Presentation on theme: "Validation and checking of crystal structures This presentation contains material from the following lectures: American Crystallographic Association Annual."— Presentation transcript:
Validation and checking of crystal structures This presentation contains material from the following lectures: American Crystallographic Association Annual Meeting, Los Angeles, July 2001; International Union of Crystallography Congress, Geneva, August 2002; University of Natal, Pietermaritzburg, South Africa, August 2003; ACS 226 th National Meeting, New York, September 2003; British Crystallographic Association, Chemical Crystallography Group Meeting, Cambridge, November 2003; European Crystallographic Meeting, Budapest, August 2004 Alexander J. Blake, University of Nottingham, UK and Anthony Linden, University of Zurich, Switzerland
G. Pattenden (Nottingham) How do we know whether this structure is correct and reliable?
Overview validation and checking Validation for Acta C, etc Myths and misunderstandings Validation for other journals The limits of validation OUTLINE
Validation involves comparison against a set of test criteria Do cell volume and cell parameters match? Do bonded atoms have compatible U ij values? Has the refinement converged? Is the space group correct? Are the assigned atom types correct? etc, etc, etc
Valid-ation Correct Appropriate Defensible
Does the structure make sense to you? Does the structure look right? Do chemically equivalent bonds agree? Are all CIF entries complete and correct? Checking is additional to validation
Automated data validation with checkCIF or PLATON Checks for –CIF construction and syntax errors –missing information –parameters outside expected norms –conformation with convention
ASerious – attention essential Item omitted or large deviation from norm Alert ANo crystal dimensions have been given Alert ARatio of Tmax/Tmin expected is > 1.30 An absorption correction is required. Alert AAtom C58A ADP max/min Ratio ALERT LEVELS
BSignificant – action needed? Item is a significant or unexpected outlier Alert BThe formula has elements in wrong order Alert BADDSYM detects Cc to Fdd2 transformation Alert BRefined extinction parameter < 1.9s Alert BStructure contains VOIDS of Å 3 ALERT LEVELS
COutside expected norms – examine May appear trivial, but do not dismiss out of hand - an extensive list may indicate problems Alert CMoiety formula not given Alert CShort inter X...Y contact: O7...C1 = 2.96 Å Alert CLow U(eq) as compared to neighbors: C1 Alert CD-H without acceptor N2–H2 ? C1 and N2 should be N and C, respectively
ALERT LEVELS G General issues – check ALERT_3_G The ratio of expected to reported Tmax/Tmin (RR') is < 0.75 Tmin and Tmax reported: Tmin' and Tmax expected: RR' Please check that your absorption correction is appropriate. 380 ALERT 4 C Likely Unrefined X(sp2)-Methyl Moiety.... C ALERT 2 C Short Intra XH3.. XHn:H19B.. H30A = 1.81 Ang. 720 ALERT 4 C Number of Unusual/Non-Standard Label(s).... 1
ALERT Type 1: CIF construction/syntax error, inconsistent or missing data ALERT Type 2: Indicator that the structure model may be wrong/deficient ALERT Type 3: Indicator that the structure quality may be low ALERT Type 4: Cosmetic improvement, query or suggestion A/B/C indicate the seriousness of the problem Not all combinations are logical, for example 4 A
Sources of outlier parameters Unresolved feature (e.g., untreated disorder) Artefact due to limited data quality Inadequate procedures (e.g., poor corrections) Incorrect structure (e.g., wrong space group) A genuinely unusual observation!!
What does validation software do? Identifies possible problems via ALERTs Provides explanations of ALERTs Suggests interpretations and possible solutions Not just for authors referees use it for assessment authors need to be aware of this how appropriate are IUCr criteria?
When to validate? software for data collection, refinement, etc - should do its own validation use PLATON in final stages of determination validate raw CIF from the refinement program must validate the final version as well avoids problems at submission, refereeing, etc
A visual examination can often be revealing: here there are some extreme ellipsoids which are also incompatible with a rigid bond model Looking at the structure
A pretty picture, but what about the numbers …
1.897 Å Br Å Å Å P.J. Cox, RGU, Aberdeen … in fact the bond lengths match the values expected
Ordered t-butyl group has all C-C distances around 1.52 Å Within the disordered group the range is 1.49 to 1.60 Å Need (better) restraints? Anon Less satisfactory
1.Check the CIF from refinement using PLATON 2.Augment CIF using e.g. XCIF and enCIFer 3.Re-check the CIF using PLATON or checkCIF 4.Look at ellipsoid plots from several directions 5.Check bond lengths are sensible and consistent 6.After any changes, re-check the CIF VALIDATION/CHECKING PROCEDURE
Validation and IUCr Journals
Results tables largely created by hand –only manual checking (if any) –laborious and time-consuming –hard to ensure consistent treatment –vital matters were easily overlooked –any revisions required laborious re-checking Pre-electronic times
allows automatic creation of tables enables full electronic submission/processing increases efficiency, faster publication times automates many editorial tasks improves appearance of the journal permits automated validation Early 1990’s - CIF introduced
authors get instant, anonymous feedback can detect and fix problems before submission fewer, shorter revision cycles consistent application of acceptance criteria editors/referees can focus on science RESULT: faster publication times Automation of syntax and data checks
Authors working with CHECKCIF
sound scientific basis is there a sound scientific basis for the outlier? put Validation Response Form (VRF) into CIF submit CIF CIF Validation Co-editor (Acta C) Co-editor (Acta B or Acta E) If you still get A alerts
VRF allows for “fine-tuning” validation criteria need some flexibility looking for sound scientific reasoning sound explanation? Pass the CIF otherwise suggest possible remedial action We try to be helpful and informative ! Assessment of VRF
A valid riposte Alert B ADDSYM detects additional (pseudo) symmetry element: I Author Response: This additional symmetry element does not hold true for one of the ether bridges, as discussed in the text.
An inadequate answer Alert A < 85% complete (theta max?) Author Response: Hemisphere of data collected.[Space group P21/n, Nonius FAST] But what is the reason for missing data: inherent geometrical limitation? mistake in data collection or reduction?
How does it work?
Author Response: It appears that the absmu- and the density-problem are related. No explanation other than it is related to the disordered triflate groups and the refinement over several partially occupied sites. Just being helpful... Alert A Given & expected crystal density differ Alert A Given & expected absorption coefficient differ Calculated density = density in CIF = Calculated mu = mu in CIF = Cause of Alert: Molecule sits over an inversion centre in P2 1 /n: Z given as 4, instead of 2.
Give ALL Alerts due consideration –appreciate validation criteria –criteria are based on normally expected results from routine analyses –Why, then, is your structure not routine? How to get a CIF through In any VRF... –avoid casual or circular responses –show you understand the causes of the outlier –explain why it is a true feature of the analysis
What causes most problems? VRN???01 Data completeness ALERT A probably spurious PASSED VRN???02 Space group ID is main subject of paper PASSED VRN???03 Some H atoms mistreated - authors to re-refine REJECT VRN???04 30 atoms isotropic in a very large structure PASSED VRN???05 Coordinates/geometry mismatch REJECT VRN???06 Max shift/su > 4.0 REJECT VRN???07 Perchlorate O atoms have extreme ADPs PASSED VRN???08 Atom labels randomly scrambled REJECT VRN???09 Extreme H U values - inappropriate H atom treatment REJECT VRN???10 Not a connected set? - probably a false positive PASSED VRN???11 Central heavy atoms have high U wrt neighbors PASSED
Common problems... VRN???12 VRN???06 again; shifts now acceptable PASSED VRN???13 H atom treatment; missing absorption correction REJECT VRN???14 Solvent disorder modeling; high mean U3/U1 PASSED VRN???15 VRN???09 again: still many problems with H atoms REJECT VRN???16 VRN???09 again: nearly there PASSED VRN???17 Spurious warning (intensity standards) but AD PASSED VRN???18 Ligands have geometric and Ueq problems PASSED VRN???19 Problems with high U3/U1 PASSED VRN???20 Dataset only 65% complete REJECT VRN???21 Completeness: theta max was too high PASSED VRN???22 Wide range of H-atom U values; very close H...H REJECT
Common problems... Data completeness or resolution too low Maltreatment of H atoms Structure not at convergence Missing or inadequate absorption correction Indications of a poor structure
Acta C CIF submissions in 2000 Tony Linden (Zurich)
Fate of CIFs with VRFs in : 58% passed as is
All Acta C submissions in 2000
97% of all submissions reach a Co-editor Validation is not a brick wall - either to run into or get over -
Introduction of validation: Acta C electronic-only submission since 1996 are validation criteria widely understood? explanations in Notes for Authors, etc but a mythology has grown up... Myths and myth-understandings
Myth 1: “Acta will not consider ‘problem’ or ‘difficult’ structures” Reality: The problems or difficulties must be explained and justified disorder twinning crystal size voids ADPs pseudosymmetry residual e - absorption H atoms
Scylla Myth 2: “ Acta will not publish any structure with R 1 > 0.05/0.07/ ” Reality: There is no formal cut-off, but a structure with a high R 1 will need to be justified. Abstract... 2-(Di-n-propylamino)-8-hydroxytetralin (8OH-DPAT) hydrochloride, C 16 H 26 NO + Cl -, M = 283.8, monoclinic, P2 1 /n, a = (7), b = (6), c = (6) Å, = (6)°, V = Å 3, Z = 4, D x = 1.151g cm -3, (CuK ) = l Å, = cm -1, F(000) = 616, T = 298 K, final R = with 1550 independent data. The structure solution of 8OH-DPAT was hindered by the poor quality of the one crystal obtained...
Gorgon Myth 3: “ Acta will not publish a structure with Z’ > 1 where one of the molecules is disordered” Reality: We welcome such interesting structures, but the disorder must be treated adequately. Acta Cryst. (1996). C52, Two C-Unsubstituted Enaminals Abstract In both 3-(N,N-diisopropylamino)-2-propenal, C 9 H 17 NO, (3), and 3-(1,2,3,4- tetrahydro-l-quinolinyl)-2-propenal, C 12 H 13 NO, (4), the entire enaminal system (O1– C1–C2–C3–N4) is approximately planar. The angles around the N atoms in (3) and (4) sum to values near 360 °, indicating planarity in both molecules. One of the two crystallographically independent molecules of (3) exhibits disorder in its isopropyl groups.
Myth 4: “Datasets must be (almost) perfectly complete” Reality: A dataset need only be essentially complete to 2 of ca. 50°/Mo, and thereafter have good completeness up to the diffraction limit. Dragon _diffrn_reflns_theta_max _diffrn_measured_fraction_theta_max _diffrn_reflns_theta_full _diffrn_measured_fraction_theta_full 1.000
Myth or not? Is the assertion based on direct experience? Check with Notes for Authors (www.iucr.org) If in any doubt, ask a Co-editor (www.iucr.org) Your case may not be the same as a similar one
checkCIF in 2004 the new home of checkCIF: service sponsored by ACS, CCDC and Elsevier an ORTEP plot is now included part of new Acta C/E submission procedures will soon have online upload of all material for Acta C and E papers (CIF + figures/schemes/structure factors)
Validation and other Journals
Standards, procedures vary widely some journals perform extensive checks some do only very basic checks some do none at all ? so what do authors do ? Perform your own validation ensure there are no serious mistakes ensure the quality is adequate submit a copy of the checking report
Example – an ACS procedure Authors submit the CIF along with the paper CIF must contain author names and paper title authors must have checked the CIF first - the check report may be requested reviewers have Web access to the CIF, along with the manuscript and any supplementary data
Other procedures Submit paper to journal get a code for the paper submit CIF under this code Submit CIF to CCDC or ICSD get deposition number include number in paper
If you have a “difficult” structure Identify and describe the problem Give details of the remedial action taken Describe the (successful?) outcome
1. Briefly in any experimental footnote Where and how? 2. At the top of the CIF use _refine_special_details 3. In any other Supplementary Data
Example of text _refine_special_details ; Disorder was identified in one of the tetrafluoroborate anions. All the F atoms were affected and two orientations were identified. Similarity restraints were applied to B-F distances, and to F-B-F angles. All F atoms were refined isotropically. The occupancies of each group of four partially-occupied F atoms were refined competitively using a free variable. Each F atom was found to be disordered over two equally occupied sites, as shown by the final group occupancies of 0.506(12) and 0.494(12). In the final model the range of B-F distances was 1.31(2)-1.42(2) Angstroms and the F-B-F angles spanned 105(2)-112(2) degrees. No difference Fourier peak in the region exceeds 0.6 e/A**3. ;
(automatic validation will not catch every problem) The limits of validation
test not (yet) implemented test not practical error not a validation issue error cannot be detected from data in CIF nonsense entries in the CIF Possible limits to validation
Test not implemented Example:High ADPs on isolated atom Not detected by rigid bond test atom type test ADP ratio test Atom is probably O rather than Cl
Test not practical C-C range is 1.49 to 1.60 Å However, C-C single bonds are found within this range
Error not a validation issue _chemical_formula_sum 'C24 H12 Fe O6' _exptl_crystal_description needle _exptl_crystal_colour colourless _exptl_crystal_size_max 0.28 _exptl_crystal_size_mid 0.24 _exptl_crystal_size_min 0.03
Prior chemical information: Complex is either Ru/Ru or Ru/Zn Refinement as Ru/Ru gave R 1 = 0.064; unusual five- coordinate Ru geometry Error not detectable from CIF data
Difference map with Ru/Ru model (R 1 = 0.064)
Difference map with Zn/Zn model (R 1 = 0.022)
AgCNAg link, AgNCAg link or disordered? could only be resolved using F maps M. Schröder (Nottingham) Other examples
need good data to distinguish Ni and Fe by refinement Ni (Z = 28) vs Fe (Z = 26) Z/Z = 2/28 M. Schröder (Nottingham) R 1 < 4 Z ? Model complexes for [NiFe] hydrogenase Use F maps to confirm and when data are poor
Lanthanide complexes Ln = Er, Tm or Yb ? Z = 68, 69, 70 Similar geometry parameters Similar co-ordination Crystallography is not much good at distinguishing these metals
Nonsense entries in the CIF * _diffrn_ambient_temperature 293(2) _diffrn_radiation_wavelength _diffrn_radiation_type synchrotron _diffrn_radiation_source 'fine-focus sealed tube' _diffrn_radiation_monochromator 'graphite' _diffrn_measurement_device_type 'SMART 1k on Daresbury SRS Station 9.8' * see W. Clegg, Acta Cryst. 2003, E59, e2-e5
Unsuitable SHELX(T)L-97 defaults ? space group notation diffractometer T = 293 K ? absorption correction total data collected index limits R int H atom treatment weighting scheme precision structure solution
SUMMARY 1. Overview of validation and checking 2. Validation for IUCr journals 3. Validation for chemical journals 4. The limits of validation
Thanks to..... George Ferguson Ton Spek Peter Strickland