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SYSTEM-S The Challenge of Automated Structure Determination

SYSTEM-S The Challenge of Automated Structure Determination. Ton Spek National Single Crystal Service Utrecht University, The Netherlands. The Challenge. Early 1990’s, with a serial detector TurboCAD4 on rotating anode producing about one data set per day ==> need for:

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SYSTEM-S The Challenge of Automated Structure Determination

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  1. SYSTEM-SThe Challenge of Automated Structure Determination Ton Spek National Single Crystal Service Utrecht University, The Netherlands

  2. The Challenge • Early 1990’s, with a serial detector TurboCAD4 on rotating anode producing about one data set per day ==> need for: • 1-Automated data collection • 2-Automated structure determination • Ad1: Argus (Schreurs/Duisenberg) • Ad2: System-S (Spek, 1991-)

  3. Routine Structure Determination Single Crystal I Data collection (CAD4/Argus: GO) I Formula I Autosolve, Refine and Validate (S: NQA) I ORTEP

  4. Current Setup KappaCCD/Rotating Anode/LNT I Collect, DENZO or EVAL-CCD (Not AUTO!) I Import.cif (includes Formula) I System-S Auto-Mode: platon -F import.cif I ORTEP/PLUTON Plots

  5. Standard System-S Example • Two files: name.ins & name.hkl • Content name.hkl : SHELX style HKLF 3/4 • Content name.ins: TITL, CELL, SFAC, UNIT, HKLF 3 or 4 • Note: No Spacegroup Info Needed • Run: s name.ins NQA.

  6. Example: with shelx.ins & shelx.hkl Structure solved/refined in 18 seconds

  7. Critical Points of Failure • Formula - Can be either incomplete or completely wrong (Example later). • Space group - Often not uniquely determined when not P-1, P21/c or Pbca (e.g. Cc or C2/c) • Phase Problem - Multiple methods (Shelxs/Sir etc) • Atom type assignment • Non-ideal crystal: Disorder, Twinning • Voids with disordered (unknown) content (solvent mixture, charges)

  8. Misassigned Atom Types (S & P)

  9. Atom Type Assignment Assignment Methods (can be) based on: 1 - the analysis of Peak heights 2 - the value of the displacement parameters 3 - Population parameter refinement (S) 4 - Refinement of each site with alternative scattering types (E.g. C,N,O) 5 - Chemistry (& CSD knowledge, Mogul)

  10. Raw Output from SHELXS86

  11. Result of the EXOR workup

  12. Space-group Determination • Use LePage Algorithm for the Metrical Symmetry Determination of the Lattice • Get Laue averages for each of the proposed (Sub)Lattices and Laue group. • Select tentative Lattice (e.g. tP, 4/m) • Get systematic absences • Select tentative space-group

  13. Phase Determination Primary: • SHELXS86 & SHELXS97 • SIR97 & SIR2002 • DIRDIF PATTY & ORIENT ‘WORKUP’ of Approximate Solutions: • EXOR(cise)

  14. SYSTEM-S DESIGN FEATURES • EASY USE OF THE BEST PUBLIC DOMAIN TOOLS (NO LOCAL MODIFICATION) • DIRECTORY TREE STRUCTURE FOR THE ARCHIVAL OF INTERMEDIATE FILES • MANAGEMENT OF MULTIPLE SPACE GROUP & STRUCTURE DETERMINATION ATTEMPTS (SHELXS, SIR, DIRDIF) • AUTOMATIC, GUIDED AND COMMAND LINE MODES OF OPERATION • BUILD-IN VALIDATION

  15. Special Features • Automatic Spacegroup determination • EXOR: Automatic workup of raw Direct Methods results (population refinement) • Automatic H-atom assignments • Automatic numbering scheme • Missed symmetry handling • Automatic (weighted) refinement • Validation

  16. Horror Story • Example: Paper submitted for publication in Acta Cryst. C • Supposedly coordination complex with composition Cu(2+) Ligand(2-), at least that was what the chemist wanted to see confirmed with a routine X-ray study • That is what he got …. With R < 7% using SHELXTL software

  17. Cu NOT coordinated ! False Structure, R < 7%

  18. Correct Structure • Cu(2+) --> Br(1-) [HBr was used during the synthesis/crystallisation] • Additional H-atoms needed/found on sp3-N and -CO2 (short intermolecular acid bridge. • Thus NOT Cu(2+) L(2-) but Br(1-)L(1+) • Problems clearly indicated with validation ALERTS

  19. Correct Structure, R < 6%

  20. What about the ORTEPS ? • Surprisingly, the ORTEPS of the false and correct structure are very similar • Ellipsoids are as expected for room-temperature data

  21. Ortep of the False Structure

  22. Ortep of the Correct Structure

  23. Redetermination with System-S • System-S / Guided Mode • Using original Room-temperature data and expected formula (CuL) • Result: Direct Methods (SIR etc) reproduce results largely consistent with the expected composition apart from some C,N & O miss-assignments, not uncommon for RT data and easy to correct.

  24. O O N N C Br Raw Result with SIR97

  25. EXPERIENCE • AUTOMATIC STRUCTURE DETERMINATION SYSTEM-S WORKS CURRENTLY BEST FOR : • - LIGHT ATOM STRUCTURES • - BASED ON LOW TEMPERTURE DATA • - WITH NO DISORDER • - WITH CORRECT FORMULE Otherwise: • The Manual GUIDED-Mode appears to be the more appropriate protocol.

  26. CONCLUDING REMARKS • SYSTEM-S can be used easily for the re-examination of structures with CIF + FCF data taken from the Acta Cryst Archives. • Future implementation: • - (C,N,O) etc. L.S. Refinement • - More chemical knowledge • - Extention of the already available procedures for Structure determination without any Content Information.

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