Crystallographic database
(Molecules need to crystallize into solids so that their regularly repeating arrangements can be taken advantage of in X-ray, neutron, and electron diffraction based crystallography).
They are routinely identified by comparing reflection intensities and lattice spacings from X-ray powder diffraction data with entries in powder-diffraction fingerprinting databases.
Crystallographic databases differ in access and usage rights and offer varying degrees of search and analysis capacity.
Newer versions are built on the relational database model and support the Crystallographic Information File (CIF) as a universal data exchange format.
In recent years, many publishers of crystallographic journals have come to interpret CIFs as formatted versions of open data, i.e. representing non-copyrightable facts, and therefore tend to make them freely available online, independent of the accessibility status of linked scientific articles.
Crystal structures are republished owing to corrections for symmetry errors, improvements of lattice and atomic parameters, and differences in diffraction technique or experimental conditions.
Crystal structures are typically categorized as minerals, metals-alloys,[4] inorganics,[5] organics,[6] nucleic acids,[7] and biological macromolecules.
[8][9] Individual crystal structure databases cater for users in specific chemical, molecular-biological, or related disciplines by covering super- or subsets of these categories.
Writing access rights (upload, edit, delete), on the other hand, determine the number and range of contributors to the database.
Scientific progress has been slowed down by restricting access or usage rights as well as limiting comprehensiveness or data integrity.
Search algorithms used for a more complex analysis of physical properties, e.g. phase transitions or structure-property relationships, might apply group-theoretical concepts.
Polycrystals are made of a large number of small single crystals, or crystallites, held together by thin layers of amorphous solid.
Crystal phases can be identified by successfully matching suitable crystallographic parameters with their counterparts in database entries.
The resulting partial-to-total overlap of symmetry-independent reflections renders the structure determination process more difficult, if not impossible.
[16] Search-match algorithms compare selected test reflections of an unknown crystal phase with entries in the database.
In this case, peak resolution is only possible in 3D reciprocal space, i.e. by applying single-crystal electron diffraction techniques.
High-Resolution Transmission Electron Microscopy (HRTEM) provides images and diffraction patterns of nanometer sized crystallites.
The vertical axis is defined as acute angle between Fourier transformed lattice fringes or electron diffraction spots.
[22][23] The Generalized Steno Law[24] states that the interfacial angles between identical faces of any single crystal of the same material are, by nature, restricted to the same value.
[26] In order to employ this technique successfully, one must consider the observed point group symmetry of the measured faces and creatively apply the rule that "crystal morphologies are often combinations of simple (i.e. low multiplicity) forms where the individual faces have the lowest possible Miller indices for any given zone axis".
[27] Provided that the crystal faces have been correctly indexed and the interfacial angles were measured to better than a few fractions of a tenth of a degree, a crystalline material can be identified quite unambiguously on the basis of angle comparisons to two rather comprehensive databases: the 'Bestimmungstabellen für Kristalle (Определитель Кристаллов)'[28] and the 'Barker Index of Crystals'.
[29] Since Steno's Law can be further generalized for a single crystal of any material to include the angles between either all identically indexed net planes (i.e. vectors of the reciprocal lattice, also known as 'potential reflections in diffraction experiments') or all identically indexed lattice directions (i.e. vectors of the direct lattice, also known as zone axes), opportunities exist for morphological fingerprinting of nanocrystals in the transmission electron microscope (TEM) by means of transmission electron goniometry.
While in optical goniometry net-plane normals (reciprocal lattice vectors) need to be successively aligned parallel to the reference direction of an optical goniometer in order to derive measurements of interfacial angles, the corresponding alignment needs to be done for zone axes (direct lattice vector) in transmission electron goniometry.
The complements to interfacial angles of external crystal faces can, on the other hand, be directly measured from a zone-axis diffraction pattern or from the Fourier transform of a high resolution TEM image that shows crossed lattice fringes.
Lattice parameters of unknown crystal phases can be obtained from X-ray, neutron, or electron diffraction data.
Alternatively, lattice parameters can be obtained from powder or polycrystal diffraction data via profile fitting without structural model (so-called 'Le Bail method').
If, on the other hand, some or all of the crystalline sample material can be ground, powder diffraction fingerprinting is usually the better option for crystal phase identification, provided that the peak resolution is good enough.
Bond distances and angles can be made available to the user in tabular form or interactively, by selecting pairs or groups of atoms or ions.
Alternatively, the crystal structure data are exchanged between the database and the visualization software, preferably using the CIF format.
More advanced visualization capabilities allow for displaying surface characteristics, imperfections inside the crystal, lighting (reflection, shadow, and translucency), and 3D effects (interactive rotatability, perspective, and stereo viewing).
