Automatic Detection of Poor or Incorrect Single Crystal Structures

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Automatic Detection of Poor or Incorrect Single
Crystal Structures

• A.L.Spek
• Utrecht University
• The Netherlands

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WHY AUTOMATED VALIDATION?

• IN THE PAST
• - Single crystal structures determined by
  professional crystallographers
• Using serial detectors ( 50 datasets/year)
• Using software they knew in detail
• Papers containing crystallographic results were
  refereed by fellow crystallographers

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Why Automated Validation?

• PRESENT
• - Diminishing number of professional small
  molecule crystallographers (sites, teaching)
• Many crystal structures done by chemists
• with limited crystallographic background
• Using CCD detectors ( 1000 datasets/year)
• Crystal structures solved using Black-Box
  crystallographic firmware

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Why Automated Validation?

• PROBLEMS
• Exploding of structural papers to review
• Limited of referees with sufficient
  crystallographic knowledge
• Limited supporting information available
• for the reviewer (footnote/deposited)
• Papers increasingly refereed by
  non-crystallographers, unaware of pitfalls

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Why Automated Validation?

• IUCR SOLUTION
• Provide and archive structural data in computer
  readable CIF format
• Automatic validation, with a computer generated
  report for authors and referees
• Journals enforcing a validation protocol
• EXAMPLE where things went wrong

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HOT STRUCTURE FAST LANE PUBLICATION
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NOT SO HOT AFTER ALL !!
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ASSIGNED BOND-TYPES
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THE CIF DATA STANDARD

• Driving Force Syd Hall (IUCr/ Acta Cryst C)
• Early Adopted by XTAL SHELX(T)L
• Currently Crystals,Texsan, Maxus etc.
• Acta Cryst. C/E Electronic Submission
• Acta Cryst.Automatic Validation at the Gate
• CIF data available for referees for detailed
  inspection (and optional calculations)
• Data retrieval from the WEB for published papers
• CCDC Deposition in CIF-FORMAT

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VALIDATION QUESTIONS

• Single crystal validation addresses three
• important questions
• 1 Is the reported information complete?
• 2 What is the quality of the analysis?
• 3 Is the Structure Correct?

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IUCR-CHECKCIF

• IUCR-TESTS
• MISSING DATA, PROPER PROCEDURE, QUALITY
• PLATON TESTS
• SYMMETRY, GEOMETRY, DISPLACEMENT PARAMETERS,
  VOIDS etc.
• ALERT LEVELS
• ALERT A - SERIOUS PROBLEM
• ALERT B - POTENTIALLY SERIOUS PROBLEM
• ALERT C - CHECK EXPLAIN

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ALERT TYPES

• 1 - CIF Construction/Syntax errors,
• Missing or Inconsistent Data.
• 2 - Indicators that the Structure Model
• may be Wrong or Deficient.
• 3 - Indicators that the quality of the results
• may be low.
• 4 - Cosmetic Improvements, Queries and
• Suggestions.

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Problems Addressed by PLATON

• Missed Higher Space Group Symmetry
• Solvent Accessible Voids in the Structure
• Unusual Displacement Parameters
• Hirshfeld Rigid Bond test
• Misassigned Atom Type
• Population/Occupancy Parameters
• Mono Coordinated/Bonded Metals
• Isolated Atoms (e.g. O, H, Transition Metals)

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Problems Addressed by PLATON

• Too Many Hydrogen Atoms on an Atom
• Missing Hydrogen Atoms
• Valence Hybridization
• Short Intra/Inter-Molecular Contacts
• O-H without Acceptor
• Unusual Bond Length/Angle
• CH3 Moiety Geometry

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Praseodymium complex
J.A.C.S. (2000),122,3413 P1, Z 2
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P-1, Z2
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Validation with PLATON

• - Details www.cryst.chem.uu.nl/platon
• Driven by the file CHECK.DEF with criteria, ALERT
  messages and advice.
• Use (UNIX) platon u structure.cif
• Result on file structure.chk
• Applicable on CIFs and CCDC-FDAT

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Example of Misplaced Hydrogen Atom
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Two ALERTS related to the misplaced Hydrogen Atom
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Unsatisfactory Hydrogen Bond Network
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Satisfactory Hydrogen Bond Network with new
H-position
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Characterization of compound isolated from marine
invertebrate
Lindquist et al., J. Amer. Chem. Soc.
(1991),113,2303-2304.
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Synthesis Li et al. (2001) Angew. Chem. 113,
4901 -gtSurprise
Solution of the riddle Li et al. (2001) Angew.
Chem. 113,4906 O --gt N-H (Analysis of the
Displacement Ellipsoids)
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Automatic Validation of the coordinate data taken
from the CSD
Result Alert on short intermolecular OO Contact
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O
N
Infinite hydrogen bonded chain
N-HOC
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COMMENTS

• Validation should not be postponed to the
  publication phase. All validation issue should be
  taken care of during the analysis.
• Everything unusual in a structure is suspect,
• mostly incorrect (artifact) and should be
  investigated and discussed in detail.
• - The CSD can be very helpful when looking for
  possible precedents (but be careful)

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CONCLUSION

• Validation Procedures are excellent Tools to
• Set Standards (Not just on R-Value)
• Save a lot of Time in Checking, both by the
  Investigators and the Journals
• - Point at Interesting Features
  (Pseudo-Symmetry,
• short Interactions etc.) to be discussed.
• Surface a problem that only an experienced
  Crystallographer might be able to Address
• Proof the Routine Status of the Determination
  in the Hands of its Investigator