- Количество слайдов: 22
State-of-the-Art Crystallographic Refereeing General Message: Deposition of Reflection Data should be Obligitary Why? Three examples Ton Spek, Utrecht University, The Netherlands ACA-Honolulu - July 23, 2013
The Purpose of Refereeing an X-RAY Study is to Check: • Is the supplied information complete for a meaningful structure report and evaluation? • Is the data quality adequate for the conclusions drawn? • Are proper data collection and structure analysis techniques used? • Is the structure correct? • Is the interpretation of the result correct? • Are there additional observations of interest but missed by the authors? • Is this a duplication with no added value or even a fraud?
Data Needed for Proper Refereeing • The Refinement Model (Coordinates, con/restraints etc. ). • The reflection data on which the Model is based. • For Acta Cryst. this implies the deposition of a parameter ‘CIF’ and an Fobs/Fcalc ‘FCF’. • The new SHELXL 2013 offers an option for the inclusion of both types of information in a single (CIF) file. • This allows for the creation of a proper automated validation report and data archival. • It also provides an option for additional independent calculations where relevant.
IUCr Check. CIF Validation • The IUCr has set up an elaborate validation system for structures published in its own Acta Cryst. Journals. • Most chemical journals now also require authors to deposit a CIF and to supply a validation report for use by the referees but do not require the deposition of the reflection data. • The problem is that authors and referees still have to understand the implication of ALERT issues. • Even with Acta Cryst. the above sometimes fails as shown in the next example (Paper withdrawn now).
Acta Cryst. (2011). E 67, m 576 -m 577 Is this structure correct ? [Co 4 Cl 4(C 3 H 6 S)4] R 1 = 0. 041 w. R 2 = 0. 125
Co Zn C 3 N 1 C 6 N 2 R 1 = 0. 028 w. R 2 = 0. 072 Identical to: Inorg. Chem. (2006) 45, 8318 Correction proved with reflection data
Problem Example from Chemical Journal Biswas et al. Eur. J. Inorg. Chem. (2012) 4479 -4485. R 1 = 0. 08, w. R 2 = 0. 30 Space Group C 2/c Fe-Complex on 2 -axis NO 3 Anion in general pos. Population = 0. 5 !?
Problematic Structure (Biswas et al. ) • Problem: NO 3 - in general position disordered over two symmetry related sites sounds strange (precedents ? ). • Significant residual density peaks up to 2. 5 e/Å3 but explained away as ‘With no chemical significance’ • Reflection data would be needed for a detailed analysis of the issue but only a CIF was deposited. • Martin Lutz et al. resynthesised the compound following the Biswas et al. protocol with a surprising result (Eur. J. Inorg. Chem. (2013) 2467 -2469) • C 2/c Cc and NO 3 + Acetic acid + H 2 O
Biswas et al. Lutz et al.
C 2/c – Biswas et al. - VOIDS Cc – Lutz et al.
Follow-Up - Biswas et al. maintain their rebuttal [Eur. J. Inorg. Chem. (2013) 2470] with their interpretation. - Referee conclusion (with no access to the reflection data): Two different structures !!! - I obtained the reflection data from one of the co-authors - A SQUEEZE test run on the Biswas et al. data, with the NO 3 - removed, recovered 279 electrons from the voids left where only 128 were expected for an NO 3 - model. - Run on Lutz et al. data, with NO 3 and solvents removed, recovered 285 electrons of the expected 296. Conclusion ?
Widely Cited Nature paper in the News Nature (2013) 495, 461
Did a Crystallographic Referee have a serious look at the data ? • The deposited CIFs bring up multiple validation issues in need of further and detailed analysis. • Important information is lacking to justify the use of the SQUEEZE technique in this MOF context. Its use is probably not valid in this application. • Of particular interest are the details of the reported structure determination of miyakosyne A with a population of 50%. • No reflection data have been deposited to allow for an independent analysis of the structures.
From Nature Paper
Major Important Error Types • • • Wrong atom type assignments (e. g. Cu for Zn) Problems with hydrogen atoms (too few or too many etc. ) Missed twinning Missed disordered solvent Artificial ‘disorder’ due to wrong structure analysis Wrong symmetry • All the above may lead to one strong ALERT but more often it leads to multiple weaker ALERTS that in combination would indicate a strong ALERT. • We usully need the reflection data to sort out those ALERTS
Plea for the deposition of both the ‘CIF’ and the reflection data • A minimum would be the parameter CIF and the Fo/Fc data from the final refinement (FCF). • Better: Embed the refinement details and the observed data in the CIF. The IUCr/Acta Cryst. provides for that purpose the data names _iucr_refine_instructions_details and _iucr_refine_reflections_details • The new SHELXL 2013 does this by embedding automatically (with data names starting with _shelx_) and adds checksums.
Final Comments • Check. CIF provides a list of issues that need to be addressed, either with a correction or giving an acceptable explanation. • ALERTS come in levels A, B & C and report possible error, missing data or quality issues. G-ALERTS are generally informative and not necessarily errors but still need to be looked at seriously. • A & B ALERTS should never automatically lead to the rejection of a paper but should be investigated by a professional crystallographer. • Everything unusual marked as ‘new’, ‘unexpected’ etc. in a paper should be approached with healthy mistrust.
For the Discussion • Do we need different validation criteria for papers in crystallographic journals such as Acta Cryst. and papers published in chemical journals ? • Should deposition of the reflection data be required by all journals (Standard now in the macromolecular crystallography community) ? • Should the validation report along with (where relevant) the authors’ comments be published as supplementary material ?
Thanks to George Sheldrick for the major 2013 update of SHELXL and my former coworker Martin Lutz and many others for useful comments and suggestions