Atom

Atom["sym"]

represents an atom with atomic symbol "sym".

Atom["sym",namevalue,]

represents an atom with atomic symbol "sym" and specified properties.

Details

  • For atoms within a Molecule expression, the following properties can be specified:
  • "FormalCharge"0the formal charge of the atom
    "MassNumber"Automaticthe mass number of the nucleus
    "UnpairedElectronCount"0unpaired (radical) electrons
  • When the "MassNumber" property is Automatic, the molecular weight is computed using the average atomic masses, as found in ElementData. When the number is specified, the mass is taken from IsotopeData.
  • Atom can act as a pattern for functions such as AtomList and MoleculeContainsQ, matching a single atom in a molecule. In this case additional, computed properties may be specified. Typical pattern properties and their values include:
  • "AromaticAtomQ"True|False
    "AtomChirality""R"|"S"
    "AtomicMass"Real
    "AtomicNumber"Integer
    "CIPRank"Integer
    "CoordinationNumber"Integer
    "FormalCharge"Integer
    "GasteigerPartialCharge"Real
    "GeometricStericEffectIndex"Real
    "HeavyAtomCoordinationNumber"Integer
    "HydrogenCount"Integer
    "ImplicitHydrogenCount"Integer
    "MassNumber"Integer
    "MMFFPartialCharge"Real
    "OrbitalHybridization""S"|"SP"
    "OuterShellElectronCount"Integer
    "PiElectronCount"Integer
    "RingAtomQ"True|False
    "TopologicalStericEffectIndex"Real
    "UnpairedElectronCount"Integer
    "UnsaturatedAtomQ"True|False
    "Valence"Integer
  • Numeric properties may also be specified using GreaterThan, LessThan, GreaterEqualThan, LessEqualThan or Between.

Examples

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Basic Examples  (2)

Build a molecule with atoms and bonds:

Retrieve the list of atoms:

Build a molecule using atoms with defined mass numbers:

Scope  (2)

Highlight all atoms with one electron:

Highlight atoms with large partial charges:

Introduced in 2019
 (12.0)