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Validation and checking of crystal structures Alexander J. Blake, University of Nottingham, UK and Validation and checking of crystal structures Alexander J. Blake, University of Nottingham, UK and Anthony Linden, University of Zurich, Switzerland 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 th National Meeting, New York, Natal, Pietermaritzburg. South Africa, August 2003; ACS 226 , September 2003; British Crystallographic Association, Chemical Crystallography Group Meeting, Cambridge, November 2003; European Crystallographic Meeting, Budapest, August 2004

How do we know whether this structure is correct and reliable? G. Pattenden (Nottingham) How do we know whether this structure is correct and reliable? G. Pattenden (Nottingham)

OUTLINE OUTLINE

Validation involves comparison agains a set of test criteria • Do cell volume and Validation involves comparison agains a set of test criteria • Do cell volume and cell parameters match? • Do bonded atoms have compatible values? Uij • Has the refinement converged? • Is the space group correct? • Are the assigned atom types correct? etc, etc

Valid -ation Correct Appropriate Defensible Valid -ation Correct Appropriate Defensible

Checking is additional to validation • Does the structure make sense to you? • Checking is additional to validation • Does the structure make sense to you? • Does the structure look right? • Do chemically equivalent bonds agree? • Are all CIF entries complete and correct?

Automated data validation with check. CIFor PLATON • Checks for – CIF construction and Automated data validation with check. CIFor PLATON • Checks for – CIF construction and syntax errors – missing information – parameters outside expected norms – conformation with convention

ALERT LEVELS A Serious – attention essential Item omitted or large deviation from norm ALERT LEVELS A Serious – attention essential Item omitted or large deviation from norm Alert A No crystal dimensions have been given Alert A Ratio of. Tmax/Tmin expected is > 1. 30 An absorption correction is required. Alert A Atom C 58 A ADP max/min Ratio 18. 00

ALERT LEVELS B Significant – action needed? Item is a significant or unexpected outlier ALERT LEVELS B Significant – action needed? Item is a significant or unexpected outlier Alert B The formula has elements in wrong order Alert B ADDSYM detects Cc to Fdd 2 transformation Alert B Refined extinction parameter < 1. 9 s 3 Alert B Structure contains VOIDS of 130. 00 Å

ALERT LEVELS C Outside expected norms – examine May appear trivial, but do not ALERT LEVELS C Outside expected norms – examine May appear trivial, but do not dismiss out of hand - an extensive list may indicate problems Alert C Moiety formula not given Alert C Short inter X. . . Y contact: O 7. . . C 1 = 2. 96 Å Alert C Low U(eq) as compared to neighbors : Alert C D-H without acceptor N 2–H 2 C 1 ? C 1 and N 2 should be N and C, respectively

ALERT LEVELS G General issues – check ALERT LEVELS G General issues – check

A/ C indicate theseriousness the problem B/ of ALERT Type 1: CIF construction/syntax error, A/ C indicate theseriousness the problem B/ of 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 Not all combinations are logical, for example 4 A

Sources of outlier parameters • Unresolved feature (e. g. , untreated disorder) • Artefact 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 ALERTs via • Provides explanations What does validation software do? • Identifies possible problems ALERTs via • 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 - shoulddo its own When to validate? • software for data collection, refinement, etc - shoulddo 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

Looking at the structure A visual examination can often be revealing: here there are Looking at the structure A visual examination can often be revealing: here there are some extreme ellipsoids which are also incompatible with a rigid bond model

A pretty picture, but what about the numbers … A pretty picture, but what about the numbers …

… in fact the bond lengths match the values expected P. J. Cox, RGU, … in fact the bond lengths match the values expected P. J. Cox, RGU, Aberdeen

Less satisfactory Orderedt-butyl group has all C-C distances around 1. 52 Å Within the Less satisfactory Orderedt-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

VALIDATION/CHECKING PROCEDURE 1. Check the CIF from refinement using PLATON 2. Augment CIF using VALIDATION/CHECKING PROCEDURE 1. Check the CIF from refinement using PLATON 2. Augment CIF using e. g. XCIF and en. CIFer 3. Re-check the CIF using PLATON or check. CIF 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 and IUCr Journals Validation and IUCr Journals

Pre-electronic times Results tables largely created by hand – only manual checking (if any) Pre-electronic times 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

Early 1990’s - CIF introduced • allows automatic creation of tables • enables full Early 1990’s - CIF introduced • allows automatic creation of tables • enables full electronic submission/processing • increases efficiency, faster publication times • automates many editorial tasks • improves appearance of the journal

Automation of syntax and data checks • authors get instant, anonymous feedback • can Automation of syntax and data checks • 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

Authors working with CHECKCIF Authors working with CHECKCIF

If you still get A alerts If you still get A alerts

Assessment of VRF • VRF allows for “fine-tuning” • validation criteria need some flexibility Assessment of VRF • 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 !

A valid riposte Alert B ADDSYM detects additional (pseudo) symmetry element: I Author Response: 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: An inadequate answer Alert A < 85% complete theta max? ) ( Author Response: Hemisphere of data collected. [Space group P 21/n, Nonius. FAST] But what is the reason for missing data: • inherent geometrical limitation? • mistake in data collection or reduction?

How does it work? How does it work?

Just being helpful. . . Alert A Given & expected crystal density differ Alert Just being helpful. . . Alert A Given & expected crystal density differ Alert A Given & expected absorption coefficient differ Calculated density = 3. 377 density in CIF = 1. 689 Calculated mu = 2. 063 mu in CIF = 1. 031 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. Cause of Alert: Molecule sits over an inversion centre in. P 21/ Z given as 4, instead of 2. n:

How to get a CIF through • Give ALL Alerts due consideration – appreciate How to get a CIF through • 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? • 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? What causes most problems?

Common problems. . . Common problems. . .

Common problems. . . Ò Data completeness or resolution too low Ò Maltreatment of Common problems. . . Ò Data completeness or resolution too low Ò Maltreatment of H atoms Ò Structure not at convergence Ò Missing or inadequate absorption correction Ò Indications of a poor structure

Acta C CIF submissions in 2000 Tony Linden (Zurich) Acta C CIF submissions in 2000 Tony Linden (Zurich)

Fate of CIFs with VRFs in 2000 2002: 58% passed as is Fate of CIFs with VRFs in 2000 2002: 58% passed as is

All Acta C submissions in 2000 All Acta C submissions in 2000

Validation is not a brick wall - either to run into or get over Validation is not a brick wall - either to run into or get over - 97% of all submissions reach a Co-editor

Myths and myth-understandings Introduction of validation: • Acta C electronic-only submission since 1996 • Myths and myth-understandings Introduction of validation: • Acta C electronic-only submission since 1996 • are validation criteria widely understood? • explanations in Notes for Authorsetc , but a mythology has grown up. . .

Myth 1 : “Acta will not consider ‘problem’ or ‘difficult’ structures” Reality The problems 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

Myth 2: “ Acta will not publish any Scylla structure with 1 > 0. Myth 2: “ Acta will not publish any Scylla structure with 1 > 0. 05/0. 07/0. 10. . . ” R Reality: There is no formal cut-off, but a structure with a high. R 1 will need to be justified.

Myth 3 “Acta will not publish a : Gorgon structure with > 1 where Myth 3 “Acta will not publish a : Gorgon structure with > 1 where one of the Z’ molecules is disordered” Reality We welcome such interesting structures, but : the disorder must be treated adequately.

Myth 4: Dragon “Datasets must be (almost) perfectly complete” Myth 4: Dragon “Datasets must be (almost) perfectly complete”

Myth or not? • Is the assertion based on direct experience? • Check with. 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

check. CIF in 2004 • the new home of check. CIF : http: // check. CIF in 2004 • the new home of check. CIF : http: // checkcif. iucr. org • 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 Acta C and E for papers (CIF + figures/schemes/structure factors)

Validation and other Journals Validation and other Journals

Example – an ACS procedure • Authors submit the CIF along with the paper Example – an ACS procedure • Authors submit the CIF along with the paper • CIF must contain uthor names andpaper title a • author must have checkedthe CIF first s - the check report may be requested • reviewershave 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 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 If you have a “difficult” structure • Identify and describe the problem • Give details of the remedial action taken • Describe the (successful? ) outcome

Where and how? 1. Briefly inany experimental footnote 2. At the top of the Where and how? 1. Briefly inany experimental footnote 2. At the top of the CIF use _refine_special_details 3. In any other Supplementary Data

Example of text Example of text

The limits of validation (automatic validation will not catch every problem) The limits of validation (automatic validation will not catch every problem)

Possible limits to validation Ð test not (yet) implemented Ð test not practical Ð Possible limits to validation Ð test not (yet) implemented Ð test not practical Ð error not a validation issue Ð error cannot be detected from data in CIF Ð nonsense entries in the CIF

Test not implemented Example: High ADPs on isolated atom Not detected by Ò rigid Test not implemented Example: High ADPs on isolated atom Not detected by Ò rigid bond test Ò atom type test Ò 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 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 C 24 H 12 Fe O 6 ' Error not a validation issue _chemical_formula_sum C 24 H 12 Fe O 6 ' ' _exptl_crystal_description needle _exptl_crystal_colourless _exptl_crystal_size_max 0. 28 _exptl_crystal_size_mid 0. 24 _exptl_crystal_size_min 0. 03

Error not detectable from CIF data Prior chemical information: Complex is either Ru/Ruor Ru/Zn Error not detectable from CIF data Prior chemical information: Complex is either Ru/Ruor Ru/Zn Refinement as Ru/Rugave R 1 = 0. 064; unusual fivecoordinate. Ru geometry

Difference map with Ru/Rumodel ( 1 = 0. 064) R Difference map with Ru/Rumodel ( 1 = 0. 064) R

Difference map with Zn/Zn model ( 1 = 0. 022) R Difference map with Zn/Zn model ( 1 = 0. 022) R

Other examples M. Schröder (Nottingham) Other examples M. Schröder (Nottingham)

Model complexes for [Ni. Fe] hydrogenase M. Schröder (Nottingham) Model complexes for [Ni. Fe] hydrogenase M. Schröder (Nottingham)

Lanthanide complexes Ln = Er, Tm or Yb ? Z = 68, 69, 70 Lanthanide complexes Ln = Er, Tm or Yb ? Z = 68, 69, 70 Similar co-ordination Similar geometry parameters Crystallography is not much good at distinguishing these metals

* Nonsense entries in the CIF _diffrn_ambient_temperature 293(2) _diffrn_radiation_wavelength 0. 69010 _diffrn_radiation_type synchrotron _diffrn_radiation_source * Nonsense entries in the CIF _diffrn_ambient_temperature 293(2) _diffrn_radiation_wavelength 0. 69010 _diffrn_radiation_type synchrotron _diffrn_radiation_source 'fine-focus sealed tube ' _diffrn_radiation_monochromator 'graphite ' _diffrn_measurement_device_type 'SMART 1 k on Daresbury SRS Station 9. 8' * see W. Clegg, Acta Cryst. 2003, E 59, e 2 -e 5

Unsuitable SHELX(T)L-97 defaults ? • space group notation • diffractometer • T = 293 Unsuitable SHELX(T)L-97 defaults ? • space group notation • diffractometer • T = 293 K ? • absorption correction • total data collected • index limits • Rint • H atom treatment • weighting scheme • precision • structure solution

SUMMARY 1. Overview of validation and checking 2. Validation for IUCr journals 3. Validation 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. . . . Thanks to . . George Ferguson Ton Spek Peter Strickland. . . .