814(12) 90.0 2112.8(3) Lattice reduction selected cell 14.5993 9.8527 16.0514 90.0061 113.7692 90.0239 mP 35 reduced cell 9.8527 14.5993 16.0514 113.7692 90.0061 90.0239 2113.0 Twin information 1: 14.5934 9.8530 16.0502 90.007 113.720 90.008 2112.9 2: 14.6015 9.8542 16.0544 90.002 113.764 90.030 2114.1 1: Total: 4970( 61.1%) Separate: 3201( 39.3%) Overlapped: 1769( 21.7%) 2: Total: 4930( 60.6%) Separate: 3161( 38.8%) Overlapped: 1769( 21.7%) Unindexed: 9 ( 0.1%)

  22. 1. Structure solution using 1st twin domain only: R ~ 17% 2. Introduction of twinning: R ~ 13%

  23. 3. Discarding partially overlapped reflections: R ~ 4%

  24. Where to stop? We want to discard as little reflections as possible 4. Using data of the second domain 5. Testing scale of domains

  25. 6. Using HKLF5 file: R ~ 5.5% without discarding reflections The diffractometer software should know more about overlaps than Jana2006

  26. Example 3.3: CsLiSO4 Simple structure with pseudo-merohedric 3-fold twinning. Finding twinning matrix from group->subgroup transformation. Transformation to four times larger reciprocal cell. Single crystal data measured with Oxford Diffraction four-circle diffractometer Input files: CsLiSO4.hkl, CsLiSO4.sum Frame scaling, absorption correction: done with software of diffractometer

  27. Good data No split reflections No overlaps

  28. Peaks projected along a*

  29. Peaks projected along b*

  30. Peaks projected along c* hexagonal unit cell • a = 10.89451(0.00058) • b = 10.88937(0.00058) • c = 8.80485(0.00041) • = 90.00104(0.00407) • = 90.02358(0.00406) • = 119.94547(0.00557) • V = 905.11

  31. From symmetry wizard this is evident that hexagonal symmetry is violated. Because cell parameters are exactly hexagonal merohedric twinning is highly probable. In order to get twinning matrices easily we shall use the highest hexagonal symmetry and use group-subgroup transformation tool. The symmetry wizard does not list orthorhombic possibilities because they are in contradiction with cell parameters. Orthorhombic cells will be available in group-subgroup transformation.

  32. Transformation to orthorhombic cell

  33. The discarded symmetry operations will be used as twinning operations. They are two -> we have created three-fold twin.

  34. Finally a transformation is offered to standard symmetry Cmcm. We can check new cell parameters in EditM50.

  35. Header of M95 now contains transformation from hexagonal to new orthorhombic elementary cell. It is applied during createng M90 before merging of reflections.

  36. Flags in M90 show that all reflections are indexed in the first domain. This is correct because the twin is merohedric.

  37. Twinning matrices Attempts to solve structure fail!!

  38. This will start Jana2006 to show Reciprocal space viewer.

  39. Can we use four times larger reciprocal cell + three-fold twinning?

  40. Transformation

  41. M95 with all transformations cumulated M90 should contain three domains: 1,2,3

  42. Solution with Superflip Correction of false Li Final refinement: R ~ 2.5%

  43. Example 3.4: Ca2Fe2O5 HT structural phase transition, coexistence of two phases in single crystal with strong overlaps. Single crystal data measured with Stoe IPDS-II imaging plate system Input files: HT_phase.M40, HT_phase.m50, HT_phase.m90, HT_phase.m95 and LT_phase.cif. The example starts from solved phases and shows how to connect them Kruger, H., Kahlenberg, V., Petřiček, V., Phillipp, F., Wertl, W. (2009): “Hightemperature structural phase transition in Ca2Fe2O5 studied by in situ X-ray diffraction and transmission electron microscopy”. J. Solid State Chem. 182, 1515-1523

  44. Low temperature (LT) phase Symmetry Pnma, a = 5.4707Å , b = 14.9897Å, c = 5.6302Å High temperature (HT) phase (> 710 °C) Symmetry Imma(00γ)s00, a = 5.4707Å , b = 14.9897Å, c = 5.6302Å

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