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Notes on Example 1.1 (Zn)

Notes on Example 1.1 (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.

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Notes on Example 1.1 (Zn)

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  1. Notes on Example 1.1 (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 Extinction correction

  3. Test of symmetry

  4. Information from merging of symmetry equiv. reflections

  5. Jana2006 and Superflip are distributed together but Superflip is an independent program. Input file: jobname.inflip Output files: electron density and jobname.sflog Jana provides interface for some frequently used commands, the others are available in the superflip manual (superflip.fzu.cz) Interface to Superflip • Interpretation of the resulting density: • Superflip finds symmetry • EDMA or Jana2006 find positions of peaks and assign chemical types

  6. Independent check of symmetry by Superflip in direct space

  7. Format of 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. Adding of hydrogen atoms

  10. Automatically created keep commands

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

  12. Refinement 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.

  13. R statistics indicates an extinction

  14. 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.

  15. 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

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

  17. No Important warnings on the bottom of the refinement listing (It may contain warnings about non-positive ADP and about large correlations)

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