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Structure Validation in Chemical Crystallography

Structure Validation in Chemical Crystallography. Ton Spek, Bijvoet Centre for Biomolecular Research, Utrecht University, The Netherlands . CCP4-Leeds, 5-Jan.-2008 . Overview of this Talk. Introduction to the Problems that are addressed by Structure Validation in Chemical Crystallography

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Structure Validation in Chemical Crystallography

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  1. Structure ValidationinChemical Crystallography Ton Spek, Bijvoet Centre for Biomolecular Research, Utrecht University, The Netherlands. CCP4-Leeds, 5-Jan.-2008.

  2. Overview of this Talk • Introduction to the Problems that are addressed by Structure Validation in Chemical Crystallography • The currently implemented IUCr Solution • Evaluation of the Performance • Possible Future work and Extensions • Summary & Conclusion

  3. Chem. Cryst. 40 Years Ago …(when I started in Xtallography) • Datacollection, Structure Solution, Refinement and Publication took generally several months or more. • For my first structure I even had to write my own Direct Methods program to solve it. • Software was not a Black Box. Ad-hoc software development was part of the job. • Paper review was done in those days by experienced crystallographers and took months to publication.

  4. Today • A Routine Datacollection, followed by • Automated Structure Determination, • SHELXL Refinement, • PublCIF Paper Preparation and • Electronic Submission to Acta Cryst., May take an experienced crystallographer just 1 day …for an Acta Cryst. E paper.

  5. Number of Yearly Published Chem. Cryst. Structures • 1967: 936 • 2007: more than 30000 • CSD Nov 2007: 450000 entries • More growth expected (China, India) …

  6. Announced Aug 2007: Tabletop ‘Black Box’ – Smart X2S Mount Crystal in a Vial Structure ?

  7. Are all those 450000 Structures Correct and Reliable? • Unfortunately not. • The result of many searches in the CSD for structures that are related to the structure under investigation will include outliers, many of which turn out to be at least suspect. • Following are just three of the examples of chemically wrong structures that obviously passed the refereeing system.

  8. Published with Wrong Composition B O BORAX ! B

  9. Entry from the CSD (IDAKUT) Found during search in CSD for short inter S…S Contacts S H

  10. But with Space Group Symmetry => Different compound with S-S Bond !

  11. Searching for structures with a Methyl Moiety bridging two metals … Structure of a strange CH3 Bridged Zr Dimer Paper has been cited 47 times ! So can we believe this structure? The Referees did …! But … H .. H = 1.32 Ang. !

  12. Comment • The methyl hydrogen atoms are expected outside the Zr2C2 ring (and indeed have been found in similar structures) • Referees likely had no access to (or did not access) the primary data other than the ORTEP illustration in the paper. • General problem: A limited number of experts is available to referee too many structural papers that offer only limited primary (deposited) data.

  13. Partial Solution A solution for the structure validation problem waspioneered by the International Union of Crystallography • Provide and archive crystallographic data in the computer readable CIF standard format. (Driving force: Syd Hall, Editor Acta Cryst. C) • Implement Automated Validation, with a computer generated report for authors, editors and referees.

  14. The CIF Data Standard - Early Adopted in 1993 by SHELX(T)L and subsequently other packages. • Around 1995: CIF-Format Electronic Submission to Acta Cryst. C/E • Ten Years Ago: Automatic Validation (and possible return to sender) of Acta Cryst. C & E papers at the Gate. • CIF & HKL data are available for referees for detailed inspection (and optional calculations). • Data retrieval from the WEB for published papers

  15. VALIDATION QUESTIONS Single crystal validation addresses three simple but important questions: 1 – Is the reported information complete? 2 – What is the quality of the analysis? 3 – Is the Structure Correct?

  16. IUCr CHECKCIF WEB-Service http://checkcif.iucr.org reports the outcome of: • IUCr standard tests Consistency, Missing Data, Proper Procedure, Quality, Comparison against test criteria etc. • + Additional PLATON based tests Missed Symmetry, Voids, Geometry, Hydrogen atoms, Displacement Parameters, etc.

  17. ALERT LEVELS CheckCif Report in terms of a list of ALERTS • ALERT A – Serious Problem • ALERT B – Potentially Serious Problem • ALERT C – Check & Explain • ALERT G – Verify or Take Notice

  18. 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.

  19. EXAMPLE OF PLATON GENERATED ALERTS FOR A RECENT PAPER PUBLISHED IN J.Amer.Chem.Soc. (2007) Attracted special attention in Chemical and Engineering News (Referees obviously did not Bother)

  20. Problems Addressed by PLATON/CIF-CHECK • Missed Higher Space Group Symmetry • Solvent Accessible Voids in the Structure • Unusual Displacement Parameters • Hirshfeld Rigid Bond test • Misassigned Atom Types • Population/Occupancy Parameters • Mono Coordinated/Bonded Metals • Isolated Atoms (e.g. O, H, Transition Metals)

  21. More 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 • To be extended with tests for new problems ‘invented’ by authors.

  22. The Missed Symmetry Problem • Up to 10 % of the structures in space groups such as Cc have higher symmetry (e.g. C2/c, R-3c, Fdd2 etc.) than was originally reported. (To be Marshed is not good for your scientific reputation as a crystallographer). • MISSYM (Y. LePage) & PLATON/ADDSYM algorithm addresses the problem. - Next Slide: Example 

  23. WRONG SPACEGROUP J.A.C.S. (2000),122,3413 – P1, Z = 2

  24. CORRECTLY REFINED STRUCTURE P-1, Z=2

  25. Example of Change of Space Group ALERT

  26. Misoriented O-H • The O-H moiety is generally, with very few exceptions, part of a D-H..A system. • An investigation of structures in the CSD brings up many ‘exceptions’. • Closer analysis shows that misplacement of the O-H hydrogen atom is in general the cause. • Molecules have an environment in the crystal ! • Example 

  27. Validation Looks at inter-molecular contacts Unsatisfactory Hydrogen Bond Network Correct ! ALERT !

  28. Solvent Accessible Void of 235 Ang3 out of 1123 Ang3 Often Not Accounted for in the Refinement Model High R-value

  29. Additional Problems Addressed byPLATON/FCF-CHECK With information from .cif and .fcf files • Report on the resolution of the data • Report about randomly missing data • Check the completeness of the data (e.g. for missing cusps of data) • Report on Missed (Pseudo) Merohedral Twinning • Report on # Friedel Pairs and Absolute Structure (comparison of Hooft y with Flack x parameter values)

  30. Missed (Pseudo) Merohedral Twinning A tool (TwinRotMat) in PLATON automatically analyses a reported structure for missed twinning Example 

  31. Evaluation and Performance • The validation scheme has been very successful for Acta Cryst. C & E in setting standards for quality and reliability. • Most major chemical journals currently have some form of a validation scheme implemented. • But does it solve all problems …

  32. Some Recent Statistics • Validation CSD Entries 2006 + early 2007 • Number of entries: 35760 • # of likely Space Group Changes: 384 • # of structures with (unaccounted for ?) voids: 3354 • Numerous problems with H, O, OH, H2O etc., etc, .

  33. Problems to be Addressed • Synthetic Chemist View: ‘Addressing Crystallographic Details holds up the Publication of Important Chemistry’ • Author Question: What does it mean “Spacegroup Incorrect” • Crystallographic Education (beyond Pushbutton and Black Box) • Referees that know how to handle ALERTS

  34. Possible Future Extensions • Validation of Structures from Powder Data • Validation of Inorganic Compounds • Validation of Incommensurate Structures • Validation of Charge Density Studies • Automated check against (average) geometry in the CSD • Check for fabricated data ?

  35. Summary & Conclusions Validation Procedures are excellent Tools to: • Set Quality Standards (Not just on R-Value) • Save a lot of Time in Checking, both by the Investigators and the Journals (referees) • Point at Interesting Structural Features (Pseudo-Symmetry, short Interactions etc.) to be discussed. • Surface a problem that only an experienced Crystallographer might be able to Address • Proof of a GOOD structure.

  36. Additional Info http://www.cryst.chem.uu.nl (including a copy of this powerpoint presentation) Thanks foryourattention !!

  37. Example of a PLATON/Check Validation Report: Two ALERTS related to the misplaced Hydrogen Atom

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