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Crystal Structure Validation : The IUCr tool to distinguish GOOD and trustable single crystal structures from BAD and UGLY reports Ton Spek Bijvoet Center.

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Presentation on theme: "Crystal Structure Validation : The IUCr tool to distinguish GOOD and trustable single crystal structures from BAD and UGLY reports Ton Spek Bijvoet Center."— Presentation transcript:

1 Crystal Structure Validation : The IUCr tool to distinguish GOOD and trustable single crystal structures from BAD and UGLY reports Ton Spek Bijvoet Center for Biomolecular Research Utrecht University,The Netherlands Aachen, Nov 10, 2006

2 Who are we ? The National facility for ‘small molecule’ single crystal structure determination since 1971 in the Netherlands. Embedded within the Crystal and Structural Chemistry group in Utrecht. Also in Utrecht most of the C & S research has moved from small molecule to protein crystallography (Structural Biology).

3 Small molecule and Protein Xtallography:Utrecht

4 Some Statistics Collaboration of the facility with most synthetic groups in the Netherlands who send their samples for analysis to Utrecht. We handled over 3500 requests over the past 35 years. Mainly organometallic and coordination chemistry. Up to now, the results are reported in over 1200 (joint) papers.

5 People Involved The last years 3 to 4 mostly PHD’s of which one on a postdoc position. Currently a permanent staff of 2 + 1 postdoc. Dr. Martin Lutz (since 1997) Dr. Lars von Chrzanowski (postdoc since Oct 15, 2006) In the past: a few trained chemists in the context of their synthetic work.

6 Associated Functions Development of crystallographic software based on local needs: PLATON package. Crystal Structure Validation (IUCr) Co-Editor of Acta Cryst. C (involved in the handling of more than 1000 CIF-formatted papers).

7 This Talk In this talk I will illustrate with a number of real world examples how the IUCr structure validation tool CHECKCIF can help to distinguish Good from Bad and Ugly crystal structures. The validation tool was developed in the context of the journal Acta Cryst. C but is now also used by many other high standard journals and pharmaceutical companies. Let me start with a quote from a Nobel lecture..

8 1964 Nobel Lecture Dorothy Hodgkin …. [The] great advantage of X-ray analysis as a method of chemical structure analysis is its power to show some totally unexpected and surprising structure with, at the same time, complete certainty...

9 With Complete Certainty ? Yes, in most cases, in particular in the hands of experienced investigators. No, when proper scientific procedures and signs of trouble have been ignored. This presentation will address a number of obvious cases where proper procedures were ignored, resulting in erroneous science. There are good scientific reasons for enforcing an automated validation procedure as illustrated by the following real world example that apparently was not properly validated by the referees.

10 THE STABLE PENTAMETHYLCYCLOPENTADIENYL CATION J.B.Lambert et al. Angew. Chem. Int. Ed. 2002, 41, 1429-1431 +

11 Pentamethylcyclopentadienyl - Common Anionic Form“New” Cationic Form Assigned Bond types Cp*


13 Enthusiastic Last Paragraph of C&E-News … The Northwestern chemists are now exploring the reactivity of C5Me5+. “You can sit down and write lots of interesting reactions on paper,” Lambert says, and it will be interesting to see if the molecule reacts as expected. But Considering this cation’s track record, it might be safer to expect more surprises. [!!]

14 NOT SO HOT AFTER ALL !! Editors Note in the next issue of Angewandte Chemie

15 Strange Bond Pattern and Ring pucker PACKING EFFECTS ?? DoDDoD Double Bond ? +

16 Corrected Structure J.N. Jones et al.,Chem. Comm. 2002,1520-1521 Additional H-Atoms

17 Where did it go Wrong ? First impression of the structure was likely based on a preliminary result (plot) without H-atoms. Rushed as a short communication into the prestigious high impact journal Angewandte Chemie. Ignoring all counter theoretical and spectroscopic evidence. No experienced crystallographer as referee ? No unbiased automated CIF-validation.

18   Validation of the Deposited CIF

19 So Why (Automated) Structure Validation? - See previous case study. VALIDATION IN THE PAST -Single crystal structures determined by experienced professional crystallographers (e.g. Dorothy Hodgkin) -Using previous generation serial detectors (with at best an output of ~ 50 datasets/year). -Using (open source) software they knew in detail. -Structures were analyzed and discussed in great detail. -Papers containing crystallographic results were refereed by fellow crystallographers.

20 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 – when pushed and given enough ‘slaves’). -Crystal structures solved using Black-Box crystallographic firmware (SHELXTL etc.) - Near Future – AutoCollect & AutoSolve

21 Why Automated Validation? PROBLEMS: -Exploding # of structural papers to review. -Limited # of referees with sufficient time and crystallographic knowledge. -Limited supporting information available for the reviewer (footnote/deposited). -Papers including structural ‘evidence’ are increasingly refereed by non-crystallographers, unaware of the many potential pitfalls.

22 SOLUTION The solution for the problem was pioneered by the International Union of Crystallography -Provide and archive crystallographic data in the computer readable CIF format. -Automated validation, with a computer generated report for authors and referees. -Journals to enforce a structure validation protocol. - The IUCr journals and most major journals now implement validation procedures.

23 THE CIF DATA STANDARD -Driving Force: Syd Hall (IUCr/ Acta Cryst C) -Early Adopted by XTAL & SHELX(T)L. -Currently: WinGX,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.

24 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?


26 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.

27 Validation with PLATON -Details: -Driven by the file CHECK.DEF with criteria, ALERT messages and advice. -Use: platon –u structure.cif -Result on file: structure.chk -Applicable on CIF’s and CCDC-FDAT -FCF-Valid: platon –V structure.cif

28 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)

29 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.

30 Problems Addressed by PLATON Reflection Data (.fcf) -Sufficient Resolution -Completeness of the data set -Missed (Pseudo-) Merohedral Twinning -Friedel pairs, Absolute Structure S

31 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.

32 Why is description in a correct space group so important ? Refinement in a too low symmetry group may result in geometry artifacts In particular when a centro-symmetric structure is refined in a non- centrosymmetric space group. Example of a Bad and Ugly Structure from JACS = 

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


35 The Missed Symmetry Problem -Another Missed symmetry EXAMPLE from a 2004 Organometallics (23, 3210- 3217) paper ==>



38 Another Missed Symmetry Case An example from the space group Cc missed symmetry family ….

39 BAMYEU Dalton Trans 2003,134-140 Cc



42 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 

43 Example of Misplaced Hydrogen Atom

44 Two ALERTS related to the misplaced Hydrogen Atom

45 Unsatisfactory Hydrogen Bond Network



48 Satisfactory Hydrogen Bond Network with new H-position

49 Problem with a Multistep Synthesis Example where synthetic chemists were seriously mislead by the results of an erroneous crystal structure in an attempt to synthesize a natural product.

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

51 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)

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

53 Infinite hydrogen bonded chain N-H…O=C O N

54 Wrong Structures Sometimes automatic structure determination procedures can come up with ‘reasonably looking’ but wrong structures. Structure validation software should send out proper ALERTS to the investigators (e.g. IUCr Checkcif)

55 Wrong Structure Example Structure submitted to Acta Cryst. C The chemist involved expects a Cu coordination complex, so that is what he reports … (confirmed by X-ray crystallography !) and tries to publish this structure with an interesting non-coordinated Cu2+ and fortunately caught by the validation software ALERTS related to short O..O and O.. N contacts

56 ORTEP of the False Structure R < 7 % Cu not Coordinated =>

57 Ortep of the Correct Structure R < 6 %

58 Thus … The original paper indeed mentioned an interesting uncoordinated Cu2+ but left it with this statement. The chemistry changed from [Cu]2+[L]2- to [L]+[Br]- by also adding some missed Hydrogen atoms. HBr was used in the synthesis (but not mentioned in the original experimental). Various ALERTS pointed to the problem but they were ignored by the authors. Interestingly, the color of the crystal changed from green to colorless in the now published revised paper …..

59 Structure Determination Artifacts Pseudo-symmetry easily results in false structures. Example: An Organometallic-AuCl compound from the CSD with the Cl in the wrong position  Very Short C-H..Cl ?! ALERTED by validation (C..Cl = 2.19 Ang) Moving Cl to the correct position drops R from 4 to 2 %



62 Consult the CSD It is a good idea to always consult the CSD for previous reports on structures related to the one at hand. The statistics provided by VISTA (CCDC) can be very helpful for this. However, be aware, such an analysis often shows outliers. Many of those appear to be errors. Example: A search for short S..S contacts gave:

63 Entry from the CSD H S

64 But with Space Group Symmetry => Different structure with S-S Bond !

65 COMMENTS -Validation should not be postponed to the publication phase. All validation issues 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 great detail and supported by independent evidence. -The CSD can be very helpful when looking for possible precedents (but be careful)

66 CONCLUSION #1 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 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.

67 Conclusion #2 Dorothy Hodgkins claim that X-ray crystallography can deliver new science is still valid as it was in 1964, Given: -Correct procedures -Structure validation -Education

68 Residual Problem EDUCATION Response of an author of a structural paper submitted to the crystallographic journal Acta Cryst. to an enquiry from a referee on the reported erroneous space group: Please teach me, what does in mean ‘ space group incorrect’ ……

69 Additional Info (including a copy of this powerpoint presentation) Thanks for your attention !!



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