Transcript Automatic Detection of Poor or Incorrect Single Crystal

Automatic Detection of Poor or
Incorrect Single Crystal
Structures
A.L.Spek
Utrecht University
The Netherlands
WHY AUTOMATED
VALIDATION?
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IN THE PAST
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Single crystal structures determined by
professional crystallographers
Using serial detectors (~ 50 datasets/year)
Using software they knew in detail
Papers containing crystallographic results
were refereed by fellow crystallographers
Why Automated Validation?
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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)
Crystal structures solved using Black-Box
crystallographic firmware
Why Automated Validation?
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PROBLEMS:
Exploding # of structural papers to review
Limited # of referees with sufficient
crystallographic knowledge
Limited supporting information available
for the reviewer (footnote/deposited)
Papers increasingly refereed by noncrystallographers, unaware of pitfalls
Why Automated Validation?
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IUCR: SOLUTION
Provide and archive structural data in
computer readable CIF format
Automatic validation, with a computer
generated report for authors and referees
Journals enforcing a validation protocol
EXAMPLE … where things went wrong
HOT STRUCTURE – FAST LANE PUBLICATION
NOT SO HOT AFTER ALL !!
ASSIGNED BOND-TYPES
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THE CIF DATA STANDARD
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Driving Force: Syd Hall (IUCr/ Acta Cryst C)
Early Adopted by XTAL & SHELX(T)L
Currently: 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
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?
IUCR-CHECKCIF
IUCR-TESTS:
- MISSING DATA, PROPER PROCEDURE, QUALITY
PLATON TESTS:
- SYMMETRY, GEOMETRY, DISPLACEMENT
PARAMETERS, VOIDS etc.
ALERT LEVELS:
- ALERT A - SERIOUS PROBLEM
- ALERT B - POTENTIALLY SERIOUS PROBLEM
- ALERT C - CHECK & EXPLAIN
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.
Problems Addressed by PLATON
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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)
Problems Addressed by PLATON
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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
Praseodymium complex
J.A.C.S. (2000),122,3413 – P1, Z = 2
P-1, Z=2
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 CIF’s and CCDC-FDAT
Example of Misplaced Hydrogen Atom
Two ALERTS related to the misplaced Hydrogen Atom
Unsatisfactory Hydrogen Bond Network
Satisfactory Hydrogen Bond Network with new H-position
Characterization of compound isolated from marine invertebrate
Lindquist et al., J. Amer. Chem. Soc. (1991),113,2303-2304.
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)
Automatic Validation of the coordinate data taken from the CSD
Result: Alert on short intermolecular O…O Contact
O
N
Infinite hydrogen bonded chain
N-H…O=C
COMMENTS
- Validation should not be postponed to the
publication phase. All validation issue
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 detail.
- The CSD can be very helpful when looking
for possible precedents (but be careful)
CONCLUSION
Validation Procedures are excellent Tools to:
- Set Standards (Not just on R-Value)
- Save a lot of Time in Checking, both by the
Investigators and the Journals
- 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