The SystemS Approach to Automated Structure Determination: Problems and Solutions

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The System-S Approach to Automated Structure
DeterminationProblems and Solutions

• Ton Spek
• National Single Crystal Service
• Utrecht University, The Netherlands

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Is a Fully Automatic Structure Determination
Possible ?

• Yes, in many cases given good quality low
  temperature reflection data and correct prior
  knowledge of the chemical composition.
• Good examples are light atom structures with no
  disorder and with no unknown solvent of
  crystallization.
• No, in all cases needing an experienced
  crystallographer (I.e. when no automated methods
  are available yet for the problem at hand)
• e.g. many/most coordination complexes.

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Current Setup in Utrecht

• KappaCCD/Rotating Anode/LNT
• I
• Collect, DENZO or EVAL-CCD (Not AUTO!)
• I
• import.cif (includes Formula Unit Cell)
• I
• Silent System-S Auto-Mode platon -F import.cif
• I
• Result files -gt ORTEP/PLUTON Plots

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Typical Import CIF Filter Job

• Unix Command Line Instruction
• platon F import.cif
• .. Wait 0.5 minute ..
• Standard Console Output
• Tentative Result on /mnt/spea/import_s.cif
• and /mnt/spea/import_s.
  res
• Validation Report /mnt/spea/import_s.chk
• Details may be found in /mnt/s/import

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0.5 Min. from import.cif to ORTEP (3GHz Linux Box)
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System-S Approach

• Crystallographic Shell around public domain tools
  (SHELX, SIR, PLATON etc.)
• Two Modes of operation
• Guided Mode Suggests/Executes next step in the
  structure determination (handles I/O)
• Automatic Mode (NQA-Mode) Executes automatically
  all default steps
• Build-in Structure Validation
• System-S is included in the UNIX PLATON exe.

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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, CELLSD, SFAC, UNIT,
  HKLF 4 (or 3)
• Note No Spacegroup Info Needed
• Run s name.ins NQA.
• 18 Seconds later for C16H20NO3P .

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Problems and Solutions

• There are still many interesting Real World
  problems to be solved for a full proof automatic
  replacement of an experienced crystallographer.
• Already the use of the Guided Mode to quickly try
  multiple approaches to solve a structure is a big
  help (even for the experienced crystallographer)
• System-S stores all relevant I/O files in a
  hierarchic directory structure for inspection
  when problems arise.

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Problem 0 Complete Failure

• Example The chemist provides us with crystals
  labeled to be a Zn-coordination complex requiring
• human Expert Forensic Crystallography to
  tell us that the inorganic salt MnK2(SO4)2 gives
  us a perfect fit with the experimental data.
• Partial Solution Check with databases (I.e.
  CELL or simulated powder patterns) and stop.

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Failure 1 Space group

• The space group can not always be determined
  uniquely from systematic absences (e.g Cc or
  C2/c).
• Some structures solve only in lower than the
  actual space group symmetry (sometimes only in
  P1)
• Solution loop over the various space group
  candidates to solve the structure and use ADDSYM
  to find out about the correct symmetry of the
  model (implemented in S).

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Failure 2 Phase Problem

• Attempts to automatically solve a structure with
  a single solution package might fail.
• Solution loop over all available packages and
  approaches until a solution is found.
• System-S SHELX86, SHELXS97, SHELXD, SIR97,
  SIR2002, DIRDIF99
• Workup with EXOR Example next

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Raw Output from SHELXS86
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Result of the EXOR workup
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Failure 3 Incorrect Atom Type Assignment

• Automatic atom type assignment is not always
  straightforward.
• A large variation in displacement parameters
  often hampers a correct atom type assignment
• Solution detailed analysis of intra- and
  intermolecular geometry and ADPs
• Example next

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Misassigned Atom Types (S P)
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Atom Type Assignment

• Assignment Methods (can be) based on
• 1 - An analysis of the Peak heights Shapes
• 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)

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Failure 4 - Disorder

• Type 1 Orientational, Conformational or
  Substitutional disorder of (part of) the
  structure.
• Solution (Expert) Crystallographer
• Type 2 Voids filled with unknown (mixtures of)
  solvents.
• Solution PLATON/SQUEEZE

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Failure 5 - Twinning

• (Pseudo) Merohedral Twinning may lead to refined
  structures with unexpectedly high final R-values
  and high residual peaks in a difference Fourier
  Map.
• Solution Software to detect the applicable twin
  law.
• E.g. Rotax (Simon Parsons Bob Gould)
  available in WINGX and CRYSTALS or
• PLATON/TwinRotMat
• Example next .

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3 independent molecules
Space group P-3 R 20
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Problem 6 Wrong Structure

• Sometimes automatic procedures can come up with
  reasonably looking but wrong structures.
• Structure validation software should send out
  proper ALERTS (e.g. IUCr Checkcif)
• Example The chemist expects a Cu-complex, so
  that is what he gets (confirmed by X-ray
  crystallography !) . and tries to publish and
  caught by a knowledgeable referee on the bases
  of Checkcif ALERTS.

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R lt 7
Cu not Coordinated gt
ORTEP of the False Structure
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R lt 6
Ortep of the Correct Structure
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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 or for
  refereeing purposes to investigate unclear
  details of the analysis.
• Future implementation
• C,N,O etc. discrimination in difficult cases
• More chemical knowledge
• Extension of the already available procedures
  for structure determination without any
  Content Information.

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End