Charge parameterization

No firm theoretical mechanism representing projectile charge structure in effective charge parameterization has yet been discovered. 

In contrast to the point charge model, which needs atom-centered charges from an external source (because of the geometry dependence of the charge distribution they cannot be parameterized and are often pre-calculated by quantum mechanics), the relatively few different bond dipoles are parameterized. An elegant way to calculate charges is by the use of so-called bond increments (Eq. (26)), which are defined as the charge contribution of each atom j bound to atom i. 

Molecular dipole moments are often used as descriptors in QPSR models. They are calculated reliably by most quantum mechanical techniques, not least because they are part of the parameterization data for semi-empirical MO techniques. Higher multipole moments are especially easily available from semi-empirical calculations using the natural atomic orbital-point charge (NAO-PC) technique [40], but can also be calculated rehably using ab-initio or DFT methods. They have been used for some QSPR models. 

A molecular modeling and simulation package with various implemented force field parameterizations. Free of charge for academic use. Available for different platforms. 

The Fenske-Hall method is a modification of crystal held theory. This is done by using a population analysis scheme, then replacing orbital interactions with point charge interactions. This has been designed for the description of inorganic metal-ligand systems. There are both parameterized and unparameterized forms of this method. 

For molecular mechanics, the charge calculation method used in parameterizing the force field should be used if possible. Otherwise, use Q-equilibrate or electrostatic charges. 

Ah initio calculations of polymer properties are either simulations of oligomers or band-structure calculations. Properties often computed with ah initio methods are conformational energies, polarizability, hyperpolarizability, optical properties, dielectric properties, and charge distributions. Ah initio calculations are also used as a spot check to verify the accuracy of molecular mechanics methods for the polymer of interest. Such calculations are used to parameterize molecular mechanics force fields when existing methods are insulficient, which does not happen too often. 

Given the diversity of different SCRF models, and the fact that solvation energies in water may range from a few kcal/mol for say ethane to perhaps 100 kcal/mol for an ion, it is difficult to evaluate just how accurately continuum methods may in principle be able to represent solvation. It seems clear, however, that molecular shaped cavities must be employed, the electiostatic polarization needs a description either in terms of atomic charges or quite high-order multipoles, and cavity and dispersion terms must be included. Properly parameterized, such models appear to be able to give absolute values with an accuracy of a few kcal/mol." Molecular properties are in many cases also sensitive to the environment, but a detailed discussion of this is outside the scope of this book. ... 

The fiuid-phase simulation approach with the longest tradition is the simulation of large numbers of the molecules in boxes with artificial periodic boundary conditions. Since quantum chemical calculations typically are unable to treat systems of the required size, the interactions of the molecules have to be represented by classical force fields as a prerequisite for such simulations. Such force fields have analytical expressions for all forces and energies, which depend on the distances, partial charges and types of atoms. Due to the overwhelming importance of the solvent water, an enormous amount of research effort has been spent in the development of good force field representations for water. Many of these water representations have additional interaction sites on the bonds, because the representation by atom-centered charges turned out to be insufficient. Unfortunately it is impossible to spend comparable parameterization work for every other solvent and... 

Patel S, Brooks CL (2004) CHARMM fluctuating charge force field for proteins I parameterization and application to bulk organic liquid simulations. J Comput Chem 25(1) 1—15... 

Stern HA, Kaminski GA, Banks JL, Zhou RH, Berne BJ, Friesner RA (1999) Huctuating charge, polarizable dipole, and combined models parameterization from ab initio quantum chemistry. J Phys Chem B 103(22) 4730 t737... 

For the metal in the electrochemical interface, one requires a model for the interaction between metal and electrolyte species. Most important in such a model are the terms which are responsible for establishing the metal-electrolyte distance, so that this distance can be calculated as a function of surface charge density. The most important such term is the repulsive pseudopotential interaction of metal electrons with the cores of solvent species, which affects the distribution of these electrons and how this distribution reacts to charging, as well as the metal-electrolyte distance. Although most calculations have used parameterized simple functional forms for this term, it can now be calculated correctly ab initio. 

In contrast, for cases where the protein is more rigid, the standard continuum approach can give excellent results. A striking example is the case of photosystems and redox proteins, where a low reorganization is needed to maintain fast charge-transfer kinetics. For these systems, carefully parameterized continumm models can give an accurate picture of redox potentials and their coupling to acid/base reactions [126-128],... 

In the last example, a serious handicap is the extreme sensitivity of the calculations to the parameterization of the metal atoms. In a paper concerning the spin states of metal dimer complexes (38) as studied by EHT, heavy manipulation of the original theory was needed. In the field of transition metal coordination compounds self-consistent charge (SCC) calculations (of the type already mentioned for electronegative atoms) are essential to obtain the diagonal elements Hu. 

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