As of Version 14.3, use the "InvertAroundAtom" method in MoleculeModify.

Function Repository Resource:

InvertAtom

Source Notebook

Invert the geometry of selected atoms in a molecule

Contributed by: Robert B. Nachbar

ResourceFunction["InvertAtom"][mol, atom]

inverts the geometry of atom in molecule mol.

ResourceFunction["InvertAtom"][mol,{atom₁,atom₂,…}]

inverts the geometry of several atom_i in molecule mol.

Details

Tetrahedral atoms are inverted by exchanging the two smallest movable ligands. Trigonal pyramidal atoms are inverted by moving the smallest movable ligand. Movable atoms are either not in rings or are in the same ring.

The coordinates of the moving atoms are transformed with a 2-fold rotation, thus preserving all other stereocenters in the molecule.

For molecules with only a single stereocenter, reflecting all the coordinates through a plane would accomplish the same effect as ResourceFunction["InvertAtom"]. However, all the atoms move. InvertAtom is parsimoneous with respect to the total change of atom coordinates and therefore some part of the molecule to remains fixed in space.

For molecules with more than one stereocenter, ResourceFunction["InvertAtom"] allows one to generate a diastereomer, an epimer more specifically. In this case, the chirality at only one atom is changed, and the rest remain geometrically unaffected.

Examples

Basic Examples (2)

Show 2-butanol:

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Invert it:

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Check the chirality:

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Invert one of the carbinol atoms of cis-cyclohexan-1,3-diol:

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Check the chirality:

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Scope (6)

Several atoms can be inverted at once. Show (-)-menthol:

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Invert atoms 2 (bearing the hydroxyl group) and 9 (bearing the methyl group) to make (+)-neoisomenthol:

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Check the chirality:

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Amines can be inverted:

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Check the out-of-plane angle:

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Atoms in rings can be inverted:

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Check the chirality:

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Spiro centers can be inverted:

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Check the chirality:

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Ring fusion atoms with sufficiently large rings can be inverted:

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Check the chirality:

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Bridgehead atoms with sufficiently large rings can be inverted:

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Applications (2)

Invert the anomeric carbon of α-D-glucose:

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Check that the stereochemistry at only atom 2 has changed:

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Possible Issues (4)

Ring fusion atoms with small rings are not inverted:

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Bridgehead atoms with small rings are not inverted:

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Bridgehead atoms in tricyclic and larger ring systems are not inverted:

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Pentacoordinate atoms cannot be inverted:

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Publisher

Requirements

Wolfram Language 13.0 (December 2021) or above

Version History

1.1.0 – 10 March 2025
1.0.1 – 08 March 2024
1.0.0 – 06 March 2024

Related Resources

License Information

This work is licensed under a Creative Commons Attribution 4.0 International License