structure validation in chemical crystallography principles and application ton spek, national...
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![Page 1: Structure Validation in Chemical Crystallography Principles and Application Ton Spek, National Single Crystal Service Facility, Utrecht University SAB-Delft,](https://reader035.vdocument.in/reader035/viewer/2022062421/56649d6c5503460f94a4c108/html5/thumbnails/1.jpg)
Structure Validationin
Chemical CrystallographyPrinciples and Application
Ton Spek,National Single Crystal Service Facility, Utrecht University
SAB-Delft, 2-10-2008.
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Overview of this Talk
• Why Crystal Structure Validation ?
• What are the Validation Questions ?
• How is Validation Implemented ?
• Which key problems are addressed ?
• Examples
• Evaluation and Performance
• Summary
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Why Crystal Structure Validation
• The explosion of structure determinations• An analyses of the nearly 500000 structures in the
CSD learns that a significant number are in error• Many analyses are done today by non-specialists• Limited number of experts to detect pitfalls• Validation provides a list of issues that need
special attention of the analyst, specialist and referee.
• Validation sets quality standards.
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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?
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How is Validation Implemented
• Computer readable structure analysis results in CIF format (Syd Hall & George Sheldrick)
• A file (Check.def) defines the issues that are tested with levels of severity and associated explanation and advise.
• The tests are executed by the program PLATON• The tests can be executed both in-house or through
the WEB-based IUCr CHECKCIF server.
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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
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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.
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EXAMPLE OF PLATON GENERATED
ALERTS FOR A RECENTPAPER PUBLISHED INJ.Amer.Chem.Soc. (2007)
Attracted special attention in Chemical and
Engineering News
(Referees obviously did not Bother)
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Which Key Issues are Addressed
• Missed symmetry (“being Marshed”)• Wrong chemistry (Misassigned atom types)• Too many, too few or misplaced H-atoms• Missed solvent accessible voids in the structure• Missed Twinning• Absolute structure• Data quality and completeness
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Examples
• Following are some examples of the type of problems addressed.
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WRONG SPACEGROUP
J.A.C.S. (2000),122,3413 – P1, Z = 2
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P-1, Z=2
CORRECTLY REFINED STRUCTURE
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Published with Wrong Composition
O
B
B
BORAX !
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Structure of a strange CH3 Bridged
Zr Dimer
Paper has been cited
47 times !
So can we believe this structure?
The Referees did …!
H .. H = 1.32 Ang. !
But …
Searching for structures with a MethylMoiety bridging two metals …
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HOT STRUCTURE – FAST LANE PUBLICATION
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NOT SO HOT AFTER ALL !!
Editors Note in the next issue of Angewandte Chemie
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THE STABLE PENTAMETHYLCYCLOPENTADIENYL CATION
J.B.Lambert et al. Angew. Chem. Int. Ed. 2002, 41, 1429-1431
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Pentamethylcyclopentadienyl Anion (Cp*-)
-
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PENTAMETHYLCYCLOPENTADIENYL CATION
ASSIGNED BOND-TYPES
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Strange Bond Pattern and Ring pucker
PACKING EFFECTS ??
DoD
Double Bond ?
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Corrected StructureJ.N. Jones et al.,Chem. Comm. 2002,1520-1521
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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 …
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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
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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.
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