MATERIAL IDENTIFICATION AND CHARACTERIZATION 10 YEARS OF DEVELOPMENT PDF-4/Organics Database
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MATERIAL IDENTIFICATION AND CHARACTERIZATION
10 YEARS OF DEVELOPMENT PDF-4/Organics Database
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Timothy G. Fawcett, Soorya N. Kabbekodu, Fangling Needham and Cyrus E. CrowderInternational Centre for Diffraction Data,
Newtown Square, PA, USA
Experimental X-Ray Diffraction Data provided by ICDD members and ICDD grantees
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MATERIAL IDENTIFICATION AND CHARACTERIZATION
All entries have powder patterns Most have spot, ring, EBSD patterns
Database contains organic, organometallic, polymer and inorganic materials
(Drugs, excipients, packaging materials, common salts, common corrosion phases)
Database has a relational database design Entries contain physical properties Entries contain instrumental and experimental conditions Entries contain bibliographic information Entries contain crystallographic information All entries have been standardized All entries have been evaluated for quality Searches based on chemistry, crystallography and analytical
data
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10 Year Growth
2003 2004 2005 2006 2007 2008 2009 2010 2011 20120
50,000
100,000
150,000
200,000
250,000
300,000
350,000
400,000
450,000
500,000
PDF-4/Organics
00- Experimental 01- FIZ 02- CCDC
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History of Continuous Improvements
2003 – Targeted pharmaceuticals for grants (2003- now) Product designed as a relational database Cross referenced ICDD (PDF No.), CSD databases (Refcode)
2004 – Added excipient file, Cross referenced ICSD (Entry numbers)
2005 – Implemented calculated pattern quality system 2006 – Implemented JAVA point and click interfaces 2007 – Implemented automated cross referencing system
Introduced integral index Crystallite size simulation program
2008 – Introduced experimental digital patterns 2009 – Expanded d-spacing ranges
Subfile enhancements for forensics and polymers 2010 – More organic subfile additions – amino acids, steroids, carbohydrates
First amorphous references for % crystallinity determinations 2012 – Significant additions of atomic coordinates
2nd Generation integral index
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PDF-4/Organics
2003 – Targeted pharmaceuticals for grants (2003- now) Product designed as a relational database Cross referenced ICDD (PDF No.), CSD databases
(Refcode) 2004 – Added excipient file,
Cross referenced ICSD (Entry numbers) 2005 – Implemented calculated pattern quality system 2006 – Implemented JAVA point and click interfaces 2007 – Implemented automated cross referencing system
Introduced integral index Crystallite size simulation program
2008 – Introduced experimental digital patterns 2009 – Expanded d-spacing ranges
Subfile enhancements for forensics and polymers 2010 – More organic subfile additions – amino acids, steroids,
carbohydrates First amorphous references
2012 – Significant additions of atomic coordinates 2nd Generation integral index
Data MiningPolymorph ID
Enhanced Phase Identification
% Crystallinity Amorphous Materials
Quantitative Phase Identification
Nanomaterials
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Material Identification and Characterization
Formulation Analysis
(Excipients, Quality System)
Polymorph Identification
(Digital Calc. Patterns)Trace Phase Identification
with Data Mining(Searches)
Nano materialsAmorphous Materials
(Digital Experimental Patterns )
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Database DevelopmentAnnual Product
Published
Customer Surveys
Customer Input (email, clinics,
workshops, symposia)
ICDD Organics Subcommittee
Software Developer Input
(Automation, Speed)
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Development of Strategic Subfiles
2004 2005 2006 2007 2008 2009 2010 2011 20120
2,000
4,000
6,000
8,000
10,000
12,000
Strategic Subfiles
PharmaceuticalsExcipientsMerck
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Pharmaceutical Materials – Release 2011Pharmaceuticals -6,370 Excipients – 1,916
ICDD53%
ICSD21%
CSD26%
NIST0%
Pharmaceuticals
ICDD38%
ICSD50%
CSD12%
NIST1%
Excipients
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ICDD Grant Programs1,396 Pharmaceutical Phases
18 % of all known XRD patterns of pharmaceuticals, both single crystal
and powder, have come from the ICDD grant program
Prof. Shao Fan Lin
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10 Year Growth
20032004200520062007200820092010201120120
50,000
100,000
150,000
200,000
250,000
300,000
350,000
400,000
450,000
500,000
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02- CCDC01- FIZ00- Experimental
FIZ (01) contributes49 % of all excipients,21 % pharmaceuticals
ICDD (00) experimentalcontributes 53 % ofall pharmaceuticals, 38 % of excipients
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Pharma associated Subfiles
Polymers – 1,302 Bioactives -13,145
ICDD87%
ICSD0%
CSD13%
PolymersICDD2%
CSD98%
Bioactives
Bioactives are materials that exhibit someBioactive behavior
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Bioactives by Publication Year13,864 Bioactives
Would include exploratory drugs, drug salts, herbicides, pesticides, gramicides
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File Size and 2θ Range- For full pattern methods
2007 2008 2009 2010 2011 20120
10,000,000
20,000,000
30,000,000
40,000,000
50,000,000
60,000,000
70,000,000
80,000,000
90,000,000
100,000,000
Interplanar Spacings
Axis Title
5.5 GB
22 GB
RietveldLeBailPauleyFullPAT
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Quality System – Disordered Structures
Missing electron density
Is the powder pattern accurate
How much electron density is missing ?
50,757 not published !
68,608 published, most with low quality marks
0 % 1-3 % 4-15 %
> 15 %
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Disordered StructuresCalculated vs Structural Density
Before Quality MarkSystem
After Quality Mark SystemDeletes removed
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Missing H atoms
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Quality System – Disordered Structures
Primary, Star Patterns
All Primary and AlternatesNo deletes
All Data
“S” Quality
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Quality of CSD sourced Data
Star Quality266,129 Entries
165,230Not Star Quality
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Sources of errors
Missing electron density- disorders- missing hydrogens- missing molecules (water, other solvates)
Non positive thermal displacement parameters
Unrealistic bond angles and distances
Chemical analysis does not match crystallographic determination(Author formula vs calculated formula)
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Sucrose – Which one is correct ?
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Sucrose – Which one is correct ?
Star, based on single crystal dataall atoms foundReflection geometry
Blank, missing 6.3 % densityfrom hydrogens
O quality from 1956 film data,Intensities visually calibratedTransmission geometry
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Closer Inspection
3 shown in previous slide
12 determinations of sucrose
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Multiphase Analyses5- Phases 4 Star, 1 I quality
8 – Phase Matchwith data mining
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Subfiles and Data Mining
Database98%
Excipients0.5% Pharmacueticals
2%
Subfiles
Dave Rendle, UKFanglingNeedham
What is in a pharmaceutical tablet ?
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SubfilesTarget Subfiles
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Target Materials
Have atomic coordinates
CrystallineHas Atomic Coordinates
Non-crystallineHas PD3 Patterns
Publications per year
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29
Experimental digital patterns
Nanocrystalline or Amorphous ?Cellulose Polystyrene
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Targeted DevelopmentInclude all target subfiles
Add atomic coordinate data sets through bibliographic extraction
Fix disorders – site occupancies included
Add anisotropic thermal displacement parameters
Extract supporting analytical data
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80-85 %
15-20 %Pepcid AC - 2012
Kaduk & Langan
McBride, Shankland, DavidShankland, Steele
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Pepcid AC
Nano
Amorphous
Highly crystalline
Calculated patternExperimental amorphous patternExperimental nano pattern
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US PatentPowder Pattern – bestReference for identification
Best Fit among single crystalpolymorphs – best reference
for quantitation
Patent exhibits orientation along (h 0 0)Data on Pepcid AC matches patent data over single crystal !
Famotidine – Similarity Index
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Amorphous and nanocrystalline patterns
Often requires support analytical data to help with the diffraction pattern interpretations.In this case the PDF confirms that in some cases the materials are nanocrystalline andin other cases the materials are amorphous. In these cases the support data are includedwith the PDF reference.
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Conclusions PDF-4/Organics is designed for
material identification and characterization
Database, data mining and identification software are all being continuously improved – expanding analysis capabilities for identification and characterization
Feedback from users and members redesigns the database (2012 Global User Survey)
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PDF-4/Organics