CCDC




What textual information does a CSD entry contain?

Each entry in the CSD contains a number of data items. These are obtained from the CIF, the published paper or derived by CCDC. Every data item is validated by CCDC Scientific Editors and/or CCDC software. The following table is a non-exhaustive list of what an entry may contain (this depends on what information is available in the CIF or the published paper). It details where we locate the data and where it can be found in the entry as viewed in the multi-pane version of ConQuest.

Other information is stored with CSD entries; details are provided elsewhere (see General Information Content).

Data Item

Source of information

Location in CSD entry

Additional comments

Author names

Published paper Author/Journal tab Some standardisation of names is applied to comply with CCDC rules.

Compound name/synonym

Published paper/CCDC Chemical tab Compound names generally try to reflect what is given by the author in the paper. A compound may have several synonyms. Both the compound name and synonym are searched when a name query is undertaken. Names given by the CCDC give reference to the IUPAC rules on the nomenclature of organic chemistry and may also utilise the ACD naming package. Polymeric compounds are always denoted with the term catena-.

Formula

CIF/CCDC Chemical tab A moiety formula with stoichiometries (and charges) is given. Discrepancies can occur with disordered compounds or in cases with partially charged molecules.

Journal Citation

Published paper Author/Journal tab The reference is usually given in standard Journal, Volume, (first ) Page, Year format. For private communications or structures from theses, details of the workplace of the contributor are given in this section.

DOI

Published paper/CCDC Author/Journal tab and CSD Internals Most papers now have a DOI reference which is hyperlinked to the publisher's website for the article.

Cell parameters

CIF/Published paper Crystal tab Any discrepancies between the unit cell dimensions given in the paper and deposited CIF are noted under the Experimental tab, CCDC notes. Occasionally, additional cell parameters will be given in the crystal tab, additional information, notes. This occurs e.g. in cases where cell dimensions are reported at a range of temperatures without a full data collection.

Space Group

CIF/Published paper Crystal tab Any discrepancies between the space group given in the paper and in the deposited CIF are noted in the Experimental tab, CCDC notes.

Z value

CIF/Published paper/CCDC Crystal tab The Z value is usually taken from the deposited CIF. In some cases (for example if a different polymeric unit is chosen) a multiple may be used.

Class

CCDC Chemical tab, CCDC class The CCDC currently include 8 sub-categories of materials to enable more efficient searching of some structure types. These are: Carbohydrates and their metal complexes (including Inositols); Nucleosides, nucleotides and their metal complexes; Amino-acids, peptides and their metal complexes ; Porphyrins, corrins and their metal complexes; Steroids; Terpenes; Alkaloids and Organic polymers. An entry can have 2 class assignments.

Radiation

CIF/Published paper Experimental tab, extra information Experiments using synchrotron and neutron radiation are noted. Radiation wavelengths are not given.

Powder

CIF/Published paper Experimental tab, extra information Data is generally assumed to have been determined from single-crystal studies. Structures determined from powder data are specifically noted.

Pressure

CIF/Published paper Experimental tab, extra information Experiments can be assumed to have taken place under atmospheric conditions unless a pressure is quoted.

R-factor

CIF/Published paper Experimental tab For single crystal studies the R factor shown is automatically chosen from the CIF by picking the lowest value from _refine_ls_wR_factor_all, _refine_ls_wR_factor_obs, _refine_ls_wR_factor_gt and _refine_ls_wR_factor_ref.

Density

CIF/CCDC Experimental tab Two density values are normally quoted; the value _exptl_crystal_density_diffrn taken from the CIF and a value calculated by CCDC software. Discrepancies may arise in disordered structures where not all atoms have been modelled. If the value from the CIF is inaccurate (e.g. if SQUEEZE/PLATON has been used) the value is not included in the entry.

Temperature

CIF/Published paper Experimental tab and CSD Internals Taken from the _diffrn_ambient_temperature line of the CIF. If this is not present the value from _cell_measurement_temperature is chosen. If values given in the CIF and paper differ by more than 10 K the other value is noted under the Experimental tab, CCDC notes. If no temperature is given, room temperature is assumed.

Melting Point

CIF/Published paper Chemical tab and CSD Internals The melting point is NOT taken from DSC/TGA analysis.

Colour

CIF/Published paper Chemical tab and CSD Internals American spelling is used for colorless. Certain descriptors are removed, such as clear and transparent.

Habit

CIF/Published paper Crystal tab and CSD Internals Author's terminology is used. Certain descriptors are removed including chip and fragment.

Crystallisation solvent

CIF/Published paper Crystal tab, additional information and CSD Internals The solvent(s) used specifically to prepare the crystal for X-ray analysis are given.

Polymorph

Published paper Crystal tab and CSD Internals Polymorphs are generally recorded using the author's terminology. Pseudopolymorphs (i.e structures with different solvent or levels of hydration) are not included. Polymorphs are categorised in the same refcode family.

Sensitivity

Published paper Chemical tab, extra information and CSD Internals Recorded if the paper makes explicit reference to sensitivity of the compound studied. General phrases such as 'All experiments were performed under an atmosphere of nitrogen' are not included.

Isostructural materials

Published paper Crystal tab, notes and CSD Internals A description of materials described by the authors as isostructural, isomorphous or isotypic analogues. Details of isoelectronic, analogous or isomeric structures are not given.

Phase-transition

Published paper Crystal tab, notes and CSD Internals This includes brief details of the temperatures, pressure or other conditions of phase transitions. Also included are details of spin-crossover transitions.

Twinning

CIF/Published paper Experimental tab, extra information and CSD Internals Twinning derived from diffraction of the crystal (i.e not from visual inspection of the bulk solid) is noted. In some cases additional information on the type of twinning (inversion, racemic etc) is given. Twin laws and batch scale factor (BASF) values are not included.

Disorder

CIF/Published paper/CCDC - In general, the major occupancy sites of disordered atoms are shown, with the minor occupancy ones being suppressed. The coordinates of the minor occupancy atoms are retained, but connectivity is only shown for the major site. In the case of mixed occupancy sites (eg mixed metal or mixed halogen) the major component is chosen and the compound named accordingly. The disorder comment will include the sum formula in these cases. Compounds with mixed occupancy sites are given a separate refcode to the full occupancy equivalent. Solvent molecules with symmetry related disorder leading to short bonds are usually suppressed. However, in the case of symmetry related disorder of the main molecules or clathrated solvents the connectivity is retained.

Disorder comments

CCDC Experimental tab, disorder A brief comment on the treatment of disorder in the structure is given. This includes cases when unmodelled disorder is mentioned. The occupancies of major and minor sites are normally given and cases of symmetry related disorder are explicitly noted.

SQUEEZE

CIF/Published paper Experimental tab, disorder Molecules modelled using the SQUEEZE/PLATON program are (if possible) included in the name, 2D representation and formula of the compound. In some cases insufficient data is available, and the term 'unknown solvate' is added to the name of the compound with additional information given under Experimental tab, disorder. If included in the deposited CIF, or paper, the comment may include the number of electrons removed and the void size.

Natural source

Published paper Chemical tab, source and CSD Internals The original source of a natural product.

Absolute configuration

CIF/Published paper Chemical tab, extra information Absolute configuration is only given if determined from the X-ray data, i.e. NOT from the synthesis or non-crystallographic methods such as circular dichroism. Absolute configuration is included if specifically mentioned in the paper or if the CIF term _chemical_absolute_configuration is given as either ad or rmad. It is also required that the Flack parameter given has a reasonable value and is quoted with an e.s.d.

Relationships between entries

Published paper/CCDC Chemical tab, extra information and CSD Internals Descriptions of the stereochemistry of the material are included in the name whenever possible. Stereoisomers (and racemates) are given separate refcodes, however the entries are cross-referenced for ease of comparison.

Structural Descriptors

Published paper Chemical tab, extra information and CSD Internals Information on the conformation or any other structural descriptors of the molecule may be given in this section, especially for macromolecules such as calixarenes.

Bioactivity

Published paper Chemical tab, extra information and CSD Internals A brief indication of any possible biological interest is given, including cases where compounds have been tested and shown to be inactive or where there is biological activity of near relatives. The intention is that users will consult the published paper for full details. English as opposed to American spelling is used.

Peptide Sequence

CCDC Chemical tab, synonym Molecules containing more than one alpha-amino acid in an independent residue (including peptides, pseudo-peptides and retro-peptides) are given a peptide sequence code. This details the linkages of the individual amino acid groups and enables additional search functionality. This is not given in cases when the amino acid is complexed to a main group element or a transition metal atom.

Other experimental properties

Published paper Chemical tab, extra information and CSD internals Certain other properties of the material, reported in the paper, are noted. The most common of these are luminescence (photoluminescence and fluorescence are also used) and magnetic properties.

Remarks

CCDC Experimental tab, CCDC notes and CSD Internals Discrepancies between values quoted in the paper and CIF, or problems noted with the structure during the abstracting process are recorded as additional remarks in this section.



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