Crystal%20Structure%20Validation%20A%20Tool%20to%20distinguish%20GOOD%20and%20reliable%20single%20crystal%20studies%20from%20BAD%20and%20UGLY%20reports. - PowerPoint PPT Presentation

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Crystal%20Structure%20Validation%20A%20Tool%20to%20distinguish%20GOOD%20and%20reliable%20single%20crystal%20studies%20from%20BAD%20and%20UGLY%20reports.

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Automated validation of crystal structures as part of the editorial ... CH3 Moiety Geometry. To be extended with tests for new problems invented' by authors. ... – PowerPoint PPT presentation

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Title: Crystal%20Structure%20Validation%20A%20Tool%20to%20distinguish%20GOOD%20and%20reliable%20single%20crystal%20studies%20from%20BAD%20and%20UGLY%20reports.


1
Crystal Structure ValidationA Tool to
distinguish GOOD and reliable single crystal
studies from BAD and UGLY reports.
  • Ton Spek
  • National Single Crystal Facility
  • Bijvoet Center of Biomolecular Research
  • Utrecht University
  • The Netherlands
  • MIT Feb 18,2006

2
Small molecule and Protein XtallographyUtrecht
3
Automated Structure Validation
  • Automated validation of crystal structures as
    part of the editorial process is currently
    implemented in one form or another by most if not
    all major chemical journals.
  • There are good scientific reasons for enforcing
    such a procedure as illustrated by the following
    real world example that apparently was not
    properly validated.

4
Example Validation of a Deposited CIF
?
?
5
THE STABLE PENTAMETHYLCYCLOPENTADIENYL
CATION J.B.Lambert et al. Angew. Chem. Int. Ed.
2002, 41, 1429-1431

-
6
HOT STRUCTURE FAST LANE PUBLICATION
7
Pentamethylcyclopentadienyl
Common Anionic Form
New Cationic Form
-
Assigned Bond types
8
Enthusiastic Last Paragraph of CE-News
  • The .. chemists are now exploring the
    reactivity of C5Me5. You can sit down and write
    lots of interesting reactions on paper, P.I.
    says, and it will be interesting to see if the
    molecule reacts as expected. But considering this
    cations track record, it might be safer to
    expect more surprises. !!

9
NOT SO HOT AFTER ALL !!
Editors Note in the next issue of Angewandte
Chemie
10
Strange Bond Pattern and Ring pucker
DoD
Double Bond ?
Commonly misused catch all explanation
PACKING EFFECTS ??
11
Example Validation of a Deposited CIF
?
?
12
Corrected StructureJ.N. Jones et al.,Chem. Comm.
2002,1520-1521
Additional H-Atoms
13
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 (theoretical) counter indications.
  • Apparently there was no experienced
    crystallographer involved as a referee ?
  • Apparently no unbiased automated CIF-validation
    was done.

14
STRUCTURE VALIDATIONIN THE PAST
  • Single crystal structures were mostly determined
    by professional crystallographers using (slow)
    serial detectors (typically 50 datasets/year).
  • Using (open source) software they knew in detail.
  • Structures were analyzed and discussed in great
    detail and all evidence was given in the paper.
  • Papers containing crystallographic results were
    generally refereed by fellow crystallographers.

15
Crystallography Today
  • - 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 Autosolve

16
Why Automated Validation?
  • PROBLEMS
  • - See previous Cp example.
  • 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.

17
SOLUTION
  • The solution for the problem was pioneered
    by the International Union of Crystallography
  • Provide and archive structural data in computer
    readable CIF format.
  • Automated validation, with a computer generated
    report for authors and referees.
  • Journals enforcing a structure validation
    protocol.
  • - All IUCr journals and most major chemical
    journals now implement validation procedures.

18
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.

19
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?

20
IUCR-CHECKCIF SERVICE
  • IUCR-TESTS
  • MISSING DATA, PROPER PROCEDURE, QUALITY
  • PLATON TESTS
  • SYMMETRY, GEOMETRY, DISPLACEMENT PARAMETERS,
    VOIDS, TWINNING etc.
  • ALERTS
  • ALERT A - SERIOUS PROBLEM
  • ALERT B - POTENTIALLY SERIOUS PROBLEM
  • ALERT C - CHECK EXPLAIN

21
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.

22
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)

23
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.

24
Problems Addressed by PLATON
  • Reflection Data (.fcf)
  • Sufficient Resolution
  • Completeness of the data set
  • Missed (Pseudo-) Merohedral Twinning
  • Absolute Structure, Flack Parameter,
  • Bijvoet pairs
  • S

25
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 PLATON/ADDSYM algorithm effectively
    addresses the problem.
  • Missed symmetry EXAMPLE from a 2004
    Organometallics (23, 3210-3217) paper gt

26
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28
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 from JACS ?

29
Praseodymium complex
J.A.C.S. (2000),122,3413 P1, Z 2
30
CORRECTLY REFINED STRUCTURE
P-1, Z2
31
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

32
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34
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 CIFs and CCDC-FDAT

35
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

36
Entry from the CSD
SS 2 Ang ?
H
S
37
But with Space Group Symmetry
gt Different structure with S-S Bond !
38
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)

39
CONCLUSION
  • Validation Procedures are excellent Tools to
  • Set Quality Standards (Not just on R-Value)
  • Saves 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 the Routine Status of the Determination
    in the Hands of its Investigator

40
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 space group
  • Please teach me, what does in mean
  • space group incorrect

41
Additional Info
  • http//www.cryst.chem.uu.nl
  • (including a copy of this powerpoint
    presentation)
  • Thanks
  • for your attention !!

42
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