StereochemistryElements

StereochemistryElements

is an option for Molecule that specifies the local stereochemical arrangement of atoms in a molecule.

Details

  • The option value describes the local geometry around an atom or bond, and does not specify the absolute stereochemistry (e.g. stereocenters "R" or "S").
  • The value of StereochemistryElements is used for generating two-dimensional structure diagrams and for embedding the molecule in three dimensions.
  • The value of the StereochemistryElements option can be obtained from a molecule via MoleculeValue using the property name "StereochemistryElements".
  • Elements are entered as a list of associations, with a "StereoType" key.
  • Possible values for "StereoType" are:
  • "Tetrahedral"for atomic stereocenters
    "DoubleBond"for geometric isomerism around nonrotatable bonds
  • For "Tetrahedral" stereo elements, the following keys are supported:
  • "ChiralCenter"the atom index of chiral center
    "FiducialAtom"index of a reference atom bonded to the chiral center
    "Ligands"an index list of three remaining atoms bonded to the chiral center
    "Direction""Clockwise" or "Counterclockwise"
  • When the ligand atoms are viewed along the vector from the fiducial atom to the chiral center, their order is given by the specified direction.
  • The chiral center may have an implicit hydrogen, in which case the "Ligands" list will have only two atoms, and the hydrogen is taken to be at the end of the list.
  • For "DoubleBond" stereo elements, the following keys are supported:
  • "StereoBond"a list of two atom indices, which have a double bond between them
    "Ligands"a list of two atom indices
    "Value""Together" or "Opposite"
  • The two atoms in the ligands list must be bonded to the two atoms in the double bond.
  • When the value is "Together", the two ligands are on the same side of the double bond. "Opposite" specifies them to be on opposite sides.
  • MoleculeEquivalentQ will return False for molecules with different stereochemistry, unless the SameTest option is set to "Stereoisomers".

Examples

Basic Examples  (3)

Create a molecule with a chiral center:

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Next create its enantiomer:

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The chirality is reflected in the "SMILES" and "InChI" identifiers:

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Create a molecule with defined geometry around a double bond:

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Next create its geometric isomer:

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The geometry is reflected in the "SMILES" and "InChI" identifiers:

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Create a molecule specifying the absolute CIP chirality:

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Introduced in 2019
(12.0)