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Automatic Detection of Poor or Incorrect Single Crystal Structures

This article discusses the need for automated validation of crystal structures due to the increasing number of structures being published and the limited expertise of reviewers. It highlights the IUCR's solution of providing and archiving structural data in CIF format and implementing automatic validation protocols.

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Automatic Detection of Poor or Incorrect Single Crystal Structures

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  1. Automatic Detection of Poor or Incorrect Single Crystal Structures A.L.Spek Utrecht University The Netherlands

  2. 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

  3. 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

  4. 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

  5. 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

  6. HOT STRUCTURE – FAST LANE PUBLICATION

  7. NOT SO HOT AFTER ALL !!

  8. ASSIGNED BOND-TYPES

  10. 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

  11. 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?

  12. 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

  13. 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.

  14. 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)

  15. 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

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

  17. P-1, Z=2

  18. 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 CIF’s and CCDC-FDAT

  19. Example of Misplaced Hydrogen Atom

  20. Two ALERTS related to the misplaced Hydrogen Atom

  21. Unsatisfactory Hydrogen Bond Network

  22. Satisfactory Hydrogen Bond Network with new H-position

  23. Characterization of compound isolated from marine invertebrate Lindquist et al., J. Amer. Chem. Soc. (1991),113,2303-2304.

  24. Synthesis: Li et al. (2001) Angew. Chem. 113, 4901 ->Surprise Solution of the riddle: Li et al. (2001) Angew. Chem. 113,4906 O --> N-H (Analysis of the Displacement Ellipsoids)

  25. Automatic Validation of the coordinate data taken from the CSD Result: Alert on short intermolecular O…O Contact

  26. O N Infinite hydrogen bonded chain N-H…O=C

  27. 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)

  28. 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

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