Guidelines for the Searching of Compounds in the Gmelin Database with CrossFire - Registration of Compounds

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In order to get good retrieval results on searching for compounds in the GMELIN database with CrossFire, the user should have some knowledge of how these compounds are stored.

Substance Hierarchy in the GMELIN file

Tree diagram of substance hierarchy

Compound Formulas with more than one component
Compound Formulas with more than one fragment
General Information on structures
Stereochemistry
Identical molecular formula - New compound?

Compound Formulas with more than one Component

Example: Pd(b),Ag(0.25) (W%), this means a palladium based alloy containing 0.25 weight % silver.

Compounds with more than one component can be given in the field LSF (linearized structure formula) in the following style:

1) ABC#XYZ the single components ABC and XYZ are

separated by a hash sign (#)

2) (A,B)Z the single component parts are separated by a comma, giving the components AZ and BZ

3) A(x)B(1-x)C x:0.9-0.95; gives the components A0.95B0.05C and A0.9B0.1C

Formulas of type 2 and 3 often refer to solid solutions, minerals or diadochous compounds. Type 1 often refers to homogeneous or heterogeneous multicomponent compounds.






Compound Formulas with more than one fragment

Compounds with more than one fragment are separated in the linearized structure formula field by an asterisk.

Example: 2Na(1+)*SO4(2-)=Na2SO4

Normally, the formula is repeated in the conventional manner after the '=' symbol as shown in the example above.

Rules whether a compound is fragmented or not are as follows:

Solid state structures and ion lattices:

a) Substances, which contain in the crystal aggregate, the gas phase, the liquid phase, or in solution

discrete polyatomic ions

are divided into formal fragments if there is at least one structurable fragment, e.g. 2Na(1+)*SO4(1-2-)=Na2SO4.

b) ion lattices, which consist exclusively of one-atomic ions, or solid state structures without discrete ions or molecules, have no structure in the database; the formula is given without fragmentation, e.g. CaTiO3.

Organometallics and Coordination Compounds:

Organometallic compounds, and coordination compounds with unknown manner of ligand coordination, are divided into fragments by separating all ligands from the metal center; e.g., if there is an unknown coordination of the dianion of oxalic acid to Fe(2+) in [Fe(OOCCOO)2](2-) (mono- or bidentate), the formula is given as Fe(2+)*2OOCCOO(2-).

Note: Clusters with unknown ligand coordination are not divided further; hydrogen atoms are not separated from the cluster units; the cluster cores get no structure; the structures of the ligands are given e.g. if the coordination of CO in the cluster H2Os3(CO)10 is unknown, the formula is given as H2Os3*10CO; the cluster core gets no structure.


General information on structures

Fragments may or may not have a structure. Especially in coordination and organometallic chemistry, compounds have a structure in nearly every case.

Single bonds, double bonds and triple bonds are available as bond types in the database, but note, the bond type is no criterion for registration. If one is not sure about the bond order, the bond type 'any bond' should be preferred in the search query. There are no tautomeric or aromatic bonds. In the case of keto/enol tautomerism, the ketonic form is always stored. Different tautomers are stored explicitly. All pi-interactions within organometallic pi-complexes are drawn as single bonds.

Structures of fragments are identical if the connectivity of the chosen atoms and the overall charge are the same. Only additional given stereodescriptors can differentiate them further.

Main group organometallic compounds

In the gray area between covalent and ionic bonds, usually both formulations occur in the original literature for main group organometallic compounds. From the point of view of input conventions the following rules are generally favoured by the GMELIN file, but one may find both alternatives, and it is recommended that you search for both structures to ensure completeness:

- Lithiumorganic compounds are stored with a covalent Li-C single bond

- Sodium- and potassiumorganic compounds are stored in ionic form (more than one fragment)

- Grignard compounds are stored in the covalent form

- Organometallic compounds with metals of the main groups III-VI are stored in the covalent form




Transition metal organometallic compounds

Transition metal organometallic compounds are input with the connectivity of atoms given in the original literature. If the connectivity is unknown, the compounds are separated formally into the central metal atoms and the surrounding ligands.

Stereochemistry

Stereochemistry is a further identification criterion of the structures in the GMELIN file. Two principal different stereochemical aspects can be searched for:

Stereochemical information on bonds and on centers

Specified double bond information (cis or trans) can be searched for if the bond attribute "Double Steric" is chosen in the structure editor, and the structure is drawn as wanted.

All stereochemical assigned centers have a three-dimensionally drawn surrounding of connected substituent or ligand atoms. Fragments with stereochemical information are assigned either an absolute or a racemic configuration.

In the case of trigonal pyramidal, tetrahedral, or octahedral centers, a stereodescriptor is set if one, or more than one, possible configuration of a stereocenter can be assigned. This also applies to all pi-descriptors and all descriptors linking two polyhedra by a chain of bonds. In all other cases the mentioning of a polyhedral center within a compound in the original literature is sufficient for the designation of a polyhedral descriptor.

The polyhedron descriptors in the GMELIN file are as follows:

a) Simple Polyhedra

Descriptor Polyhedron
P-3 trigonal pyramid
T-4 tetrahedron
SP-4 square planar
SP-5 square pyramid
TB-5 trigonal bipyramid
OC-6 octahedron
TP-6 trigonal prism
PB-7 pentagonal bipyramid
CU-8 cube
SA-8 square antiprism
DD-8 dodecahedron
HB-8 hexagonal bipyramid
TPS-9 tricapped trigonal prism
HB-9 heptagonal bipyramid


b) Two polyhedra, linked by a chain of bonds

Descriptor Polyhedron
22E two triangles (eclipsed)
22S 22S two triangles (staggered)
23E triangle plus tetrahedron (eclipsed)
23S triangle plus tetrahedron (staggered)
33E two tetrahedra (eclipsed)
33S two tetrahedra (staggered)
24E triangle plus square pyramid (eclipsed)
24S triangle plus square pyramid (staggered)
25E triangle plus octahedron (eclipsed)
25S triangle plus octahedron (staggered)
44E two square pyramids (eclipsed)
44S two square pyramids (staggered)
45E square pyramid plus octahedron (eclipsed)
45S square pyramid plus octahedron (staggered)
55E two octahedra (eclipsed)
55S two octahedra (staggered)





Identical molecular formula - New compound?

Searching for a certain molecular formula may often give more than one hit.

The following criteria are responsible for a further registration of a compound with molecular formula identical to another:

- different charge

- isotope marked atoms in the formula

- the substance types

Isomorphous, diadochous compounds, solid solutions

Minerals

Isotope or isotope containing compounds

Polymer

- modifications of inorganic compounds

- different connectivity of atoms in the structure

- additional stereodescriptors