Partial charges are created due to the asymmetric distribution of electrons in chemical bonds. The resulting partial charges are a property only of zones within the distribution, and not the assemblage as a whole. For example, chemists often choose to look at a small space surrounding the nucleus of an atom: When an electrically neutral atom bonds chemically to another neutral atom that is more electronegative, its electrons are partially drawn away. This leaves the region about that atom's nucleus with a partial positive charge, and it creates a partial negative charge on the atom to which it is bonded.
In such a situation, the distributed charges taken as a group always carries a whole number of elementary charge units. Yet one can point to zones within the assemblage where less than a full charge resides, such as the area around an atom's nucleus. This is possible in part because particles are not like mathematical points--which must be either inside a zone or outside it--but are smeared out by the uncertainty principle of quantum mechanics. Because of this smearing effect, if one defines a sufficiently small zone, a fundamental particle may be both partly inside and partly outside it.
Partial atomic charges are used in molecular mechanics force fields to compute the electrostatic interaction energy using Coulomb's law. They are also often used for a qualitative understanding of the structure and reactivity of molecules.
Despite its usefulness, the concept of a partial atomic charge is somewhat arbitrary, because it depends on the method used to delimit between one atom and the next (in reality, atoms have no clear boundaries). As a consequence, there are many methods for estimating the partial charges. According to Cramer (2002), all methods can be classified in one of four classes:
The following is a detailed list of methods, based on Meister and Schwarz (1994).
J. Meister, W. H. E. Schwarz. Principal Components of Ionicity. J. Phys. Chem. 1994, 98, 8245-8252. C. J. Cramer. Essentials of Computational Chemistry: Theories and Methods. Wiley, 2002, pp. 278-289.