On the Proper Reporting and Archival of Crystal Structure Data
On the Proper Reporting and Archival of Crystal Structure Data Ton Spek Utrecht University, NL (ACA2015-Philadelphia) Summary Message Crystal structures should be published with their experimental
(reflection) data archived Two supporting examples follow Boring Structure ? Let me start with a story about a BORING looking published structure. The authors think that it is hot. Published in the high-impact journal
Angew. Chem. Int. Ed. 2015, 54, 164-168 Why an Interesting Structure ? Title: Crystallographic Snapshot of an Arrested Intermediate in the Biomimetic Activation of CO2 Product of the bubbling of CO2 through a solution of n-tetrabutylammonium hydroxide
[N(C4H9)4]+[OH]- + CO2 [N(C4H9)4]+[HCO3]-] Study motivated by CO2 fixation/conversion research. Tetrabutylammonium Hydrogencarbonate Note the slightly higher Uij for O3]- Authors interpretation of the experimental data
-O3]--H without acceptor -The unusually long C17O3]- bond of 1.563]-(6) Ang. But interpreted that as: H-OCO2 , stabilized by interactions with the cation scaffold Referees accepted that strange argument No reflection data were deposited for independent evaluation Acetate anion might fit as well
A few months later A paper appeared entitled: Comment on Crystallographic Snapshot of an Arrested Intermediate in the Biomimetic Activation of CO2 by J.A.C. Clyburn et al. (2015). Angew. Chem., 54, 7484-7487. New data collection with acetate as anion => The previously described mystery species is likely a
common acetate ion (O-H CH3]-) Now supported by deposited reflection data in SHELXL2014 format Comparison of the hydrogen carbonate and acetate structures Observe the close resemblance of the displacement ellipsoids
Contoured CH3]- density section in the acetate structure We would expect to see a similar section prepared with the HCO 3]- data Last Month Update Afterall a dull structure .. but perfectly illustrating my message
By-the-way, where did the acetate anion come from? Important Message Unusual structural features are most likely wrong A reported crystal structure (i.e. coordinates and atom type assignment) is just the authors interpretation of the data and open for debate Deposition of the data is needed to prove/disprove an authors interpretation (by referees and readers)
Not all chemical journals enforce the good scientific practice of the deposition of the reflection data yet Programs like SHELXL2014 now automatically include the reflection data in the deposited CIF. Those data should not be deleted for whatever reason Deposition/Archival The IUCr journals require as a minimum the deposition of Fo/Fc data. Better now: include
the unmerged reflection data into the CIF. Some programs do that now automatically, including the refinement instructions. The CCDC is now fully equipped and happy to accept reflection data for archival. Private communications to the CCDC should include reflection data to make more sense. Structure Validation
A crystal structure needs to be fully validated before publication on the basis of both the refinement results and experimental (reflection) data on which they are based. Tools available to authors, referees and readers should include checkCIF, the Cambridge Crystallographic database, a rerefinement program and very important: chemical knowledge All non-standard procedures used (e.g. constraints/restraints, disorder, SQUEEZE) should be sufficiently detailed in a structure report All unusual structural features should be investigated and
discussed in sufficient detail. A refereeing example of an actual structure report follows. A Structure Report submitted to Acta Cryst. C (2015) Title: The synthesis and DFT calculation of a four-coordinated manganese compound Mn2(BPTC). 3]-D-Network
Prepared in a stainless steel reactor at 443]-K from Mn(ClO4)2.6H2O + H4BPTC ligand. Relevant section of the 3]-D-network 293]- K Is this structure correct?
The Mn 4-coordination is somewhat unusual: Coordination generally square planar rather than tetrahedral. An isomorphous Zn complex was reported previously (no deposited reflection data, thus no comparison of reflection data possible) The coordination around Zn closely fits the one of the Mn complex
Published Zn structure (No reflection data) CrystEngComm (2013]-, 15, 4606) Zn1 O1 Zn1 O2i Zn1 O3]-g Zn1 O4a
1.910(2) 1.974(2) 1.963]-(2) 1.93]-3]-(2) checkCIF What can checkCIF tell us about the Mn complex?
Also, always inspect the difference density map for unusual features Refined with Mn substituted by Zn R1 = 0.047 wR2 = 0.113]S = 1.03]-9
Improvement of the model is hardly visible, But the R-values improved significantly Structure Comparison Mn Zn Zn
The displacement ellipsoids are surprisingly similar (both RT) Unfortunately, the two reflection sets can not be compared Paper rejected ! Common checkCIF Issues
ADDSYM is designed to warn for possible higher symmetry between the supplied coordinate set with a suggestion for a revised space group. The tolerances used are relatively high in order to catch most known misassignments. An ALERT not necessarily means an error, just something to investigated and reported on. With multiple components in the unit cell or with polymers it is not always
clear what the best choise is for the formula unit. CheckCIF might make a different choise than an author on the basis of chemical insight. The main issue is that the reported Z and related quantities are consistent with the reported formula unit. CheckCIF uses its own f and f anomalous dispersion parameter values for a synchrotron based wavelength as a check against those supplied. The actual values can be listed with the ANOM instruction in PLATON. Details on missing reflection and outlier ALERTS can be found in the FCF validation report.
Concluding Remarks CheckCIF is intended to be helpful and to protect against oversights rather than being annoying Many ALERTS have their origin in previous incidents Some ALERTS can point to interesting features in a structure and relevant to be discussed Some ALERTS may be less important in a given context Sometimes, a combination of minor ALERTS can point to a problem
that needs to be resolved The set of ALERTS is still fine tuned and extended on the bases of reported new incidents. Please send suggestions and examples of annoying issues to [email protected] Thanks ! [email protected] www.platonsoft.nl
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