Isomers in JChem for Excel

Most compound collections (corporate databases, screening libraries, compound-provider catalogs) are comprised of 2D structures with incomplete indications of stereochemistry or tautomeric state. This inevitably leads to ambiguous stereochemistry or tautomerization when these structures are converted to 3D. The enumeration of tautomers and stereoisomers of molecules is essential for virtual screening applications such as docking, 3D-searching, or 3D-QSAR facilitating drug discovery and development processes.

Conformer

The calculation generates the stable 3D structures, conformers of a given molecule. The stability of the conformers is estimated through comparing their energy content, calculated in the framework of a molecular mechanics force-field. The 3D structure (conformation) strongly affects the properties and the reactions of molecules.

For more information regarding this plugin, see Conformer Plugin.

JCConformerCount

Returns the number of conformers.

JCHasValidConformer

Returns whether a valid conformer exists for the specified structure.

Stereoisomer

The Stereoisomer Plugin produces all possible stereoisomers of a given compound. The plugin handles both tetrahedral and double bond stereogenic centers. Identical stereo-isomers of a molecule are filtered out; energetically impossible conformations can also be filtered.

For more information regarding this plugin, see Stereoisomer Generator Plugin and Stereo Analysis - calculating stereo descriptors.

JCStereoIsomerCount

Returns the number of generated stereoisomers of the input molecule.

JCDoubleBondStereoisomerCount

Returns the number of generated double bond stereoisomers of the input molecule.

JCTetrahedralStereoisomerCount

Returns the number of generated tetrahedral stereoisomers of the input molecule.

Resonance

Lone pair, radical electron, or formal charge of certain atoms in a molecule can migrate within a delocalized system. Some resonance structures are stable, these structures are called mesomer structures. Our resonance structure generator creates all resonance forms of a molecule.

For more information regarding this plugin, see Resonance Plugin.

JCResonantCount

Returns the number of resonant structures.