Function Repository Resource:

CoordinationMoleculeStereochemistry

Source Notebook

Determine the configuration of stereoisomers

Contributed by: William Choi-Kim

ResourceFunction["CoordinationMoleculeStereochemistry"][mol]

determines whether the stereoisomer mol is "cis", "trans", "fac" or "mer".

Details and Options

The input mol must be a coordination complex as a Molecule.

Coordination complexes (coordination molecules) are molecules with ligands bonded to a central atom.

ResourceFunction["CoordinationMoleculeStereochemistry"] accepts the option "LabelPseudoSymmetric" which can be True or False. When set to True, ResourceFunction["CoordinationMoleculeStereochemistry"] identifies the stereoisomer type of mol even if mol is pseudo-symmetric.

Geometric square-planar molecules can be "cis" or "trans".

Geometric octahedral molecules can be "cis", "trans", "fac", or "mer".

In a molecule, the functional groups (atoms coming out from the central metal ion) define the stereoisomer type of a molecule:

cis

functional groups are on the same side of a plane

trans

functional groups are on opposite sides of a plane

fac

functional groups occupy a face of an octahedron

mer

functional groups and metal ion are on one plane

"cis" and "trans" molecules both involve two central-adjacent functional groups, while "fac" and "mer" involve three.

The internal geometry of optical isomers can be described as left- or right- handed —"lambda" or "delta" — defining the chirality of the molecule.

Examples

Basic Examples (12)

Identify a"cis" square-planar molecule, with same-element atoms next to each other::

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(* Evaluate this cell to get the example input *) CloudGet["https://www.wolframcloud.com/obj/c38aff0e-381f-4703-9623-f90dd81242f2"]

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Identifying "trans" square-planar molecules, with same-element atoms across from each other:

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(* Evaluate this cell to get the example input *) CloudGet["https://www.wolframcloud.com/obj/8b7226dd-db3d-4984-9998-6d04cd148274"]

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Identifying "cis" octahedral molecules, with a same-element pair in a 90 degree angle:

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(* Evaluate this cell to get the example input *) CloudGet["https://www.wolframcloud.com/obj/c438091e-eea6-41c9-8a16-56642a8351cb"]

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Identifying "trans" octahedral molecules, with a same-element pair opposite each other:

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(* Evaluate this cell to get the example input *) CloudGet["https://www.wolframcloud.com/obj/abae2437-898a-40a6-a44e-27f05ef1ed67"]

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Identifying "fac" octahedral molecules, with three same-element atoms forming a face:

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(* Evaluate this cell to get the example input *) CloudGet["https://www.wolframcloud.com/obj/8a817c13-52eb-4c2e-95a7-db0b2d8d760b"]

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Identifying "mer" octahedral molecules, with three same-element atoms and the central atom forming a plane:

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(* Evaluate this cell to get the example input *) CloudGet["https://www.wolframcloud.com/obj/a87c0f22-56bb-4b36-b4bc-b71f54d255d2"]

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Passing molecules that can't be labeled — that is, molecules that aren't "cis", "trans", "fac", or "mer" — gives you Missing["NotApplicable"]:

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missingSqPlanar = Molecule[{"F", "Xe", "F", "F", "F"}, {
Bond[{1, 2}, "Single"],
Bond[{2, 3}, "Single"],
Bond[{2, 4}, "Single"],
Bond[{2, 5}, "Single"]}, {AtomCoordinates -> QuantityArray[
StructuredArray`StructuredData[{5, 3}, {{{-1.9203440781716368`, -0.00020447666174505663`, 0.2491154580653996}, {0.000020308462388228532`, 0.00003493564780035485, 0.24881110716492194`}, {
0.0003201650326992592, -1.3578246300191237`, 1.606708105251621}, {1.9200783914456754`, 0.0002795748233125339, 0.24920407308871928`}, {-0.0002795403776389982, 1.3578594957792525`, -1.1090508844212998`}}, "Angstroms", {{
1}, {2}}}]]}];
MoleculePlot3D[missingSqPlanar]

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The same is true for octahedral molecules:

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(* Evaluate this cell to get the example input *) CloudGet["https://www.wolframcloud.com/obj/50224f22-bd3f-4254-bc19-9b3b465252f3"]

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CoordinationMoleculeStereochemistry can handle molecules with polyatomic ligands — central adjacent groups of atoms, rather than singular atoms — as well:

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(* Evaluate this cell to get the example input *) CloudGet["https://www.wolframcloud.com/obj/e9d2b5c8-1d1e-455e-9e5a-086d488e13b5"]

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Delta molecules — right-handed molecules, so-called because of the direction in which they turn plane-polarized light — are classified as such:

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(* Evaluate this cell to get the example input *) CloudGet["https://www.wolframcloud.com/obj/ba32fc26-f4c6-476d-ad69-0dc91d69d8d4"]

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Lambda molecules — left-handed, named similarly for how they turn light — are classified as such:

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(* Evaluate this cell to get the example input *) CloudGet["https://www.wolframcloud.com/obj/564ad1e8-dcce-4956-afeb-3a0bb9c407dd"]

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Molecules that are neither lambda nor delta isotopes are labeled Missing["NotApplicable"]:

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(* Evaluate this cell to get the example input *) CloudGet["https://www.wolframcloud.com/obj/c32e0b5d-b550-47f9-9c43-8602bd9f1a14"]

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Options (4)

LabelPseudoSymmetric (4)

Pseudo-symmetric molecules — molecules whose central-adjacent atoms taken alone can be identified, but not the molecule as a whole — are usually labeled Missing["NotApplicable"]:

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