1. Data Validation and Quality Marks
Suri Kabekkodu
ICDD

2. Background
Powder Diffraction File population (Inorganic+Organic) is more than half a million now !!
Quality marks are essential while working with larger database with similar diffraction patterns
Data validation and the quality mark assignments is the most important step in the editorial process

3. Quality Mark (QM) Types
Experimental patterns
Calculated Patterns (based on experimentally determined crystal structures)

4. QM for Experimental Patterns
Star (Well characterized chemically and crystallographyically, No unindexed lines,∆2ө≤0.03º)
I (Well characterized chemically No unindexed strong lines,∆2ө≤0.06º)
O (Poorly characterized, with editorial comment explaining the reason)
B (Do not meet the criteria for *, I, O)
R (d values from Rietveld refinement)
C (author calculated d values)
H (Hypothetical)

5. What are calculated patterns?
If we know the crystal structure, we can calculate the diffraction pattern using the equation
LP factor
Cell Volume
Multiplicity
Structure factor
Crystal structure
Displacement parameters
(temp. factors)

6. It is extremely important to make sure that the crystal structure used for the calculation is correct. In fact it is the rate determining step in the editorial process

7. Reference Intensity Ratio
All the calculated patterns have I/Ic
I/Ic =   c /c c   (2)
 = Linear attenuation coefficient
 = Absolute scale factor
 = Density
(“c “ corresponds to corundum)
Scale factor depends on the structural parameters used.
Incomplete or incorrect structure will result in wrong RIR and will lead to misleading results in quantative phase analysis

8. We need to have a reliability index
Which is the Quality Mark in Powder Diffraction File
Powder Diffraction File is the only crystallographic database that categorizes data on its quality

9. QM for Calculated Patterns
A calculated patterns quality mark task group was formed during the ICDD spring meeting 2003 in order to develop a method to assign quality marks to calculated patterns.
S. Kabekkodu (Chair), C. Hubbard, J. Kaduk, E. Antipov, M. Bennett, P. Wallace, F. Rotella

10. Calculated Patterns Quality Mark
The major step in this method involves several crystallographic and editorial checks by the ICDD, followed by the extraction and flagging of the structural database warnings/comments. Resulting calculated patterns will be classified into various categories based on the significance and nature of the warnings/comments. In the final step, a quality mark (QM) will be assigned to a calculated pattern based on its category.

11. The Method ICDD editorial checks (mainly crystallographic, chemistry)
Identification and extraction of external database comments

12. The Method Editor classifies and flags warnings
Minor warning (W1)
Significant warning (W2)
Major warning (W3)
QM will be assigned SQL query based on warning code.

13. Calc. QM Notations Category QM No Warning * Minor Warning I
Significant warning B
Assigned structure (Prototype) P
Hypothetical H
Major warning O

14. ICDD Editorial Checks
In this step, crystal structure from structural databases (ICSD, CSD, LPF, NIST) will be tested for completeness and various possible errors. Based on the test result, the database will be updated with appropriate warnings.

15. ICDD Editorial Checks Atomic coordinates Vs Space group description
That is ~21 million coordinates are verified with their symmetry operator
Transformation of non-standard space groups,
author’s choice of origin
Reported site multiplicity from the source database should match one generated by symmetry operators
Typographic error in space group symbol etc.
Consistency between reported Z and the sum of site multiplicity

16. Example Mg2 (SiO4), Fd-3m, a=8.12, Z=8 Space group origin at 4-3m
So if we operate all the 192 symmetry operators of Fd-3m (Int. Tbl for Crystallography Volume A), by the lattice description we should get
16 Mg, 8 Si and 32 O atoms
We get 8 Mg, 16 Si and 32 O atoms!
What could be wrong?

17. Answer Lets change the origin to -3m
Now we get 16 Mg, 8 Si and 32 O atoms
Using incorrect origin will result in wrong diffraction patterns and RIR

18. Wrong
Significantly different diffraction patterns

19. Does the space group represent true symmetry?
Several crystal structures get published (in non-crystallographic journals) without checking for possible higher symmetry
When looked carefully some structures are reported in sub group
They may have reasonable bond lengths and angles but does not represent the true symmetry (important from the physical property point of view)

20. Example LiRhO2 in F4132 Rh 16c 1/8,1/8,1/8 Li 16d 5/8,5/8,5/8
O 32e x,x,x
LiRhO2 in Fd-3m
Rh 16c 1/8,1/8,1/8
Li 16d 5/8,5/8,5/8
O 32e x,x,x
F4132 is a subgroup of Fd-3m

21. Application of reduced cell to identify incorrect space groups
a=6.609 b=7.318 c=7.485 Å, α=69.08 β=62.24 γ=64.72° in P-1 with Z=1
Reduced cell
a=6.609 b=7.318 c=7.323 Å, α=88.83 β=64.76 γ=64.72°
Vectors 011, 0-11,100 defines a C-centered lattice
a= b= c=6.609 Å, α=89.99 β= γ=89.96°
The correct space group is C2/m

22. ICDD Editorial Checks on Temperature factors (Displacement Parameters)
Temperature factors are good indicator of quality refinement. Usually Editor’s favorite one when we look beyond popular statistical parameters like R-factors
There are good number of published structures (more than 8,000 found) with attractive R-factors but meaningless temperature factors
ICDD’s editorial system checks all the anisotropic tensor coefficients for the positive definite matrix (i.e all the eigenvalues must be positive)
Non positive definite temperature factors are physically meaningless

23. ICDD Editorial Checks on Temperature factors (Displacement Parameters)
Anisotropic tensor coefficient is not permitted by the site symmetry
Magnitude of temperature factor is outside the range (0.001<U<0.1)
Isotropic temperature factor is negative
Identify and convert mixed type of temperature factors (U+B, Beta+U, etc) to a standard type.

24. ICDD Editorial Checks
Check the cell dimensions for missing decimal point, e.s.d and magnitude of the e.s.d etc.
Check the R factors close to the theoretical limit (0.83 for centrosymmetric and 0.59 for noncentrosymmetric structure) (useful check for % to value conversion)
Check for site occupation factor >1.0

25. ICDD Editorial Checks
Part of the structure was refined as a group without locating positions of the constituent atoms (e.g. C60 compounds)
Means approximation of scattering factors
Check for possible typographic errors in the element symbol by comparing chemical formula, atomic coordinate list and chemical name (e.g., frequently observed misprints in case of: Mn,Mg; Ti,Tl etc.)
Trivial fix once found. Can result in major error in the calculated intensities
When measured density is available, check the percentage of difference in measured and calculated density (check cell dimension, Z and related parameters when the difference is significant)

26. Structure Vs Lattice comparison
For a completely solved crystal structure
Z*FW / N*V = ( M*SOF*AW )/N*V
Z=Total number of molecules per unit cell
FW= Formula weight calculated based on reported composition
M= Site multiplicity factor
SOF= Site occupation factor
AW= Atomic weight of the occupying atom
N= Avogadro’s number
V= Unit cell volume
Summation is over number of occupied sites in the structure
On simplification,
Z*FW =  M*SOF*AW

27. Structure Vs Lattice comparison
Inequality in equation (2) arise when
Missing atoms in the refined structure
Incorrect/poor refinement of occupation factor
Z is inconsistent with the refined structure
Misspelled atom symbol in coordinate list or formula
Improper choice of space group origin
In the case of incomplete structures the value [Z*FW - M*SOF*AW / Z*FW]*100 is proportional to the percentage of missing electron density.

28. External Database Warnings/Comments
Editorial comments on unusually short or long bond lengths or questionable bond angles (comment needs to be very specific for structures showing disorder or partial/mixed occupancy)
Comment on questionnable space groups, cell dimensions etc.
Published coordinates are wrong
Type of experiment (single crystal/powder)

29. External Database Warnings/Comments
Radiation used (X-ray, Neutron, Synchrotron, Electron)
Temperature/Pressure of data collection
Comments on method of structure solution/refinement (Rietveld, ab-initio calculation etc)
Editorial comment on the structure
Reference to a contradicting structure

30. External Database Warnings/Comments
Description of type of disorder
Comments on modulated structure
Atomic coordinates are assigned based on structure prototype (LPF entries)
R factor not reported
Any correction to the published coordinates

31. Warning Classification
Minor Warning
Significant Warning
Major Warning
Density calculated from reported and calculated compositions differ (1%< x 3%)
Density calculated from reported and calculated compositions differ (3%<x15%)
Density calculated from reported and calculated compositions differ (15%<x)
No e.s.d. Reported/abstracted on the cell dimension
Unit cell dimensions taken from figure (approximated)
Incorrect cell dimension
Magnitude of e.s.d. on cell dimension is >1000 ppm
Missing decimal point in the cell dimension
Incorrect space group

32. Warning Classification (Contd-)
Minor Warning
Significant Warning
Major Warning
7%<R factor <12% (for single crystal), 10%<Rfactor>15% (powder)
12%<R factor (for single crystal), 15%<R factor (powder)
Incommensurate modulated structure. Only average structure of the sub cell is given
No R factor Reported/abstracted
Anisotropic temperature factor is non positive definite
Published atomic coordinates are wrong
Reported Z is inconsistent with the sum of site multiplicity
Anisotropic tensor coefficient is not permitted by the site symmetry
Structural database removed the entry corresponding to a published calculated pattern

33. Warning Classification (Contd-)
Minor Warning
Significant Warning
Major Warning
Type of experiment (single crystal/powder) not mentioned. (When unspecified, powder is assumed for ICSD, NIST,LPF entries)
Magnitude of temperature factor is outside the range (0.001<U<0.1)
Structure corrected by the editor (usually for cases with obvious abstraction/possible typographical error)
Negative isotropic temperature factor
Metric symmetry exceeds crystal symmetry
Source database (LPF/ICSD/NIST/CSD) warning on bond length/angle

34. Warning Classification (Contd-)
Minor Warning
Significant Warning
Major Warning
Misprint in the original paper was corrected in the database
Average structure of the modulated structure.
Site occupation factor>1.0
Probable site occupation factor is deduced from the nominal composition
Percentage of difference in measured and calculated density differ>2% (for non-porous materials) >5%
Part of the structure was refined as a group without locating position of the constituent atoms

35. Warning Classification (Contd-)
Minor Warning
Significant Warning
Major Warning
Comments containing reference to a contradicting crystal structure exist
Structure determined from projections
Structure determined using electron diffraction

37. Population of star patterns in the experimental set

38. R-factor trend by year

39. Quality Mark Population

40. Incomplete Structures

41. Example PDF Card

42. Structure Type Assignments and Classifications

43. Structure Type Notation
Popular structure type descriptions are
Traditional Notation
Based on unit cell, Pearson Symbol and chemistry (usually assigned manually by comparing the diffraction patterns)
ANX Formula
Based on type of ion and their site occupation
Example
Ca Ti O3 is of ABX3 type
Fe3O4 is of AB2X4 type
Long descriptive Notation following Parthe’s method
Based on detailed crystallographic analysis
Example Cu3 As,cI64,220 (Structure Type Formula, Pearson Symbol, Space group number)
Sensitive to prototype branching based on atomic environment

44. Structure Type requirements
Must crystallize in the same space group
Similar cell parameter ratio
Same Wyckoff positions (Wyckoff sequence)
When all the above 3 conditions satisfy, we have similar atomic environments

45. Possible structural representations
Lets take diamond structure as an example. This structure belongs to Fd-3m. Atomic coordinates can be expressed as
Origin choice 1, C at 8a site (0,0,0)
Origin choice 1, C at 8b site (1/2,1/2,1/2)
Origin choice 2, C at 8a site (1/8,1/8,1/8)
Origin choice 2, C at 8a site (3/8,3/8,3/8)

46. Standardization of Crystal Structure
First proposed by Parthe and Gelato (Acta Cryst. (1984), A40, )
The method uses standardization parameter
N is number of atom sites, x,y,z are fractional coordinates

47. Standardization Procedure
Represent the structure in standard space group (i.e. Int. Tbl. Crystallography)
Derive Niggli reduced cell or cell with a<b<c
Choice of representative coordinate triple considering permitted origins, rotation of coordinate system and eantiomorphic structure representation
Ordering and renumbering atoms in the final list

48. Standardization Criteria (-Contd)
Additional constraints
Triclinic space groups: Niggli reduced cell
Monoclinic with b-axis unique
Orthorhombic a b  c (when not fixed by the space group)
Trigonal space group with R lattice (triple hexagonal cell)
Choice of origin: at the inversion center
Enantiomorphic space groups: smallest index on the relevant screw axis

49. How to account for shape of the unit cell?
Γ is based exclusively on fractional coordinates.
Centre of Gravity (CG) parameter is useful to identify unit cell shape difference when we encounter same space group and wyckoff sequence
N=Number of atom sites, V=cell volume, a,b,c,α,β,γ Unit cell dimensions, x,y,z are atomic coordinates

50. Special Cases
In general standardization procedure can directly compare candidates for isotypic compounds. However there are some special cases:
Refinable coordinate very close to zero

51. Lets standardize diamond structure
Possible structure reprenation in Fd-3m are
Origin choice 1, C at 8a site (0,0,0)
Origin choice 1, C at 8b site (1/2,1/2,1/2)
Origin choice 2, C at 8a site (1/8,1/8,1/8)
Origin choice 2, C at 8a site (3/8,3/8,3/8)
After applying the condition that inversion center as the standard choice of origin we have excluded representation 1 and 2
Γ values for 3 and 4 are 0.22 and 0.65
Standard representation is #3

52. Why standardized data for comparison?
CeCu2, Imma, a=4.425,b=7.057, c=7.475
Cu (8h)
Ce (4e)
KHg2, Imma, a=8.10,b=5.16, c=8.77
Hg (8i)
K (4e)
Standardization
Standardization
CeCu2, Imma, a=4.425,b=7.057, c=7.475
Cu (8h)
Ce (4e)
KHg2, Imma, a=5.16,b=8.10, c=8.77
Hg (8i)
K (4e)

53. Stored procedure seeking for Ca Ti O3 like structure (1% Tolerance)

54. The result set of 165 patterns were imported into HighScorePlus and the comparison of their diffraction patterns corroborates the method.

55. Structure Type Applications
Deriving Starting Model for Rietveld Refinements
Traditionally starting model for Rietveld refinements was developed based on chemical/crystallographic intuition. In other words it is individual’s knowledge of structure types
Databases with Structure Type information can make seminal contributions to this effort. Powder Diffraction File in particular is advantageous as one can perform search match based on their diffraction pattern to explore the possible models.

56. Structure Type Applications
Structural chemistry information
Database search results can also be sorted based on their structural chemistry
Can be used to explore the database from the materials design point of view
3D crystalline structure related properties
Ferrolectric, Piezoelectric, Non Linear Optics,Transport

57. Database Classifications
Primary Patterns
When multiple entries are available, primary pattern is chosen by the editor based on QM and experimental conditions
Alternate Patterns
Closely related to primary pattern.
Deleted Patterns
Low precision pattern (and better pattern is in the database)
Major error identified by the editor that can not be fixed (or to be fixed (rare))

58. Subfiles
Classified into various categories based on chemistry, properties and application
Each subfile is defined by set of rules approved by the concerned subcommittee
Subcommittee members review the file and continuously improvise it

59. Classification Overview

60. Mineral Classification
Family-Related by partial structural similarities such as framework, chain etc
Subfamily-Collection within the family based on specific similarities
Homologous- Composed of two structural units interlayered in differenet proportions (e.g. Humite, Mg2SiO4•xMg(OH)2
Homotypes- Derivative structures based on a master structure (e.g.Perovskite)

61. Mineral Classification
Supergroup- Highest symmetry phases where the structure arrangement remains unchanged.
Group- Composed of Isostructural phases
Subgroup- Groups further classified based on chemistry (oxides, sulfides)
Related Structures- Based on structural distortions from the group structure (e.g. Bunsenite (NiO) is distortion of NaCl structure)

62. Example: Mineral and Zeolite Classification

63. Example: Sphalerite

64. Crystallographic basis of Symmetry Relationship

65. Zeolite Classification
Zeolite Name
Framework Code

66. Example Zeolite Names

67. Example- Zeolite Classification
Aluminum Silicate, Mutinaite