Validation of the Crystallography Open Database using the Crystallographic Information Framework

Data curation practices of the Crystallography Open Database (COD) are described with additional focus being placed on the formal validation using the Crystallographic Information Framework (CIF). The cif_validate program, capable of validating CIF files against both the DDL1 and the DDLm dictionaries, is presented and used to process the entirety of the COD. Validation results collected from over 450 000 CIF files are demonstrated to be a useful resource in the data maintenance process as well as the development of the underlying ontologies. A set of programs intended to aid in the dictionary migration from DDL1 to DDLm is also presented.

High-throughput computational screening for two-dimensional magnetic materials based on experimental databases of three-dimensional compounds

We perform a computational screening for two-dimensional (2D) magnetic materials based on experimental bulk compounds present in the Inorganic Crystal Structure Database and Crystallography Open Database. A recently proposed geometric descriptor is used to extract materials that are exfoliable into 2D derivatives and we find 85 ferromagnetic and 61 antiferromagnetic materials for which we obtain magnetic exchange and anisotropy parameters using density functional theory. For the easy-axis ferromagnetic insulators we calculate the Curie temperature based on a fit to classical Monte Carlo simulations of anisotropic Heisenberg models. We find good agreement with the experimentally reported Curie temperatures of known 2D ferromagnets and identify 10 potentially exfoliable 2D ferromagnets that have not been reported previously. In addition, we find 18 easy-axis antiferromagnetic insulators with several compounds exhibiting very strong exchange coupling and magnetic anisotropy.

Determining dimensionalities and multiplicities of crystal nets

Low-dimensional materials have attracted significant attention over the past decade. To discover new low-dimensional materials, high-throughput screening methods for structures with target dimensionality have been applied in different materials databases. For this purpose, the reliability of dimensionality identification is therefore highly important. In this work, we find that the existence of self-penetrating nets may lead to incorrect results by previous methods. Instead of this, we use the quotient graph to analyse the topologies of structures and compute their dimensionalities. Based on the quotient graph, we can calculate not only the dimensionality but also the multiplicity of self-penetrating structures. As a demonstration, we screened the Crystallography Open Database using the method and find hundreds of structures with different dimensionalities and high multiplicities up to 11. Some of the self-penetrating materials may have application values in gas storage, selective catalysis or photocatalysis because of their high gas sorption capacities and various electronic structures.

A comprehensive review of database resources in chemistry

As scientific community worldwide is publishing a huge number of research articles in various fields; it is necessary to distinguish between databases that are efficient and objective for literature searches. This review offers information on the important points of the database. None of the databases are complete and perfect, but they complement each other. If a library can only afford one, choice must be based on the priorities of institutional needs. The benefits that databases can provide in the preparation of the literature review for developing future studies and dissemination of research are discussed. This paper provides an overview of the most frequently used free chemistry databases such as PubChem, Crystallography Open Database, PubMed, ZINC, ChemSpider, and Google Scholar. It also gives a brief description of three major commercial databases such as Scopus, Web of Science, and SciFinder. Thus, substance and citation databases that covers almost all areas of chemistry, has become an invaluable tool in bibliometric analysis.

Raman Open Database: first interconnected Raman–X-ray diffraction open-access resource for material identification

Detailed crystallographic information provided by X-ray diffraction (XRD) is complementary to molecular information provided by Raman spectroscopy. Accordingly, the combined use of these techniques allows the identification of an unknown compound without ambiguity. However, a full combination of Raman and XRD results requires an appropriate and reliable reference database with complete information. This is already available for XRD. The main objective of this paper is to introduce and describe the recently developed Raman Open Database (ROD, http://solsa.crystallography.net/rod). It comprises a collection of high-quality uncorrected Raman spectra. The novelty of this database is its interconnectedness with other open databases like the Crystallography Open Database (http://www.crystallography.net/cod and Theoretical Crystallography Open Database (http://www.crystallography.net/tcod/). The syntax adopted to format entries in the ROD is based on the worldwide recognized and used CIF format, which offers a simple way for data exchange, writing and description. ROD also uses JCAMP-DX files as an alternative format for submitted spectra. JCAMP-DX files are compatible to varying degrees with most commercial Raman software and can be read and edited using standard text editors.

OChemDb: the free online Open Chemistry Database portal for searching and analysing crystal structure information

The Open Chemistry Database (OChemDb) is a new free online portal which uses an appropriately designed database of already solved crystal structures. It makes freely available computational and graphical tools for searching and analysing crystal-chemical information of organic, metal–organic and inorganic structures, and providing statistics on desired bond distances, bond angles, torsion angles and space groups. Atom types have been classified by an identifier code containing information about the chemical topology and local environment. The crystallographic data used by OChemDb are acquired from the CIFs contained in the free small-molecule Crystallography Open Database (COD). OChemDb offers easy-to-use and intuitive options for searching. It is updated by following the continuous growth of information stored in the COD. It can be of great utility for structural chemistry, in particular in the process of determination of a new crystal structure, and for any discipline involving crystalline structure knowledge. The use of OChemDb requires only a web browser and an internet connection. Every device (mobile or desktop) and every operating system is able to use OChemDb by accessing its web page. Examples of application of OChemDb are reported.