Volume 1 Chapter 2 Coverage

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2.3 Fundamental Concepts - Entry, Reference Code, Residue, Asymmetric Unit and Crystal Chemical Unit

2.3.1 Entry

The information reported in a particular publication for the structure of compound X constitutes a database entry.

If, for example, the literature contains three publications on the crystal structure of compound X, then the database will contain three discrete entries. There is no amalgamation of information to create a single entry for compound X.

2.3.2 Reference Code

To each database entry we assign a "label", known as the reference code, or simply refcode.

The refcode consists of six alphabetic characters which "define" the chemical compound and a possible further two numeric digits which "trace the publication history".

The six alphabetic characters have a role which is similar to the Chemical Abstracts Service Registry Number.

Ex. Consider a series of publications on the structure of sodium 1-pyrrolidinyl-carbodithioate dihydrate.

NAPYCT
X-ray study at room temperature, by Oskarsson et al., published in 1979 in Eur. Cryst. Mtg.

NAPYCT01
X-ray study at 150K, by Oskarsson et al., published in 1979 in Eur.Cryst.Mtg.

NAPYCT02
X-ray study at 27K, by Oskarsson et al., published in 1979 in Eur.Cryst.Mtg.

NAPYCT03
neutron study at room temperature, by Ymen, published in 1982 in Acta Crystallogr., Sect.B.

NAPYCT10
X-ray study at room temperature, by Oskarsson et al., published in 1980 inActa Crystallogr., Sect.B.

NAPYCT11
X-ray study at room temperature, by Oskarsson et al., published in 1980 in Acta Crystallogr., Sect.B.

NAPYCT12
X-ray study at room temperature, by Oskarsson et al., published in 1980 in Acta Crystallogr., Sect.B.

The preliminary publications NAPYCT, NAPYCT01, NAPYCT02 and NAPYCT03 are independent studies, referred to as supplementary entries

The full publication NAPYCT10 supersedes NAPYCT.

Likewise NAPYCT11 supersedes NAPYCT01 and NAPYCT12 supersedes NAPYCT02.

We refer to the "family" of entries which are tied together by the common 6-letter code NAPYCT.

In the database entries are ordered alphanumerically by refcode and thus all members of a refcode family are clustered together.

It should be noted that conference abstracts are no longer input to the database; also, for earlier entries, when an entry PQRSTU was superseded by PQRSTU10 then the entry PQRSTU was deleted from the database.

This practice was discontinued in the mid- to late-1970's.

It should be noted that stereoisomers of a compound are assigned different 6-letter codes; likewise for deuterated analogues of the normal hydrogen species.

2.3.3 Residue

Most chemical information systems are concerned with one molecule per entry. A crystal structure, however, often contains more than one type of molecular or ionic species and hence we use the concept of residue to express the formula of a substance.

A residue is a discrete molecule or ionic species and in the database each residue is formulated separately.

Ex.1

One residue of formula C10 H18

Ex.2

There are two residues, the quinone molecule and the water molecule having formulae C6 H2 Br2 O4 and 2(H2 O1)

Ex.3

There are three residues:

This formulation, residue-by-residue, greatly enhances the specificity of searching based on formulae.

2.3.4 Asymmetric Unit and Crystal Chemical Unit

The determination of a crystal structure involves the location of the atomic coordinates of the asymmetric unit.

The asymmetric unit is the smallest structural unit which, when operated upon by the symmetry elements of the space group, yields the total crystal structure.

In the database the atomic coordinates of the asymmetric unit are stored in ATOM records.

Additionally, the coordinates of any atoms which are symmetry-related and bonded to atoms of the asymmetric unit are stored in SATOM records.

The total set of ATOM and SATOM records constitutes the crystal chemical unit.

Ex.1
Consider the structure of potassium methyltrifluoroborate shown in (a) below.

In this structure the asymmetric unit consists of one anion and one cation.

Thus the asymmetric unit consists of 9 atoms: C1, B1, F1, F2, F3, H1, H2, H3, K1.

In the database the coordinates of these atoms are stored in ATOM records.

No other atoms are symmetry-related and bonded to any of the atoms of the asymmetric unit.

In this case the crystal chemical unit is the asymmetric unit, composed of the 9 ATOMs.

Ex.2
Consider the structure of fumaronitrile shown in (b) below.

In this structure the centre of the double bond is located at a crystallographic centre of symmetry with the result that the asymmetric unit consists of one half-molecule: C1, H1, C10, N1.

In the database the coordinates of these atoms are stored in ATOM records.

The atoms C1B, H1B, C10B, N1B are symmetry-related and bonded to the atoms of the asymmetric unit.

In the database the coordinates of these atoms are stored in SATOM records.

In this case the crystal chemical unit consists of the 4 ATOMs and the 4 SATOMs.

Ex.3
Consider the structure of monochloroacetic acid shown in (c) below.

In this structure the asymmetric unit consists of two molecules.

Thus the asymmetric unit consists of 16 atoms: 4 carbons, 2 chlorines, 6 hydrogens, 4 oxygens.

In the database the coordinates of these atoms are stored in ATOM records.

No other atoms are symmetry-related and bonded to any of the atoms of the asymmetric unit.

In this case the crystal chemical unit is the asymmetric unit, composed of the 16 ATOMs.

Ex.4
Consider the structure of the pyrazine : tetrabromoethylene complexs shown in (d) below.

In this structure the asymmetric unit consists of two half-molecules.

The centre of the pyrazine ring lies at a crystallographic centre of symmetry, as does the centre of the ethylenic double bond.

The hydrogen atoms of the pyrazine were not reported by the authors.

Thus the asymmetric unit consists of 6 atoms: N1, C2, C3 of the pyrazine

C1, Br1, Br2 of the tetrabromoethylene.

In the database the coordinates of these atoms are stored in ATOM records.

The atoms N1B, C2B, C3B are symmetry-related and bonded to the atoms N1, C2, C3.

Likewise the atoms C1B, Br1B, Br2B are symmetry-related and bonded to the atoms C1, Br1, Br2.

In the database the coordinates of these atoms are stored in SATOM records.

In this case the crystal chemical unit consists of the 6 ATOMs and the 6 SATOMs.

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Volume 1 Chapter 2 Types of Searches.