Use of Powder Diffraction File – PDF4+, open structure databases

R. Kužel

Charles University in Prague, Faculty of Mathematics and Physics, Ke Karlovu 5, 121 16 Praha 2

 

Inorganic structural databases and related databases were described for example in [1]. However, the text needs some updates.

Powder Diffraction File - PDF

The database has already long history. It was started in a form of card sets – ASTM in Fifties, later on as JCPDS and in last decades it is called PDF. It is developed, edited and maintained by the ICDD - the International Centre for Diffraction Data [2] and it is now offered in several versions declared as follows.

Table 1. PDF versions available

 

Single license of the first four versions for one year is 8 660 USD (5 775 USD for Academics), one year renewal for 1 760 USD (1 150 USD). See icdd.com for 3-year, 5-year or site licenses.

In the following paragraphs some text from the website (icdd.com) is used.

Release 2014 of the Powder Diffraction File (PDF) contains 799,700+ unique material data sets. Each data set contains diffraction, crystallographic and bibliographic data, as well as experimental, instrument and sampling conditions, and select physical properties in a common standardized format.

Traditional form of the database is PDF-2 and it is a collaborative product between ICDD, FIZ (Karlsruhe) and NIST (National Institute of Standards). It is designed for inorganic materials analyses. Many common organic materials from ICDD are added to this database to facilitate rapid material identification. It must be take into account that quite often more records correspond to single phase. Each record contains table of interplanar spacings (d), relative intensities (I) and often also diffraction indices (hkl). In addition, chemical formula, chemical name, mineral name for minerals, crystal system, some physical characteristics, experimental parameters, bibliographic information and mark of data quality.  The PDF-2 licence is lifetime, of course, without updates.

Preferred form of database distribution is now PDF-4+.  It is designed for both phase identification and quantitative analysis. It contains the data from both the PDF-2 and ICDD's collaboration with MPDS. This database has comprehensive material coverage for inorganic materials and it contains numerous additional features such as digitized patterns, molecular graphics, and atomic parameters. Some features were included to enhance the ability to do quantitative analysis using third party software by any of three methods: Rietveld Analysis, Reference Intensity Ratio (RIR) Method or Total Pattern Analysis. In latest version, the ICDD added modulated entries with atomic coordinates. In 2015, new molecular graphics that visualize various modulations will be included. These entries are part of the new data source, designated '05', which contains crystal structures abstracted and quality checked by ICDD.

The database has the following features (2014)

• All 354,264 entries have digital patterns for use in total pattern analysis
• 258,125 entries have I/I_c values for quantitative analysis by Reference Intensity Ratio (RIR)
• 239,568 entries with atomic coordinates for quantitative analysis by the Rietveld method
• Experimental digital reference patterns for non-crystalline materials

The PDF-4 license is strictly limited to a single computer (for single license) and also time limited. If expired, nothing works.

WebPDF-4+ provides the needed portability for accessing the PDF-4+ database via the internet. It enables full functionality of the PDF-4+ database using a high-speed internet connection. WebPDF-4+ is delivered as a USB compatible dongle.

PDF-4/Organics is a highly targeted database with the world's largest collection of pharmaceutical excipients and polymer materials. It is designed for a multitude of applications in pharmaceutical, regulatory, specialty chemical, biomaterial, and forensic fields. The product has all of the display software and data mining capabilities contained in the PDF-4 family of products.

Comparison of database features can be found at http://www.icdd.com/products/pdf4-2-comparison.htm

The ICDD and the collaborating database organizations each have editorial mechanisms for updating historic data. Updates are frequently made by authors. Corrections in the data are made by users of the database or editorial reviewers. Typically, tens of thousands of historical entries are updated each year.

ICDD's search indexing programs, SIeve for PDF-2 and SIeve+ for PDF-4, are designed to search and identify unknown materials. SIeve and SIeve+ are integrated into the ICDD databases to allow the use of the extensive data mining interfaces, searches, and sorts available to improve accuracy and precision of the identification process. For example, users can utilize the extensive permutable searches in each database, then define their own search subfile or use any of the "application or expert-defined" subfiles and subclasses to increase the accuracy of their phase identification. In many cases, this provides a unique capability to analyze the most difficult problems.

SIeve and SIeve+ offer a variety of algorithms and options that allow users to optimize results for particular chemistries and both standard and non-standard diffraction systems. SIeve and SIeve+ features automatic rotation of the eight strongest lines (Hanawalt) or the eight longest of the strongest lines (Fink) or the eight longest lines (Long8) to look for entries that exhibit the best Goodness of Match (GOM). In the last few years, new algorithms have been added to identify non-crystalline materials and complex multi-phase specimens. Most of the algorithms were developed and optimized for a particular type of analysis and the selection options provide the user with a wide breadth of analytical capability. Since the fundamental algorithms used by SIeve/SIeve+ are different than those used by most commercial software programs, they can be strongly complimentary.

Several useful presentations on the use of PDF can be downloaded from http://www.icdd.com/resources/tutorials/index.htm

Some of them will be used during the presentation which will be focussed on new features and possibilites like to plot different graphs – dependencies in the database (for example, lattice parameters vs. stoichiometry, temperature etc.), using the approximate fields, multiple space group search, more powder diffraction pattern simulation options, experimental data corrections etc.

Figure 1.  Example of search output for one phase with d-spacings, intensities, hkl indices and simulated powder pattern.

Figure 2.  Example of search output for one phase. If structure is known (atomic coordinates), the structure can be visualized, Kikuchi lines, 2D diffraction pattern (back-reflection) and electron diffraction can be calculated.

 

Open structural and related databases

A list of primary and secondary crystallographic databases can be found at http://www.iucr.org/resources/data. However, one is still missing there and it is the COD – Crystallography Open Database [3] that is - Open-access collection of crystal structures of organic, inorganic, metal-organic compounds and minerals, excluding biopolymers [4]. Currently (June 2015) there are 315 590 entries in the database which is fully open access as it has been constructed this way from the very beginning. Only simple search is available including basically text, up to 8 elements chemical search (Boolean logics),  cell volume limits, journal, year, volume, issue, Z-limits, lattice parameters limits. However, then CIF files are available containing all necessary structural information as well as JSmol structure preview.

Mineralogical databases are essentially also open.

American Mineralogist Crystal Structure Database [5] includes every structure published in the American Mineralogist, The Canadian Mineralogist, European Journal of Mineralogy and Physics and Chemistry of Minerals, as well as selected datasets from other journals. The database is maintained under the care of the Mineralogical Society of America and the Mineralogical Association of Canada, and financed by the National Science Foundation. The interface offers chemistry, diffraction, lattice, author and mineral searches.

Mineralogy Database [6] contains 4714 minerals with a links and a comprehensive image library. Each mineral has a page linked to tables devoted to crystallography, crystal structures, X-Ray powder diffraction, chemical composition, physical and optical properties, Dana's New classification, Strunz classification, mineral specimen images, and alphabetical listings of mineral species. There also are extensive links to other external sources of mineral data and information. Structures can be visualized in Jmol applets.

Mincryst [7] the Russian database (Institute of Experimental Mineralogy, Moscow) was created in 1997 and it is called "Crystallographic and Crystallochemical Database for Mineral and their Structural Analogues" and can be entered via English or Russian gate. Currently it contains 9016 entries. It is a combination of structural database, theoretical powder patterns and software. Each entry has a mineral name, chemical formula, space group, lattice parameters, atomic coordinates, temperature factors, occupation and bibliographic information. Software package includes calculation of powder pattern or mixture of phases, standardless phase analysis, structure visualization etc.

Specialized databases can be found for zeolites [8].

Crystallographic server in Bilbao [9] provides information on space groups (e.g. generators of positions in individual space groups, subgroups etc.) similar to the information in International Tables for Crystallography vol. 1. It is continuously developed and it is also a base for theoretical crystallography.

Data of general interest like periodic element tables can be found at [10-12]. The last one [20] is focused on X-ray characteristics.

Pearson´s Crystal Data

In the end one commercial database should  be mentioned and this is Pearson’s Crystal Data – crystal structure database for inorganic compounds [13]. The database is published by y ASM International (Materials Park, Ohio, USA), edited by Pierre Villars and Karin Cenzual. It contains crystal structures of a large variety of inorganic materials and compounds. The "PCD" (as it is typically abbreviated) is a collaboration between ASM International and Material Phases Data System, Vitznau, Switzerland (MPDS), aiming to create and maintain the world's largest critically evaluated "Non-organic database". The current release contains nearly 258,500 structural data sets (including atom coordinates and displacement parameters, when determined) for about 150,000 different chemical formulas, roughly 16,800 experimental powder diffraction patterns and about 232,000 calculated patterns (interplanar spacings, intensities, Miller indices).

Main advantage is very user –friendly software with many features which allows really easy work. It all structural information, list of distances, structure 3D visualization, powder pattern simulation, selection criteria, entry data sheet etc. from a single page. It includes the so-called perpetual restraining giving estimation of results during defining search criteria. We have an experience that users in our lab and newcomers usually select primarily this database for their work.

1.         R. Kužel, S. Daniš, Materials Structure, 14 (2007) 89-96.

2.        International Centre for Diffraction Data – http://iccd.com

3.        http://www.crystallography.net/ 

4.         S. Grazulsi et. al. J. Appl. Cryst. 42 (2009) 726-729. Open access.

5.         http://rruff.geo.arizona.edu/AMS/amcsd.php

6.         http://webmineral.com/

7.         http://database.iem.ac.ru/mincryst/

8.         http://www.iza-structure.org/databases/

9.         http://www.cryst.ehu.es

10.       http://www.webelements.com/

11.       http://www.physics.nist.gov/PhysRefData/Elements/cover.html

12.       http://www.csrri.iit.edu/periodic-table.html

13.       http://www.crystalimpact.com/pcd/