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A crystal is a solid with a regular repeating internal three-dimensional arrangement of atoms. This periodic arrangement can be exploited to determine molecular identity and structure when the crystal is exposed to x-rays. X-rays are used because their wavelengths correspond to inter-atomic distances. The arrangement of atoms within the crystal acts as an x-ray diffraction grating. When a crystal is subjected to x-rays, diffraction intensity data is collected resulting in a diffraction pattern. A typical small molecule crystal (>350 atoms) may have 1800 exposures to generate the diffraction pattern. Pattern location and intensity are used to determine size and composition of the molecule respectively. The phase relations of the diffracted beams are resolved mathematically before a model structure is deduced (referred to as the "Phase Problem"). Using computer software, structure parameters are systematically adjusted to give the best fit between observed intensities and calculations from the model structure. The final determination yields atom identities and positions in the unit cell and bond lengths and angles derived from the atom positions.
Probably the most famous X-ray diffraction image is the photograph of the B form of DNA taken by Rosalind Franklin in May 1952 ( http://www.physicstoday.org/vol-56/iss-3/captions/p42cap3.html ). With the help of Oxford crystallographer Dorothy Hodgkin, Franklin described the helical backbone and correct crystallographic space group for DNA . Her work was instrumental in Watson's and Crick's correct modeling of DNA, for which they received the Nobel Prize.
The author gratefully acknowledges Dr. Ilia Guzei, Director of the Molecular Structure Laboratory, University of Wisconsin-Madison, for his continued interest in x-ray cryatallography information.
Repositories/Databases
American Mineralogist Crystal Structure Database. http://www.geo.arizona.edu/AMS/amcsd.php (accessed 8/18/08)
Contents: Every structure published in the American Mineralogist, The Canadian Mineralogist, and the European Journal of Mineralogy.
Searchable: Mineral, Author, Element, Cell parameters, Text
Bilbao Crystallographic Server. Materials Laboratory, University of Basque Country , Spain . http://www.cryst.ehu.es/ (accessed 8/18/08)
Contents: Crystallographic programs and databases
Searchable: Space group, Point group, Subperiodic group
Cambridge Crystallographic Data Centre. Cambridge Structural Database. http://www.ccdc.cam.ac.uk/products/csd/ (accessed 8/18/08)
Contents: organic molecules, organometallic compounds
Searchable: Structure/substructure, Molecular Formula, Compound name, Peptide, Cell parameters, Text
Repository: Yes
License required (available in UW-Madison Chemistry Library)
Crystallography Open Database. http://www.crystallography.net/ (accessed 8/18/08). Also available: Predicted Crystallography Open Database
Contents: 12000 entries
Searchable: Text, Element, Cell parameters
Repository: Yes
CRYSTMET (http://www.tothcanada.com/databases.htm) (accessed 8/18/08).
Contents: ~93000 entries - metals, intermetallics, and alloys
Searchable: Text, Element, Unit cell, symmetry, Formula
Repository: No
License required.
Inorganic Crystal Structure Database. http://icsd.ill.fr/icsd/index.html (accessed 8/18/08)
Contents: Inorganic crystal structures, with atomic coordinates, published since 1913
Searchable: License required to access database
Repository: Yes
License required
Mineralogy Database. http://webmineral.com/ (accessed 8/18/08)
Contents: 4,300+ individual mineral species
Searchable: Mineral data linked to Crystal system, X-ray powder diffraction, Chemical composition, Dana classification, Strunz classification, Physical properties, Optical properties
Nucleic Acids Database. http://ndbserver.rutgers.edu/ (accessed 8/18/08)
Contents: 2300+ Nucleic acids
Searchable: Quick Search -- PDB ID, NAB ID, Classification, Structure description, Modifiers; Full Search - defined by specific tables.
Repository: Yes
Powder Diffraction File (PDF). International Centre for Diffraction Data (ICDD). http://www.icdd.com/products/pdf4.htm (accessed 8/18/08)
PDF-4 Contents: minerals, organics, organometallics: 255,000 data sets with digital patterns; 166,000 data sets with relative intensities; 98,000 data sets with atomic parameters.
PDF-2 Contents: 186,107 entries (159,809 inorganic & 28,610 organic)
Repository: Yes. Data acquired through contributions, literature surveys, and a Grant-in-Aid program.
License required to access database. Available to UW-Madison users of Materials Science Center facilities.
Protein Data Bank. http://www.rcsb.org/pdb/ [also http://rutgers.rcsb.org/pdb/ ] (accessed 8/18/08)
Contents: Proteins and Nucleic acids
Searchable: PDB ID, author, Keyword, Chain type. Can customize search form to include EC Number, Space group, Unit cell dimension, etc.
Repository: Yes
Reciprocal Net.Common Molecules. http://www.reciprocalnet.org/edumodules/commonmolecules/index.html (accessed 8/18/08)
Contents: compounds encountered in daily life.
Searchable: Name, Formula, Parameters, Space group, keywords.
Repository: Yes, by participating crystallography labs
Southampton Crystal Reports. Crystal Structure Report Archive. http://ecrystals.chem.soton.ac.uk/ (accessed 8/18/08)
Contents: 105 compounds deposited by University of Southhamption researchers
Searchable: Name, Author, Keyword, Class, Journal/publication name .
Repository: Yes by registration
Structure Commission, International Zeolite Association. Database of Zeolite Structures. http://www.iza-structure.org/databases/ (accessed 8/18/08)
Contents: Structural information on all zeolite structure types
Searchable: Framework type properties, Cell parameters, Text, Author
Collection of Simulated XRD Powder Patterns for Zeolites. http://topaz.ethz.ch/IZA-SC/XRDpatterns.htm (accessed 8/18/08)
United States Department of the Navy, and the Naval Research Laboratory. Crystal Lattice Structures. Last updated 27 June 2006. http://cst-www.nrl.navy.mil/lattice/index.html (accessed 8/18/08)
Contents: 264 structures in 94 of the 230 space groups.
Searchable: Indexed by Strukturbericht designation, Pearson symbol, Space group, Prototype, Intermetallic alloy phases.
Online Learning
International Union of Crystallography. Crystallographic Education Online. http://www.iucr.org/cww-top/edu.index.html (accessed 8/18/08)
International Union of Crystallography. Commission on Crystallographic Teaching Pamphlets. http://www.iucr.org/iucr-top/comm/cteach/pamphlets.html (accessed 8/18/08
Cowtan, K. Interactive Structure Factor Tutorial. http://www.ysbl.york.ac.uk/~cowtan/sfapplet/sfintro.html (accessed 8/18/08)
Ecole Polytechnique Federale de Lausanne. e-Crystallography course: Crystallography 1. http://escher.epfl.ch/eCrystallography/ (accessed 8/18/08)
Hardaker, W.; Chapuis, G. Escher Web Sketch. http://escher.epfl.ch/escher/ (accessed 8/18/08)
Jasinski, Jerry P.; Foxman, Bruce M. Symmetry and Space Group Tutorial. http://people.brandeis.edu/~foxman1/teaching/indexpr.html. Site contains a donwloadable PowerPoint tutorial. The authors ask for feedback and invite users to register for updates. (accessed 8/18/08)
Proffen, T.; Neder, R.B. Interactive Tutorial about Diffraction, ver. 2.1. 2003. http://www.lks.physik.uni-erlangen.de/diffraction/ (accessed 8/18/08)
Reciprocal.Net. Learn About. http://www.reciprocalnet.org/edumodules/index.html (accessed 8/18/08)
Rupp, B. Crystallography 101. http://ruppweb.dyndns.org/Xray/101index.html (accessed 8/18/08)
Vela, Michael J.; Cho, Tae H.; Foxman, Bruce M. Crystalline Insights: An X-ray Lab-Based Tutorial and Structure Determination Demo. http://people.brandeis.edu/~foxman1/teaching/indexhs.html. Site contains a donwloadable PowerPoint tutorial suitable for advanced high school and above.The tutorial will run on a PC or Mac with MS PowerPoint installed. The authors ask for feedback and invite users to register for updates. (accessed 8/18/08)
Organizations
American Crystallographic Association. http://www.hwi.buffalo.edu/ACA/ (accessed 8/18/08)
British Crystallographic Association. http://bca.cryst.bbk.ac.uk/bca/welcome.htm (accessed 8/18/08)
European Crystallographic Association. http://www.ecanews.org/ (accessed 8/18/08)
International Union of Crystallography. http://www.iucr.org (accessed 8/18/08)
International Zeolite Association. http://www.iza-online.org/ (accessed 8/18/08)
Society of Crystallographers in Australia and New Zealand . http://www.sca.asn.au/ (accessed 8/18/08)
Swiss Crystallographic Association. http://www.sgk-sscr.ch/ (accessed 8/18/08)
Books and Reference Works
Elkin, L. O. Physics Today . February 2003, p. 61. http://www.physicstoday.org/vol-56/iss-3/p42.html . (accessed 12/15/06).
Giacovazzo, C.; Monsaco, H. L.; Artioli, G.; Viterbo, D.; Ferraris, G.; Gilli, G.; Zanotti, G.; Catti, M. Fundamentals of Crystallography; 2 nd ed. Giacovazzo, C., Ed.; Oxford : Oxford University Press, 2002 (Chem Lib: QD905.2 F86 2002).
Glusker, J. P.; Lewis, M.; Rossi, M. Crystal structure analysis for chemists and biologists; New York : VCH, 1994 (Chem Lib: QD945 G583 1994).
Hammond, C. The basics of crystallography and diffraction; 2nd ed.; New York: Oxford University Press, 2001 (Chem Lib: QD905.2 H355 2001).
International tables for crystallography: Volume A Space-group symmetry; Hahn, T., Ed.; 5 th ed.; Dordrecht : Kluwer Academic Publishers, 2002 (Chem Lib Reference: QD908 I56 2002 ).
Library Call Numbers: QD 910 - 9999 Crystallography
MadCat
Use BASIC "Subject Browse" Search to locate narrower subject terms:
Selected Journals
Acta crystallographica. Section A, Foundations of crystallography. http://journals.iucr.org/a/journalhomepage.html. Geology & Geophysics Lib: MC AC8 C882
Acta crystallographica. Section B, Structural science. http://journals.iucr.org/b/journalhomepage.html. Chem Lib: LN AC75 B1
Acta crystallographica. Section C: Crystal structure communications. http://journals.iucr.org/c/journalhomepage.html. Chem Lib: LN AC75 C1
Acta crystallographica. Section D, Biological crystallography. http://journals.iucr.org/a/journalhomepage.html. Chem Lib: LN AC75 D
CrystEngComm. Royal Society of Chemistry. http://www.rsc.org/crystengcomm (1999-)
Journal of applied crystallography. http://journals.iucr.org/j/journalhomepage.html Chem Lib: LN J82 AP51
Journal of crystal growth. http://www.sciencedirect.com/science/journal/00220248 (1995-)
Polyhedron. ScienceDirect (1982-2005). Chem Lib: LN P739
Journal Databases
BEILSTEIN/GMELIN
To launch Beilstein/Gmelin from a campus library workstation, click HERE. The client may be installed on local workstations for access outside campus libraries. See Remote Access and Client Distribution for more information about local installation. For search help, see Beilstein and Gmelin Help
Locate Beilstein crystallographic data in CRYSTALS data fields:
Locate Gmelin crystallographic data in CRYSTAL STRUCTURE Pre-Defined Search Form:
SCIFINDER SCHOLAR
Click HERE to launch SciFinder Scholar on a campus library computer (not on a DoIT Info Lab computer located inside a campus library).The client may be installed on local workstations for access outside campus libraries. See Remote Access and Client Distribution for more information about local installation. For search help, see SciFinder Scholar Help
Limit substance GET REFERENCES to CRYSTAL STRUCTURE role. Roles have been applied since 1967.
Refine RESEARCH TOPIC SEARCH using REFINE BY RESEARCH TOPIC and "crystal structure"
Glossary
Ångström unit (Å): unit of length. 1 Ångström unit = 10 -8 cm
Crystal lattice: Three-dimensional imaginary array of points (hkl). Each point represents a unit cell.
Crystal system: Unit cell type
Cubic = Three equal axes at right angles.
Tetragonal = Three axes at right angles, two equal.
Orthorhombic = Three unequal axes at right angles.
Rhombohedral = Three equal axes, equally inclined.
Hexagonal = Two equal coplanar axes at 120º, third axis at right angles.
Monoclinic = Three unequal axes, one pair not at right angles.
Triclinic = Three unequal axes, unequally inclined and none at right angles.
Plane group: Symmetry group of a two-dimensional crystal pattern. There are 17 plane groups.
Point group: Symmetry operations applied to a single point fixed in space. There are 32 three-dimensional crystallographic point groups.
Site-Symmetry Group: Symmetry operations applied to a point fixed in space. There are 32 unique crystallographic point groups.
Space group: Symmetry operations applied to points arranged on a crystal lattice. There are 230 unique crystallographic space groups. Space groups are numbered 1-230. Each space group is identified with an international space group symbol which is generated from its point group symbols.
Unit cell: Basic building block of a crystal, repeated indefinitely in three dimensions. Characterized by three vectors ( a , b , c ) and the angles between the vectors ( alph a - angle between b and c ; beta - angle between a and c ; and gamma - angle between a and b ).
The author gratefully acknowledges Dr. Ilia Guzei, Director of the X-Ray Laboratory, University of Wisconsin-Madison, for his continued interest in x-ray cryatallography information.
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