15th Group

Nitrogen (N)

  • Default: NH3

  • Molecules:

    • Neutral atoms

      • Implicit hydrogens are added to have 3 bonds (if nitrogen has at least 1 bond).
        More than 3 bonds are forbidden.
        If nitrogen has 4 ligands, charge is not set, hence not accepted
        Pentavalent N is accepted in traditional form by default, but keep in mind that these forms are not correct. Use the "ylide" from of the N atom which satisfies the correct valence electron count:

        traditional form

        "ylide" form

        images/download/attachments/1806267/trad1.png

        images/download/attachments/1806267/octet1.png

        images/download/attachments/1806267/trad2.png

        images/download/attachments/1806267/octet2.png

        images/download/attachments/1806267/trad3.png

        images/download/attachments/1806267/octet3.png

        images/download/attachments/1806267/vc1t.png

        images/download/attachments/1806267/vc1y.png

      • It's possible to accept only the "ylide" form using the MoleculeGraph.setValenceCheckOptions() function.

    • Charged atoms in a molecule:

      • Positive charge:

        • 1+: 4 bonds needed (incluing implicit hydrogens)

        • 2+: 3 bonds needed (incluing implicit hydrogens)

        • 3+: 2 bonds needed (incluing implicit hydrogens)

        • 4+: 1 bonds needed (incluing implicit hydrogens)

        • 5+: 0 bonds needed (incluing implicit hydrogens)

        • 6+ or more: not allowed

      • Negative charge: Every added negative charge decreases by one the number of possible bonds. Maximum charge accepted is -3.

    • Radical: Every added radical on these atoms decreases by one the number of bonds. Maximum three added radical is allowed.

    • Aromatic compounds: Nitrogen may form aromatic bonds as well.

Phosphorus (P), Arsenic (As), Antimony (Sb), Bismuth (Bi)

  • Default: PH3, AsH3, SbH3, Bi

  • Molecules:

    • Neutral atoms:

      • 1 bond: 2 implicit Hydrogens are added.

      • 2 bond: 1 implicit Hydrogen is added.

      • 3 bond: 0 implicit Hydrogen is added.

      • 4 bond: 1 implicit Hydrogen is added.

      • 5 bond: 0 implicit Hydrogen is added.

      • More than 5 bonds are forbidden

    • Charged atoms in a molecule:

      • Positive charge:

        • 1+: 4 bonds are necessary (including implicit Hydrogens).

        • 2+: 3 bond is necessary (including implicit Hydrogens).

        • 3+: 2 bond is allowed.

        • 4+: 1 bond is necessary (including implicit Hydrogens).

        • 5+: 0 bond is allowed.

        • 6+ or more: not allowed

      • Negative charge: Every added negative charge decreases by one the number of possible bonds. Maximum charge accepted is -3.

    • Radical: Every added radical on these atoms decreases by one the number of bonds. Maximum three added radicals are allowed.

    • Aromatic compounds: Phosphorus may form aromatic bonds as well.