15th Group
Nitrogen (N)
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Default: NH3
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Molecules:
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Neutral atoms
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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
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It's possible to accept only the "ylide" form using the MoleculeGraph.setValenceCheckOptions() function.
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Charged atoms in a molecule:
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Positive charge:
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1+: 4 bonds needed (incluing implicit hydrogens)
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2+: 3 bonds needed (incluing implicit hydrogens)
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3+: 2 bonds needed (incluing implicit hydrogens)
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4+: 1 bonds needed (incluing implicit hydrogens)
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5+: 0 bonds needed (incluing implicit hydrogens)
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6+ or more: not allowed
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Negative charge: Every added negative charge decreases by one the number of possible bonds. Maximum charge accepted is -3.
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Radical: Every added radical on these atoms decreases by one the number of bonds. Maximum three added radical is allowed.
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Aromatic compounds: Nitrogen may form aromatic bonds as well.
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Phosphorus (P), Arsenic (As), Antimony (Sb), Bismuth (Bi)
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Default: PH3, AsH3, SbH3, Bi
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Molecules:
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Neutral atoms:
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1 bond: 2 implicit Hydrogens are added.
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2 bond: 1 implicit Hydrogen is added.
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3 bond: 0 implicit Hydrogen is added.
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4 bond: 1 implicit Hydrogen is added.
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5 bond: 0 implicit Hydrogen is added.
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More than 5 bonds are forbidden
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Charged atoms in a molecule:
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Positive charge:
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1+: 4 bonds are necessary (including implicit Hydrogens).
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2+: 3 bond is necessary (including implicit Hydrogens).
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3+: 2 bond is allowed.
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4+: 1 bond is necessary (including implicit Hydrogens).
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5+: 0 bond is allowed.
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6+ or more: not allowed
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Negative charge: Every added negative charge decreases by one the number of possible bonds. Maximum charge accepted is -3.
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Radical: Every added radical on these atoms decreases by one the number of bonds. Maximum three added radicals are allowed.
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Aromatic compounds: Phosphorus may form aromatic bonds as well.
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