4.2 Theory

4.2.1 Marsili-Gasteiger Partial Charges

Marsili-Gasteiger partial charges are assigned using a two stage algorithm. In the first stage, seed charges are assigned to each atom in the molecule. For example, carboxylate oxygens are each assigned the value -0.5. During the second stage, these initial charges are then shared across bonds, moving a certain amount of charge from one atom to another. The partial charge moved and its direction is determined by difference in electronegativities of the atoms on each end of the bond. The relaxation algorithm is then iterated several times (by default eight passes), attenuating the charge moved with each iteration. OpenEye does not recommend use of this charge model. However, it is included for comparison.

4.2.2 MMFF94 Partial Charges

The partial charges used by the MMFF94 and MMFF94s force fields are assigned using a four stage algorithm. In the first stage, each atom of the molecule is assigned an MMFF94 atom type. In the second stage, an initial seed partial charge is assigned to each atom based upon it's atom type. For a few atom types, the initial partial charge also depends upon the local environment. In the third stage, the initial charges assigned to aromatic rings are shared between all atoms of the aromatic ring. Finally, in the fourth stage, a table of bond charge increments (BCI) is used to move charges across bonds based upon the bond type of the bond (single, double, triple) and the atom types of the atoms at each end.

4.2.3 AM1 Charges

AM1 charges are a set of Mulliken-type charges derived from a semi-empirical quantum-mechanical calculation. For further discussion of this method, please see Dewar et. al.

4.2.4 AM1BCC Charges

AM1BCC charges start with partial charges derived from the AM1 wave-function. In a second stage, bond-charge corrections (BCC) are applied to the partial charges on each atom to generate the final partial charges. For further discussion, please see the work of Chris Bayly.

The method of assigning AM1BCC charges to a set conformations was proposed by Chris Bayly and colleagues It is based on the following procedure: Coulomb electrostatic energy is calculated for every conformer using MMFF94 absolute values partial charges (original negative charges are replaced with their absolute values). The standard AM1BCC calculation is then performed for the lowest electrostatic energy conforner determined in previous step, and the AM1BCC charges obtained are assigned to all conformers.

OpenEye considers AM1BCC charges to be the best partial charge model currently available.

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