Atomic partial charges calculation

Physticochemical coiiatrainla Further constraints can be imposed on the atoms and bonds of the reaction center, such as those physicochemical factors calculated by the PETRA package (see Section 7.1). For example, the partial charges calculated by the PEOE method can be used to extract the chemically feasible reaction from the two conceivable ones as illustrated in Figure 10.3-11. 

Rao and Singh32 calculated relative solvation free energies for alkyl- and tetra-alkylammonium ions using same conditions as described before for neutral molecules (except, atomic partial charges were not scaled for ions). The values obtained with coordinate coupling were in better agreement with... 

We have derived three sets of (easily calculated) molecular descriptors based on atomic contributions to logP, molar refractivity, and atomic partial charge. The individual descriptors were found to be weakly correlated with each other... 

An alternative physical observable that has been used to define partial atomic charges is the electron density. In X-ray crystallography, the electron density is direedy measured, and by comparison to, say, spherically symmetric neutral atoms, atomic partial charges may be defined experimentally, following some decisions about what to do with respect to partitioning space between the atoms (Coppens 1992). Bader and co-workers have adopted a particular partitioning scheme for use with electronic structure calculations that defines the atoms-in-molecules (AIM) method (Bader 1990). In particular, an atomic volume is... 

Of course, the simplicity of the QM/MM operator does not imply diat it has only a small effect. Large atomic partial charges placed near the QM fragment would be expected to polarize the system strongly. Table 13.2 compares the dipole moments of the standard nucleic acid bases at the AMI level evaluated in the gas phase and in a QM/MM calculation carried out modeling aqueous solvation with a periodic box of TIP31 water molecules. Eor comparison, results from the AM1-SM2 aqueous continuum solvation model are also provided. 

FIGURE 28. Calculated bond lengths and atomic partial charges (in parentheses) of PhsELi (E = Sn, Pb) at the HF level. Bond distances are in A, angles in deg. Reproduced by permission of The Royal Society of Chemistry from Reference 141... 

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