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

8. NOT SO HOT AFTER ALL !!

9. ASSIGNED BOND-TYPES

11.  

12. 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

13. 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?

14. 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

15. 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.

16. 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)

17. 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

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

19. P-1, Z=2

20. 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

21. Example of Misplaced Hydrogen Atom

22. Two ALERTS related to the misplaced Hydrogen Atom

23. Unsatisfactory Hydrogen Bond Network

24. Satisfactory Hydrogen Bond Network with new H-position

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

26. 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)

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

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

29. 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)

30. 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