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The MISSYM Family : Software for the detection of Missed or Pseudo Symmetry

The MISSYM Family : Software for the detection of Missed or Pseudo Symmetry. A.L.Spek Utrecht University The Netherlands. OVERVIEW. Correct space group assignment to a crystal structure is not always trivial.

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The MISSYM Family : Software for the detection of Missed or Pseudo Symmetry

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  1. The MISSYM Family:Software for the detection ofMissed or Pseudo Symmetry A.L.Spek Utrecht University The Netherlands

  2. OVERVIEW • Correct space group assignment to a crystal structure is not always trivial. • As a result, many (uncorrected) errors can be found in the literature and databases. • Some errors are harmful others are of a more esthetic nature. • Bob Sparks was addressing this issue with the program FINDSYM he has been working on. • For this reason I choose this topic for my presentation in this Bob Sparks Symposium.

  3. CrystallineMaterial • Type A: 3-D Translation Lattice 230 Space groups. • Type B: non-3D Translation Lattice Incommensurate, Misfit, Quasicrystal. We will Focus here on Type A structures.

  4. PreliminaryStructureDetermination • All 3D structures can be solved in principle in space group P1 (Direct Methods etc.) • Subsequent standard least-squares refinement of the model requires classification as either: - non-centrosymmetric (P1) or - (pseudo) centrosymmetric (P-1)

  5. Centro or Non-centrosymmetric ? • Correct assignment is not always trivial. • Refinement of (close to) centrosymmetric structures in P1 is mathematically unstable. • Mis-assignment -> geometry artifacts. • Dick Marsh: Borderline cases are best treated as centro-symmetric (static/dynamic disorder) • Inspect Fo/Fc of weak reflection data. • In general: chiral molecules-> non-centro SpGr. • Literature Example P1 <-> P-1.

  6. Praseodymium complex J.A.C.S. (2000),122,3413 – P1, Z = 2

  7. P-1, Z=2

  8. Praseodymium complex J.A.C.S. (2000),122,3413 – P1, Z = 2

  9. Lattice Symmetry • 229 higher symmetry groups than P1 • 1979, Dick Marsh paper in Inorg. Chem. ‘Some Incorrect Space groups in Inorganic Chemistry Volume 16’ (7!) • Change of Laue Group and/or crystal system (e.g. –1 to 2/m, i.e. triclinic to monoclinic; 4/m to 4/mmm) • Example Triclinic P-1 to Monoclinic C2/c Orthorhombic Pbca to Cubic Pa-3

  10. New Algorithm • 1982: CREDUC, Y Le Page J.A.C.,15,255. • Determination of the Metrical Symmetry of the lattice from the number of compatible two-fold axes. E.g. 5  tetragonal, 9  cubic • Two-axis = coinciding low-index (0,1,2) direct and reciprocal lattice vectors within a tolerance. • Actual symmetry can be lower, not higher than the metrical symmetry. • Extended version => Twin laws.

  11. The MISSYM Algorithm • Y. Le Page published in 1987 a follow-up to CREDUC called MISSYM (J.A.C.,20,264). • MISSYM Looks for support in the actual structure (I.e. coordinate set) for the proposed metrical symmetry elements. • Liberal tolerances are used in general. • Reflection data are needed for follow-up analysis by least-squares refinement.

  12. MISSYM Implementations • Y. Le Page – MISSYM/NRCVAX Leaves evaluation and implementation of reported higher symmetry to the researcher. • Hannemann et al. Part of ICSD Software • Bob Sparks, FINDSYM (Bruker Nonius) • A.L.Spek, ADDSYM (PLATON) • ?? MSI – Insight II ???

  13. PLATON/ADDSYM Extensions • Suggests automatically a revised space group, unit cell and origin transformation. • Generation of new ‘.res’ file for SHELXL refinm. • Allows for a number of non-fitting atoms. • Handles sub-cells. (structure prediction) • Accepts data in ‘.res’ and ‘.cif’ format. • Runs on files with multiple entries (CSD/CIF). • Display of revised (averaged) structure.

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  15. Comments • Hydrogen atoms and Disordered atoms are not included in the analysis. • Pseudo-symmetry can be both problematic and/or interesting (Inorganic Structures) • Missing Atoms (Incomplete structures) • Algorithm not suitable for macromolecules

  16. ADDSYM run on CSD • April 2002 release • Space group C2 (#5) • 2190 entries • 162 entries to be inspected for missed or pseudo-symmetry • About 90 entries pseudo-symmetric • Transformations to: C2/m, C2/c, I222, C2221, Aba2, Fddd, R32, R-3m, R-3c, P3121, I-4 • See also Acta Cryst. (2001), B57, 800-805.

  17. Section out of complete suspect entry list Section out of suspect entry list

  18. J.A.C.S. 2001 T

  19. Pseudo Symmetry Example

  20. Concluding Remarks • Software to check for missed/pseudo symmetry is now readily available e.g. www.cryst.chem.uu.nl/platon/ • ADDSYM included in IUCR/CHECKCIF • Proposed higher symmetry should either be implemented or convincingly discussed as pseudo-symmetry in a structure report. • Thanks Bob & Yvonne !

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