Valence Calculations

Introduction

The Valence Calculator has 3 functionality:

• calculate if there is valence error.
• set the appropriate amount of implicit hydrogen

The functionality of the Valence Calculator is focused mainly on the organic compounds, although the inorganic compounds not containing transition-metal atoms are also supported.

Molecules

1st Group

Hydrogen

• Default: H⁺
• Molecules:
  • Neutral atoms:1 bond is accepted
  • Charged atoms: Not allowed in molecules.
  • Radical: Not allowed in molecules.
• Ions: H⁺, H^-
• Radical:
  • H· is accepted
  • H without radical and charge or bond is not accepted.

Lithium (Li), Sodium (Na), Potassium (K), Rubidium (Rb), Caesium (Cs), Francium (Fr)

• Default: Li, Na, K, Rb, Cs, Fr respectively.
• Molecules:
  • Neutral atoms:1 bond is accepted.
  • Charged atoms: Not allowed in molecules.
  • Radical: Not allowed in molecules.
• Ions: Li⁺, Na⁺, K⁺, Rb⁺, Cs⁺, Fr⁺ are accepted.
• Radical: Me· is accepted

2nd Group

• Default: Be, Mg, Ca, Sr, Ba, Ra respectively.
• Molecules:
  • Neutral atoms: 2 bonds are accepted.
  • Charged atoms: Each added charge decreases by one the number of possible bonds.
  • Radical: Each added radical decreases by one the number of possible bonds
• Ions:
  • Be²⁺, Mg²⁺, Ca²⁺, Sr²⁺, Ba²⁺ Ra²⁺ are accepted
• Radicals: ·Me⁺ is accepted

13th Group

Boron

• Default: BH₃
• Molecules:
  • Neutral atoms:
    • Implicit Hydrogens are added to have 3 bonds.
    • 4 bonds are accepted with 1 negative charge on the boron atom.
    • 5 or more bonds are forbidden.
  • Charged atoms:
    • Positive charge: Every added charge decreases by one the number of possible bonds. Maximum charge accepted is +3.
    • Negative charge: BH₄^-, BH₃^2- BH₂^3- BH^4- and B^5- are accepted.
  • Radicals: Every added radical on these atoms decreases by one the number of necessary bonds.
  • Aromatic compounds: Boron may form aromatic bonds as well.

Aluminium (Al), Gallium (Ga), Indium (In), Thallium (Th)

• Default: Al, Ga, In, Th respectively.
• Molecules:
  • Neutral Atoms: 3 bonds around these atoms are accepted.
  • Charged atoms:
    • Positive charge: Every added charge decreases by one the number of possible bonds. Maximum charge accepted is +3.
    • Negative charge: 4- charge with 4 ligands is accepted.
  • Radicals: Every added radical on these atoms decreases by one the number of necessary bonds.
• Ions:
  • Al⁺, Ga⁺, In⁺, Rb⁺, Al³⁺, Ga³⁺, In³⁺, Rb³⁺ are accepted.
• Radical: ·Me²⁺ and ·̣Me· are allowed.

14th Group

Carbon (C), Silicon (Si), Germanium (Ge)

• Default: CH₄, SiH₄, GeH₄ respectively.
• Molecules:
  • Neutral atoms Implicit Hydrogens are added to have 4 bonds. 5 or more bonds are forbidden.
  • Charged atoms: Every added charge on these atoms (no matter it is positive or negative) decreases by one the number of possible bonds. Maximum charge accepted is ±4.
  • Radical: Every added radical on these atoms decreases by one the number accepted of bonds.
  • Aromatic compounds: Carbon may form aromatic bonds as well.

Tin (Sn)

• Default: Sn
• Molecules:
  • Neutral atoms: Implicit Hydrogens are added to have 4 bonds (if Tin has at least 1 bond). 5 or 6 bonds are also accepted.
  • Charged atoms:
    • Positive charge: Every added charge (no matter it is positive or negative) decreases by one the number of possible bonds. Maximum charge accepted is +4.
    • Negative charge: Not allowed.
  • Radical: Every added radical on these atoms decreases by one the number accepted of bonds.
• Ions:
  • Sn²⁺ and Sn⁴⁺ are accepted.
• Other:
  • Sn with 2 electrons in bonds and with at least to coordinate bonds are accepted.

Lead (Pb)

• Default: Pb
• Molecules:
  • Neutral atom:
    • 1 or 2 bonds: 1 or 0 implicit hydrogen is added, respectively.
    • 3 or 4 bonds: 1 or 0 implicit hydrogen is added, respectively.
    • 5 or 6 bonds are accepted.
    • More than 6 bonds are forbidden.
  • Charged atom:
    • Positive charge: Every added charge (no matter it is positive or negative) decreases by one the number of possible bonds. Maximum charge accepted is +4.
    • Negative charge: Not allowed.
  • Radical: Every added radical on these atoms decreases by one the number accepted of bonds.
• Ions:
  • Pb²⁺ and Pb⁴⁺ are accepted.

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

    • 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.

16th Group

Oxygen (O)

• Default: H₂O
• Molecules:
  • Neutral atom:
    • Implicit Hydrogens are added to have 2 bonds (if Oxygen has at least 1 bond).
    • More than 2 bonds are forbidden
  • Charged atom:
    • Positive charge:
      • 1+: 3 bonds are necessary (including implicit Hydrogens).
      • 2+: 4 bonds are necessary (including implicit Hydrogens).
      • 3+: 3 bonds are necessary (including implicit Hydrogens).
      • 4+: 2 bonds are necessary (including implicit Hydrogens).
      • 5+: 1 bonds are necessary (including implicit Hydrogens).
      • 6+: 0 bonds are necessary (including implicit Hydrogens).
    • Negative charge: One or two the negative charges are accepted, with one or zero ligands, respectively.
  • Radical: Every added radical on these atoms decreases by one the number of bonds. Maximum two added radical is allowed.
  • Aromatic compounds: Oxygen may form aromatic bonds as well.

Sulfur (S), Selenium (Se), Tellurium (Te), Polonium (Po)

• Default: H₂S, H₂Se, H₂Te, H₂Po
• Molecules:
  • Neutral atom:
    • 1 bond: 1 implicit Hydrogen is added
    • 2 bond: 0 implicit Hydrogen is added
    • 3 bond: valence error on S/Se/Te/Po atom
    • 4 bond: 0 implicit Hydrogen is added
    • 5 bond: 1 implicit Hydrogen is added
    • 6 bond: 0 implicit Hydrogen is added
    • More than 6 bonds are forbidden
  • Charged atom:
    • Positive charge:
      • Sulfur (S):
        • 1+: 3 or 5 bonds are necessary (including implicit Hydrogens).
        • 2+: 4 bonds are necessary (including implicit Hydrogens).
        • 3+: 3 bonds are necessary (including implicit Hydrogens).
        • 4+: 2 bonds are necessary (including implicit Hydrogens).
        • 5+: 1 bond is necessary (including implicit Hydrogens).
        • 6+: 0 bond is allowed.
        • 7+ or more: not allowed.
      • Selenium (Se), Tellurium (Te), Polonium (Po):
        • 1+: 1, 3 or 5 bonds are necessary (including implicit Hydrogens).
        • 2+: 0 or 4 bonds are necessary (including implicit Hydrogens).
        • 3+: 1 or 3 bonds are necessary (including implicit Hydrogens).
        • 4+: 0 or 2 bonds are necessary (including implicit Hydrogens).
        • 5+: 1 bond is necessary (including implicit Hydrogens).
        • 6+: 0 bond is allowed.
        • 7+ or more: not allowed.
    • Negative charge:
      • 1-: 1 bond accepted. (Exception: 2 double bonded oxygens and 1 more ligand connected by a single bond)
      • 2-: Zero ligand is accepted
  • Radical: Every added radical on these atoms decreases by one the number of bonds. Maximum 2 added radical is allowed.
  • Aromatic compounds: Sulfur may form aromatic bonds as well.

17th Group

• Default:HF, HCl, HBr, HI, HAt
• Molecules:
  • Neutral atoms: 1 bond is allowed.
    Exceptions:
    • 3 valence:
      • Two of the ligands should be F, Cl or oxygen; and one more atom from the 14th, 15th, 16th columns.
      • Double bonded oxygen and one any other atom from 14th, 15th, 16th columns are also accepted.
    • 5 valence:
      • Four of the ligands should be F, Cl or oxygen; and one more atom from the 14th, 15th, 16th columns. Double bonded oxygens are accepted.
    • 7 valence:
      • IF₇ is accepted.
    • Halogen oxoacids:
      • HXO_y, where X = Cl, Br, I or At; and y = 2, 3 or 4.
  • Charged atom:
    • 1+: 2 bonds are necessary.
• Ions:
  • F^-, Cl^-, Br^-, I^-, At^- are accepted.
• Radicals:
  • 1 Radical with 0 bond around the halogen atom is accepted.

18th Group

• Default:He, Ne, Ar, Kr, Xe, Rd
• Molecules: 0 bond is accepted.
  • Exceptions: The following xenon compounds are accepted: XeF₂, XeF₄, XeF₆, XeO₃, XeO₄ XeOF₄, XeO₂F₂, XeO₃F₂.
• Ions: 0 charge is accepted
• Radicals: 0 radical is accepted

Aromatic Systems

Valence calculator provides two ways to check the valence of an atom having aromatic bonds:

• Local Aromatic Valence Calculator uses only the bond and ligand information of the considered atom to do valence calculations. Hence, this method is faster, but often chemically incorrect.
• Global Aromatic Valence Calculator examine the whole aromatic ring system to calculate the valence of one of its atoms. This method is, therefore, slower but chemically more reliable. We recommend the usage of this method, when the not the speed but the chemical reliablity of the valence calculations are important.

Local Aromatic Valence Calculator

Aromatic atoms are sorted into four groups, i.e. boron-like, carbon-like, nitrogen-like and oxygen-like atoms according to their behavior.

Boron-like atoms

• Boron-like atoms: B, C⁺
• Valence can not be calculated exactly.
• One aromatic bond:
  • Accepted with two implicit hydrogens.
  • Accepted with one single bond.
  • Accepted with one single bond and one other single bond or one radical or one implicit hydrogen or one attachment point.
  • Accepted with one double bond.
• Two aromatic bonds:
  • Accepted with no other bond, one single bond, one implicit hydrogen or one radical or one attachment point.
• Three aromatic bonds:
  • Accepted with no other bonds, implicit hydrogens, radical or attachment point.

Carbon-like atoms

• Carbon-like atoms: B^-, C, N⁺, P⁺
• Valence can be calculated exactly.
• One aromatic bond:
  • Accepted with two implicit hydrogens.
  • Accepted with one single bond.
  • Accepted with one single bond and one other single bond or one double bond or one radical or one implicit hydrogen or one attachment point.
  • Accepted with one double bond.
  • Accepted with one double bond and one radical or one implicit hydrogen or one attachment point.
• Two aromatic bonds:
  • Accepted with no other bond, one single bond, one implicit hydrogen or one radical or one attachment point.
• Three aromatic bonds:
  • Accepted with no other bond, implicit hydrogen, radical or attachment point.

Nitrogen-like atoms

• Nitrogen-like atoms: C^-, N , P, O⁺, S⁺
• Valence can not be calculated exactly.
• One aromatic bond:
  • Accepted with two implicit hydrogens.
  • Accepted with one single bond.
  • Accepted with one single bond and one other single bond or one radical or one implicit hydrogen or one attachment point.
  • Accepted with one double bond.
• Two aromatic bonds:
  • Accepted with no other bond, one single bond, one implicit hydrogen or one radical or one attachment point.
• Three aromatic bonds:
  • Accepted with no other bond, implicit hydrogen, radical or attachment point.

Oxygen-like atoms

• Oxygen-like atoms: N^-, P^-, O, S
• Valence can be calculated exactly.
• One aromatic bond:
  • Accepted with zero implicit hydrogens.
  • Accepted with one single bond.
• Two aromatic bonds:
  • Accepted with no other bond, implicit hydrogen, radical or attachment point.
• Three aromatic bonds:
  • Not acceptable.

Exocyclic double bonds

When an atom two aromatic bonds, it may have a double bond with specific ligand:

• Carbon: C, N, P, O, S atoms are possible ligand atoms.
• Nitrogen, Phosphorous, Sulfur: Only O is possible ligand atom.
• Nitrogen and Phosphorous with 1+ charge: Any atom can be ligand.

Global Aromatic Valence Calculator

Global Aromatic Valence Calculator is not yet implemented.

Superatom S-Groups

• There is one S-group attachment point around the investigated atom, that abbreviates one single bond;
• There are two S-group attachment points around the investigated atom, both of them abbreviate one single bond;
• There is one S-group attachment point around the investigated atom, that abbreviates one double bond.

Query Properties

• Default: AH_v
• Molecules:
  • Neutral atoms: Maximum v bonds are accepted.
• Ions and Radicals: According to the definition of the valence property, charge and radical is not taken into account when the valence is calculated.

Special atoms

Special atoms are not handled by the valence calculator.