IncludeHydrogens

IncludeHydrogens

is an option for Molecule and related functions that specifies whether hydrogen atoms should be explicitly included in the results.

Details

  • The following settings can be given:
  • Trueinclude or add in all necessary hydrogens explicitly
    Falsedo not include or add in any hydrogens explicitly
    Automaticinclude only hydrogens that are explicitly listed
  • With the default setting of Automatic, hydrogens not listed in the molecule expression are treated as implicit.
  • Physical properties such as molecular mass and formula will account for implicit hydrogens.

Examples

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Basic Examples  (2)

Create a molecule from an entity:

Create the same molecule with implicit hydrogen atoms:

Create a molecule only listing heavy atoms:

The hydrogens are not present in the expression, but influence properties such as mass and formula:

Three implicit hydrogens are bonded to the carbon atom, and one to the oxygen. These do not count toward structural operations such as AtomCount and AtomList:

Properties such as molecular mass and formula that reference the physical molecule will account for the hydrogens:

Possible Issues  (1)

For molecules with aromatic heterocycles, removing hydrogens introduces ambiguity. For example, in tetrazole, where all bonds are marked with type "Aromatic", it makes it ambiguous which nitrogen the hydrogen would be attached to:

When this molecule is created with implicit hydrogens, it is necessary to mark the hydrogen count of the relevant nitrogen:

Use the option IncludeAromaticBonds->False to remove the ambiguity:

Introduced in 2019
 (12.0)