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MoleculeEquivalentQ[mol1,mol2]

gives True if mol1 and mol2 represent equivalent molecules and gives False otherwise.

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Basic Examples  
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MoleculeEquivalentQ

As of Version 13.0, MoleculeEquivalentQ has been superseded by MoleculeMatchQ.

MoleculeEquivalentQ[mol1,mol2]

gives True if mol1 and mol2 represent equivalent molecules and gives False otherwise.

Details

  • Two molecules are by default considered equivalent if there is a reordering of atom and bond lists that makes them the same, including any defined stereochemistry.
  • Atoms are considered equal if their atomic number, charge and mass number are the same. Bonds are considered equal if they have the same bond order.
  • For the purpose of equivalence testing, implicit and explicit hydrogen atoms are treated the same.
  • MoleculeEquivalentQ[mol1,mol2,…] gives True if all of the moli are equivalent.

Examples

Basic Examples  (4)

Methane and the ammonium ion have identical connectivity but different atoms, so they are not equivalent:

Wolfram Language code: mol1 = Molecule["methane"]
Wolfram Language code: mol2 = Molecule["ammonium"]

Even though the underlying graphs are isomorphic, the molecules are not equivalent:

Wolfram Language code: IsomorphicGraphQ[MoleculeGraph[mol1], MoleculeGraph[mol2]]
Wolfram Language code: MoleculeEquivalentQ[mol1, mol2]

When molecules are the same, apart from the ordering of their atoms and bonds, MoleculeEquivalentQ will return True:

Wolfram Language code: mol1 = Molecule["C[C@H](Cc1c[nH]c2c1ccc(c2)O)N"]
Wolfram Language code: mol2 = MoleculeModify[mol1, {"RenumberAtoms", Reverse[Range[AtomCount[mol1]]]}]
Wolfram Language code: MoleculeEquivalentQ[mol1, mol2]

If the stereochemistry is different, then the molecules are not considered equivalent:

Wolfram Language code: mol3 = MoleculeModify[mol1, "RemoveStereochemistry"]
Wolfram Language code: MoleculeEquivalentQ[mol1, mol3]

Test molecules with isotopic substitutions:

Wolfram Language code: m1 = Molecule[["water"]]
Wolfram Language code: m2 = Molecule[["heavy water"]]
Wolfram Language code: MoleculeEquivalentQ[m1, m2]

Implicit and explicit hydrogen atoms are treated the same by MoleculeEquivalentQ:

Wolfram Language code: m1 = Molecule["benzene", IncludeHydrogens -> False]
Wolfram Language code: m2 = MoleculeModify[m1, "MakeHydrogensExplicit"]
Wolfram Language code: MoleculeEquivalentQ[m1, m2]
Wolfram Research (2019), MoleculeEquivalentQ, Wolfram Language function, https://reference.wolfram.com/language/ref/MoleculeEquivalentQ.html.

Text

Wolfram Research (2019), MoleculeEquivalentQ, Wolfram Language function, https://reference.wolfram.com/language/ref/MoleculeEquivalentQ.html.

CMS

Wolfram Language. 2019. "MoleculeEquivalentQ." Wolfram Language & System Documentation Center. Wolfram Research. https://reference.wolfram.com/language/ref/MoleculeEquivalentQ.html.

APA

Wolfram Language. (2019). MoleculeEquivalentQ. Wolfram Language & System Documentation Center. Retrieved from https://reference.wolfram.com/language/ref/MoleculeEquivalentQ.html

BibTeX

@misc{reference.wolfram_2026_moleculeequivalentq, author="Wolfram Research", title="{MoleculeEquivalentQ}", year="2019", howpublished="\url{https://reference.wolfram.com/language/ref/MoleculeEquivalentQ.html}", note=[Accessed: 16-June-2026]}

BibLaTeX

@online{reference.wolfram_2026_moleculeequivalentq, organization={Wolfram Research}, title={MoleculeEquivalentQ}, year={2019}, url={https://reference.wolfram.com/language/ref/MoleculeEquivalentQ.html}, note=[Accessed: 16-June-2026]}