Structure Validation in Chemical Crystallography Principles and Application

1
Structure ValidationinChemical
CrystallographyPrinciples and Application

• Ton Spek,
• National Single Crystal Service Facility, Utrecht
  University
• SAB-Delft, 2-10-2008.

2
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

3
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.

4
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?

5
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.

6
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

7
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.

8
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)
9
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

10
Examples

• Following are some examples of the type of
  problems addressed.

11
WRONG SPACEGROUP
J.A.C.S. (2000),122,3413 P1, Z 2
12
CORRECTLY REFINED STRUCTURE
P-1, Z2
13
Published with Wrong Composition
B
O
BORAX !
B
14
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. !
15
HOT STRUCTURE FAST LANE PUBLICATION
16
NOT SO HOT AFTER ALL !!
Editors Note in the next issue of Angewandte
Chemie
17
THE STABLE PENTAMETHYLCYCLOPENTADIENYL
CATION J.B.Lambert et al. Angew. Chem. Int. Ed.
2002, 41, 1429-1431
18
Pentamethylcyclopentadienyl Anion (Cp-)
-
19
PENTAMETHYLCYCLOPENTADIENYL CATION
ASSIGNED BOND-TYPES
20
Strange Bond Pattern and Ring pucker
DoD
Double Bond ?
PACKING EFFECTS ??
21
Corrected StructureJ.N. Jones et al.,Chem. Comm.
2002,1520-1521
22
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

23
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

24
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.

25
(No Transcript)