PLATON/CheckCIF Issues

Ton Spek

Utrecht UniversityThe Netherlands

Bruker User MeetingUCSD, La Jolla, March 22-24, 2012

Selected Validation Issues

Structure validation is an ongoing project due to changes in procedures, software and hardware

Many validation criteria are empirical and might need a theoretical background.

Proper correction for absorption was considered very important in the 1990's and is currently a lesser issue (The SADABS effect)

Absolute structure determination of light atom structure has changed in view of the supposedly more sensitive Hooft y and Parsons z parameters as compared with the Flack x parameter

Cell Parameters and s.u.'s

• Unit cell parameters determined with serial detectors were generally based on the setting angles of 25 reflections and generally produced realistic looking s.u.'s.

• Currently, cell dimensions are determined from the detector positions of many thousands of reflections. Their s.u.'s are often unrealistically small.

• It is probably best not to artificially increase the s.u.'s in a report with a guessed factor but leave that to the user of the data

Unit cell Volume s.u.

• SHELXL calculates the volume s.u. assuming 3 independent parameters. Angle s.u.'s are not taken into account (CheckCIF does)

• PLATON/CheckCIF calculates the more appropriate cubic crystal cell volume s.u. as 3a2 x sigma(a) which often leads to an ALERT when calculated with SHELXL.

• Reporting the same s.u. for a,b and c can be confusing

Connected Sets of Atoms

- Atoms should be transformed by symmetry operations into a suitable connected set

- Centers of gravity of the species of the asymmetric unit should generally lie within the bounds of the unit cell

- Exceptions are small molecules (e.g. H2O) that

should be close to the main species in order to avoid unnecessary symmetry operations in H-bond tables

This is an example of bad practice

Symmetry- PLATON accepts the specification of the spacegroup symmetry in various formats:

a) Explicit: SYMM and LATT records

b) Hermann-Mauguin symbol (PLATON knows about many variations beyond the standard 230)

c) Hall Symbol (Explicit and eventually used to generate the set of symmetry operations used)

- a), b) and c) info in the CIF is cross checked

n_hkl Symmetry Codes - PLATON adheres to the set of symmetry codes

consistent with those in the International Tables (i.e. produced from the generators implicit in the Hall symbol of the space group at hand).

- SHELXL allows for a more flexible specification and ordering of non-centering and inversion operations. Translation components can be negative (e.g -1/2).

- The validation software takes this difference into account for the n_hkl symmetry codes in e.g. H-bonding geometry: H-bond tables in PLATON list both the 'PLATON' and 'SHELXL' codes.

Shelxl s.o.f. versus CIF occupancy The SHELXL definition of occupancy in the .res and

the CIF definition of occupancy are different This often results in confusion, wrong formula and

related ALERTS The difference shows up for atoms on special

positions SHELXL generally handles (but not always) this issue

when creating a .cif Unfortunately there exists an inconsistency related to

the specification of the multiplicity as well (see below)

SHELXL definition of s.o.f.

.. the site occupation factor is normally given as 11 (i.e. fixed at 1). The site occupation factor for an atom in a special position should be multiplied by the multiplicity of that position (as given in International Tables, Volume A) and devided by the multiplicity of the general position for that space group.

.. an atom on a fourfold axes example will usually have s.o.f. = 10.25 .. and a fully occupied atom on an inversion center s.o.f. = 10.5

CIF Definition of Occupancy _atom_site_occupancy

… the fraction of the atom type present at this site … _atom_site_symmetry_multiplicity

.. the multiplicity of a site due to space-group symmetry as given in International Tables for Crystallography Vol. A (2002) .. the permitted range is 1 -> 192 ..

Thus 'multiplicity' for atom on fourfold axis in P4 ??

SHELXL CIF .. 1.0 4 (sometimes 0.25 1)

Officially …..... 1.0 1 ??

Other occupancy Issues

- SHELXL s.o.f.'s should be given with sufficient number of decimals for atoms on special positions. Thus 0.33333 and 0.66667 rather than 0.33 and 0.666

- The rounding of refined occupation numbers may lead to non-unity sums for the total occupancy of a chemically relevant atom, leading to non-integer atom counts in the formula.

Disorder

- PLATON by default automatically detects disorder fragments on the basis of occupation numbers: Bonds are assumed either between a fully occupied atom and a partially occupied site or between to atoms with the same population. Might fail in exactly 50:50% disorder cases

- SHELXL introduced the 'PART' concept many years after the the design of PLATON. Implementation of the PART concept in PLATON is now underway.

Formula & Z

- The Moiety Formula should be consistent with the reported Z value. There should be generally no problem with one species only in a general position (Z = general position multiplicity)

- The proper choice of Z in the case of multiple species in the asymmetric unit (and their order) is likely best dictated by the underlying chemistry.

Standard Setting

- Reporting a structure in a standard setting can often make the search for similar structures easier.

- Available rules: Niggli reduced, a<b<c etc.

- Hot issues: P211/c versus P2

1/n (closer to 90 deg)

- For (in particular inorganic compounds)

'Structure Tidy'

Resolution of the Dataset

- Acta Cryst. prefers a dataset that is essentially complete up to sin(theta)/lambda = 0.6

- Exceptions can be beamstop reflections and hardware constraints such as a high pressure cell

- Generally all observed reflections above sin(theta)/lambda = 0.6 should be retained

- The values for the data names for completeness and theta_full can be changed from the values given in the CIF by SHELXL to satisfy the first condition.

- Missing cusps of data can usually be avoided

Do Not remove by default data beyond sin(theta)/lambda = 0.6

Absolute Structure

• The reported Flack parameter value is checked against the value of the Hooft parameter.

• The Hooft parameter requires a high Bijvoet pair coverage

• The Flack parameter is best determined with the BASF/TWIN instruction (without matrix !)

• R & S configuration assignments are suggested (unfortunately, the algorithm used may error for complicated ring systems)

f' and f'' and mu values

– SHELXL and XL include (for all atom types) proper values for f', f'' and mu exclusively for the three wavelengths CuKa, MoKa and AgKa

– Resonance values for other wavelengths (synchrotron) have to be added manually with DISP and SFAC records in the .ins. Also the wavelength should be given with its actual value.

– PLATON offers suitable values following Brennan & Cowan (1962)

– CheckCIF compaires the values in the .cif with the expected values for the reported wavelength.

Resonance Scattering data calculated with PLATON for lambda = 1.8 Angstrom (following Brennan & Cowan)

Weight Optimization

– SHELXL provides two parameters for automatic reflection weight optimisation ( a & b). The S value is expected to converge to a value close to zero.

– Large values generally indicate model or data problems. Examples are twinning, wrong symmetry, wrong atom type assignments, unresolved disorder and solvent.

Weight Optimization

– SHELXL provides two parameters for automatic reflection weight optimisation ( a & b). The S value is expected to converge to a value close to zero.

– Large values generally indicate model or data problems. Examples are twinning, wrong symmetry, wrong atom type assignments, unresolved disorder and solvent.

Hydrogen Atom Treatment

• The parameters of hydrogen atoms on hetero atoms are best refined to prove their validity.

• Other hydrogen atoms are generally best taken into account in the riding mode to secure a good data over parameter ratio.

Missed or Pseudo symmetry

• The ADDSYM routine in PLATON analyses a coordinate set for additional symmetry.

• The tolerances are set on values intended to catch both missed and (interesting) pseudo symmetry.

• Corresponding ALERTS should be investigated and either corrected or discussed

Difference Electron Density Map• The difference electron density map should be

essentially featureless

• Significant positive or negative density on atom positions may indicate wrong atom type assignment or inadequate correction for absorption.

• Another cause may be the improper use of the SHELXL 'DAMP 0' for a non-converged refinement.

• Disorder in solvent regions may not show up in a peak list.

• Seriously in error strong reflections show up as positive and negative bands.

• Density peaks in chemically unreasonable positions may indicate twinning.

Voids and SQUEEZE

• Generally, crystal structures contain no significant solvent accessible voids. Most will collapse when their solvent of crystallization evaporates

• The SQUEEZE tool may be used to show either that there is no residual density in a VOID or to correct for its contribution

• In the latter case, info should be added to the CIF and FCF

Automated Twinning Detection• TwinRotMat attempts to report on twinning

based on the data in the .fcf.

• The related ALERTS may either confirm cases of twinning that have been addressed in the structure refinement or cases of missed twinning.

• Unfortunately no official datanames to report on twinning in the CIF are available yet.

Hirshfeld Rigid Bond Test

– CheckCIF uses the Hirshfeld Rigid Bond test outside its originally intended context (i.e. light atom structures).

– Large values may indicate misassigned atom types or disorder.

– ALERT levels are to be a function of the associated chemistry (e.g. M..C=O), data quality and resolution.

Unusual Molecular Geometry

• Unusual hybridization

• Unusual bond distances

• Phenyl ring with a large difference of the average bond distance from the expected 1.395 (due to wrong cell dimensions ?)

Short Intermolecular Contacts

• Short intermolecular contacts should be investigated. They can indicate

– Missing Hydrogen atom in a hydrogen bond

– wrong structure / wrong H-atom positions

– improper description of a disorder

– improperly modelled solvent

– Interesting contact to be discussed (e.g. halogen-halogen)

Analysis of the Reflection Data

– The data names and cell dimensions in the CIF and FCF should be identical.

– The CIF and FCF should be from the same refinement.

– Missing low order reflection data along with their expected values are reported

– Outliers with large Fo/Fc differences are reported

– Checks for the consistency of CIF & FCF data

– Calculation of the 'non weight optimized S value

Residual Issues and Challenges

- SHELXL/CIF provided defaults should be updated to their actual values.

- Validation of Powder, Charge Density and Incommensurate structures still open for development (experts needed)

- Avoid False positive and negative ALERTS

- Fabricated reflection data. Can we detect them ?

- Education – what is thye meaning of a particular ALERT

- Should validation criteria be different for structures published in chemical journals ?

References

A.L.Spek, J. Appl. Cryst. (2003). 36, 7-13. A.L.Spek, Acta Cryst. D65, 148-155.