Charge, atomic

The charge attributed to an atom A within a molecule, defined as = Za — where Za is the atomic number of atom A and A is the electron density (see Atoms in Molecules) assigned to A. The calculation of q depends on the partitioning of the electron density. In the framework of Mulliken population analysis (see Electronic Wavefunctions Analysis), cja is related to the gross atomic population H q, where q is the gross 

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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... 

Wberg K B and Rablen P R 1993 Comparison of atomic charges by different procedures J. Comput. Chem. 14 1504... 

The solvent dielectric constant, ionic strength and temperature are chosen to fit the conditions of the experimental studies. The protein dielectric constant is assigned some small value, e.g. 4. The PB calculations are currently carried out with the atomic charges and radii of the PARSE parameter set, developed by Honig and coworkers [17] or that for CHARMM [12]. The PARSE parameter set... 

Molecular surfaces can express various chemical and physical properties, such as electrostatic potential, atomic charges or hydrophobicity, using colored mapping. 

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... 

Many problems in force field investigations arise from the calculation of Coulomb interactions with fixed charges, thereby neglecting possible mutual polarization. With that obvious drawback in mind, Ulrich Sternberg developed the COSMOS (Computer Simulation of Molecular Structures) force field [30], which extends a classical molecular mechanics force field by serai-empirical charge calculation based on bond polarization theory [31, 32]. This approach has the advantage that the atomic charges depend on the three-dimensional structure of the molecule. Parts of the functional form of COSMOS were taken from the PIMM force field of Lindner et al., which combines self-consistent field theory for r-orbitals ( nr-SCF) with molecular mechanics [33, 34]. 

The MEP at the molecular surface has been used for many QSAR and QSPR applications. Quantum mechanically calculated MEPs are more detailed and accurate at the important areas of the surface than those derived from net atomic charges and are therefore usually preferable [Ij. However, any of the techniques based on MEPs calculated from net atomic charges can be used for full quantum mechanical calculations, and vice versa. The best-known descriptors based on the statistics of the MEP at the molecular surface are those introduced by Murray and Politzer [44]. These were originally formulated for DFT calculations using an isodensity surface. They have also been used very extensively with semi-empirical MO techniques and solvent-accessible surfaces [1, 2]. The charged polar surface area (CPSA) descriptors proposed by Stanton and Jurs [45] are also based on charges derived from semi-empirical MO calculations. 

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. 

Quantum chemical descriptors such as atomic charges, HOMO and LUMO energies, HOMO and LUMO orbital energy differences, atom-atom polarizabilities, super-delocalizabilities, molecular polarizabilities, dipole moments, and energies sucb as the beat of formation, ionization potential, electron affinity, and energy of protonation are applicable in QSAR/QSPR studies. A review is given by Karelson et al. [45]. 

UvHV tff cctivc Diameter V Potential of positive atomic charges... 

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. 

Despite th ese reservation s. Mu Ilikeri population -derived atomic charges arc easy to compute. Empirical investigation shows that they have various uses, they provide approximate representation of the 3D charge distribution within a molecule. 

AMBER. BlO-t-. and OPLS calciilations use information on atomic charges. Atomic charges can come from these sources ... 

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