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 OEAtomBase::SetFormalCharge and OEAtomBase::GetFormalCharge methods respectively. Similarly, the partial charges are stored and retrieved with the OEAtomBase::SetPartialCharge and OEAtomBase::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 - C++ Theory Manual Version 1.3.1

				OEChem - C++ Theory Manual Version 1.3.1