Formal and Partial Charges¶
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 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.
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. different partial
charging algorithms may assign significantly different partial charges to the same atom
(for example benzene can be represented as
Formal Charges Assignment¶
Normally, file formats such as SMILES, SLN or MDL’s SDF format, specify the formal
charges on each atom of a connection table.
However, when reading from other file formats or when repairing ‘broken’ molecules,
it may be convenient to assign formal charges to each atom such that the atomic
valence is consistent.
OEChem TK provides this functionality via the
This function requires that bond orders and implicit hydrogen counts have been set
on a molecule.
It then adjusts the formal charge on each uncharged atom to correct common valence
For example, quaternary nitrogens are assigned a +1 formal charge, and terminal
oxygen connected only by a single bond (with no implicit hydrogens) is assigned a
-1 formal charge.
A more technical discussion of the formal charges that are assigned by this function are described in the OpenEye Charge Model section.
Gasteiger Partial Charge Calculation¶
To assign Marsilli-Gasteiger partial charges to a molecule, OEChem TK provides the
This sets the partial charge property of each atom, using the
The algorithm itself reproduces the partial charges as calculated by Tripos Inc’s Sybyl
software, with default parameter settings, which is the de facto
reference implementation for Gasteiger charges.
The Gasteiger partial charge algorithm currently assumes that all hydrogen atoms are
represented explicitly, for example by calling
The current version of
should return the same results independent of the currently assigned aromaticity
models and the values of each atom’s “integer atom type” property.
Early versions of OEChem TK allowed customization of the Gasteiger charge calculation
by explicitly assigning the Tripos atoms types of each atom of the molecule.
Unfortunately, this required assigning Tripos’ aromaticity and assigning Tripos
atom types before each call to
The more recent behavior is less error-prone (as it’s no longer possible to forget
to prepare a molecule) and greatly simplifies common usage.
The first stage of the Marsilli-Gasteiger “Partial Equalization of Orbital
Electronegativities” (PEOE)” calculation [Gasteiger-1980] is assignment of
seed charges to each atom.
Typically for neutral atoms the partial charge seed is zero, but for example,
each oxygen in a carboxylate is assigned -0.5, and the net formal charge on
conjugated rings is shared equally amongst the atoms of the ring system.
These seed charges may also be useful in some applications, and can be assigned