Atomic partial charges

Momany F A 1978 Determination of partial atomic charges from ab initio molecular electrostatic potentials. Application to formamide, methanol and formic acid J. Phys. Chem. 82 592... 

Two other atomic properties have been used in the definition of atom type, thereby increasing its fuzziness relative to that in the ap and tt descriptors - atomic log P contribution (yielding hydrophobic pairs, hps, and torsions, hts) and partial atomic charges (charge pairs, cps, and charge torsions, cts). 

The authors emphasize on their web pages that UFF is not designed to be used in conjunction with partial atomic charges, as it is the default option in several software packages. A second point is that UFF is often used to model biological... 

A range of physicochemical properties such as partial atomic charges [9] or measures of the polarizabihty [10] can be calculated, for example with the program package PETRA [11]. The topological autocorrelation vector is invariant with respect to translation, rotation, and the conformer of the molecule considered. An alignment of molecules is not necessary for the calculation of their autocorrelation vectors. 

The chirality code of a molecule is based on atomic properties and on the 3D structure. Examples of atomic properties arc partial atomic charges and polarizabilities, which are easily accessible by fast empirical methods contained in the PETRA package. Other atomic properties, calculated by other methods, can in principle be used. It is convenient, however, if the chosen atomic property discriminates as much as possible between non-equivalent atoms. 3D molecular structures are easily generated by the GORINA software package (see Section 2.13), but other sources of 3D structures can be used as well. 

Figure 8-11. iD structure and representation offcoccia) versus u for (fi)-4 and [S)-4 at two different conformations (a and b) sampled at 50 evenly separated values between -0,100 e A and i-0.100 e A. Partial atomic charge was used as the atomic property. 

An extended set of physicochemical descriptors was used in this study, including, for example, partial atomic charge and effective polari2 ability of the protons, average of electronegativities of atoms two bonds away, or maximum, T-atomic charge of atoms two bonds away. 

In Eq. (16 i denotes an atom up to lour non-rotatable bonds away from the proton and is the total number of those atoms. A bond is deRned as non-rotatable if it belongs to a ring, to a. T-system, or to an amide functional group q- is the partial atomic charge of the atom i, and is the 3D distance between the proton j and the atom i. Figure 10.2-5 shows an example of a proton RDF descriptor. 

Given the widespread use of the partial atomic charge model, it is important to consider how the charges are obtained. For simple species the atomic charges required to reproduce the... 

Partial atomic charge, polarisability 3D or 2D structure See Section 4.9... 

Calculations performed using MC BOSS [66] with the CHARMM combination rules. Partial atomic charges (C = —0.27 and H = 0.09) were identical for all three simulations. 

Assign atom types Assign connectivity Assign partial atomic charges -------Assigninitiai-parameters. "... 

Partial Atomic Charges. Determination of the partial atomic charges requires minimum interaction energies and geometries for individual water molecules interacting with different sites on the model compounds. An example of the different interaction orientations is shown in Eigure 3c for model compound 1, Eigure 3a. As may be seen. 

A classical description of M can for example be a standard force field with (partial) atomic charges, while a quantum description involves calculation of the electronic wave function. The latter may be either a semi-empirical model, such as AMI or PM3, or any of the ab initio methods, i.e. HF, MCSCF, CISD, MP2 etc. Although the electrostatic potential can be derived directly from the electronic wave function, it is usually fitted to a set of atomic charges or multipoles, as discussed in Section 9.2, which then are used in the actual solvent model. 

---