The OpenEye formal charge model assigns formal charges to elements based upon
their total valence. In OEChem, this functionality is invoked by the
OEAssignFormalCharges function. If the formal charge on an atom is non-zero,
it is left unchanged.
- Hydrogen
- If the valence isn't one, the formal charge is +1.
- Boron
- If the valence is four, the formal charge is +1.
- Carbon
- If the valence is three, the formal charge is +1 if the atom has
a polar neighbor, i.e. N, O or S, and formal charge -1 otherwise.
- Nitrogen
- If the valence is two, the formal charge is -1, and if the
valence is four the formal charge is +1.
- Oxygen
- If the valence is one, the formal charge is -1, and if the
valence is three the formal charge is +1.
- Phosphorous
- If the valence is four, the formal charge is +1.
- Sulfur
- If the valence is 1, the formal charge is -1, if the valence is
three the formal charge is +1, if the valence is 5, the formal charge is -1, if
the valence is four and the degree is four the charge is +2.
- Chlorine
- If the valence is 0 the formal charge is -1, if the valence is
four the formal charge is +3.
- Fluorine, Bromine, Iodine
- If the valence is zero, the formal charge is
-1.
- Magnesium, Calcium, Zinc
- If the valence is zero, the formal charge is
+2.
- Lithium, Sodium, Potassium
- If the valence is zero, the formal charge is
+1.
- Iron
- If the valence is zero, the formal charge is +3 if the partial
charge is 3.0, and +2 otherwise.
- Copper
- If the valence is zero, the formal charge is +2 if the partial
charge is 2.0, and +1 otherwise.
For the remaining elements, if the valence of an atom is zero, its formal
charge is set from its partial charge.
