16. Formal and Partial Charges

Each OEAtomBase keeps track of two types of charges. The first, formal charge, is an integer property that is essential for the correct valence representation of a molecule. Together with atomic valences, bond order and the connectivity, this field is defines the identity of a molecule. The second type of charge, partial charge, is a floating point property used in computational chemistry and molecular modeling. This value is used to represent the electronic distribution/wave-function of a molecule by approximating the molecule's electrostatic field with a set of point charges located at each atom.

The formal charges on an atom may be stored and retrieved using the SetFormalCharge and GetFormalCharge methods respectively. Similarly, the partial charges are stored and retrieved with the SetPartialCharge and GetPartialCharge methods.

Neither the formal charge nor the partial charge is a directly observable property of an atom. Instead the same molecule may be represented by different valence representations each placing the formal charges in different locations, i.e. [cH+]1[cH-][cH+][cH-][cH+][cH-]1 Benzene, and different partial charging algorithms may assign significantly different partial charges to the same atom.

Subsections

				OEChem - Python Theory Manual Version 1.3.1

				OEChem - Python Theory Manual Version 1.3.1