Wolfram Cloud Document

Molecules

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The Wolfram|Alpha Chemistry Team

Molecules can be created in silico by passing a variety of information into the

Molecule

function.

Creation

Let’s consider propane which is the gas used in barbeque grills all over the world.

Build up a propane molecule atom by atom, bond by bond or use the corresponding chemical

Entity

propaneAtomBond=Molecule[{"C","H","H","H","C","H","H","C","H","H","H"},{Bond[{1,2},"Single"],Bond[{1,3},"Single"],Bond[{1,4},"Single"],Bond[{1,5},"Single"],Bond[{5,6},"Single"],Bond[{5,7},"Single"],Bond[{5,8},"Single"],Bond[{8,9},"Single"],Bond[{8,10},"Single"],Bond[{8,11},"Single"]}]

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Molecule

Formula:

Atoms: 11 Bonds: 10

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propaneEntity=Molecule

propane

CHEMICAL

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Molecule

Formula:

Atoms: 11 Bonds: 10



Create propane from its common or Systematic International Union of Pure and Applied Chemistry (IUPAC) name:

propaneCommonName=Molecule["propane"]

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Molecule

Formula:

Atoms: 11 Bonds: 10

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propaneIUPACName=Molecule["Tricarbane"]

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Molecule

Formula:

Atoms: 11 Bonds: 10



Create propane from identifiers such as SMILES (Simplified Molecular-Input Line-Entry System) or InChI (International Chemical Identifier):

propaneSMILES=Molecule["CCC"]

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Molecule

Formula:

Atoms:

Bonds:

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propaneInChI=Molecule["InChI=1S/C3H8/c1-3-2/h3H2,1-2H3"]

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Molecule

Formula:

Atoms:

Bonds:

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MoleculeMatchQ

combined with

AllTrue

can be used to verify that the different representations give the same molecule:

propaneList={propaneAtomBond,propaneEntity,propaneCommonName,propaneIUPACName,propaneSMILES,propaneInChI};AllTrue[propaneList,MoleculeMatchQ[propaneAtomBond,#]&]

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True