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Automatic Detection of Poor or Incorrect Single Crystal Structures

Automatic Detection of Poor or Incorrect Single Crystal Structures. A.L.Spek Utrecht University The Netherlands. WHY AUTOMATED VALIDATION?. IN THE PAST ========== - Single crystal structures determined by professional crystallographers Using serial detectors (~ 50 datasets/year)

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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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