system-s the challenge of automated structure determination
DESCRIPTION
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: - PowerPoint PPT PresentationTRANSCRIPT
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SYSTEM-SThe Challenge of Automated Structure
Determination
Ton SpekNational Single Crystal Service
Utrecht University, The Netherlands
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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-)
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Routine Structure Determination
Single CrystalI
Data collection (CAD4/Argus: GO)I
FormulaI
Autosolve, Refine and Validate (S: NQA)I
ORTEP
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Current Setup
KappaCCD/Rotating Anode/LNTI
Collect, DENZO or EVAL-CCD (Not AUTO!)I
Import.cif (includes Formula)I
System-S Auto-Mode: platon -F import.cifI
ORTEP/PLUTON Plots
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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.
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Example: with shelx.ins & shelx.hkl
Structure solved/refined in 18 seconds
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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)
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Misassigned Atom Types (S & P)
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Atom Type Assignment
Assignment Methods (can be) based on:1 - the analysis of Peak heights2 - the value of the displacement parameters3 - Population parameter refinement (S)4 - Refinement of each site with alternative scattering types (E.g. C,N,O)5 - Chemistry (& CSD knowledge, Mogul)
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Raw Output from SHELXS86
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Result of the EXOR workup
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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
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Phase Determination
Primary:• SHELXS86 & SHELXS97• SIR97 & SIR2002• DIRDIF PATTY & ORIENT
‘WORKUP’ of Approximate Solutions:• EXOR(cise)
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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
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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
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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
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False Structure, R < 7%
Cu NOT coordinated !
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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
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Correct Structure, R < 6%
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What about the ORTEPS ?
• Surprisingly, the ORTEPS of the false and correct structure are very similar
• Ellipsoids are as expected for room-temperature data
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Ortep of the False Structure
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Ortep of the Correct Structure
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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.
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Raw Result with SIR97
O O
CN N
Br
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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.
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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.