Single Crystal to Single Crystal Transformations in Metal Organic Frameworks
Crystal Structure Validation A Tool to distinguish GOOD and reliable single crystal studies from BAD...
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Transcript of Crystal Structure Validation A Tool to distinguish GOOD and reliable single crystal studies from BAD...
![Page 1: Crystal Structure Validation A Tool to distinguish GOOD and reliable single crystal studies from BAD and UGLY reports. Ton Spek National Single Crystal.](https://reader035.fdocuments.net/reader035/viewer/2022062417/551ae2295503466b6a8b5c6c/html5/thumbnails/1.jpg)
Crystal Structure Validation
A Tool to distinguish GOOD and reliable single crystal studies from BAD and UGLY reports.
Ton Spek
National Single Crystal FacilityBijvoet Center of Biomolecular Research
Utrecht University
The NetherlandsMIT Feb 18,2006
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Small molecule and Protein Xtallography:Utrecht
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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.
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Example: Validation of a Deposited CIF
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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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HOT STRUCTURE – FAST LANE PUBLICATION
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Pentamethylcyclopentadienyl
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Common Anionic Form “New” Cationic Form
Assigned Bond types
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Enthusiastic Last Paragraph of C&E-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 cation’s track record, it might be safer to expect more surprises. [!!]
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NOT SO HOT AFTER ALL !!
Editors Note in the next issue of Angewandte Chemie
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Strange Bond Pattern and Ring pucker
Commonly misused “catch all’ explanation: PACKING EFFECTS ??
DoD
Double Bond ?
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Example: Validation of a Deposited CIF
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Corrected StructureJ.N. Jones et al.,Chem. Comm. 2002,1520-1521
Additional H-Atoms
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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.
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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.
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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 …
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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.
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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.
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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.
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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?
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IUCR-CHECKCIF SERVICEIUCR-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
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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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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)
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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.
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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
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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 ==>
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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 =
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Praseodymium complex
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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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 %
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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
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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:
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Entry from the CSD
HSS…S = 2 Ang ?
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But with Space Group Symmetry
=> Different structure with S-S Bond !
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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)
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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
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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’ ……
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Additional Info
http://www.cryst.chem.uu.nl (including a copy of this powerpoint presentation)
Thanks
for your attention !!
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