Charge interaction

Changes in DNA topology caused by intercalators can impair or prevent DNA replication, a key process for cell division. Therefore, DNA intercalators have the potential 

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Electrostatic terms other than the simple charge interactions above are commonly included in molecular mechanics calculations. particularly dipole-dipole interactions. More recently, second-order electrostatic interactions like those describing polarizability have been added to some force fields. 

MM+ calculations do not usually have an electrostatic charge-charge interaction nor define a set of atomic charges for atoms. 

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. 

The other term that is very widely used is a Coulombic charge interaction of the form... 

The energy of solvation can be further broken down into terms that are a function of the bulk solvent and terms that are specifically associated with the first solvation shell. The bulk solvent contribution is primarily the result of dielectric shielding of electrostatic charge interactions. In the simplest form, this can be included in electrostatic interactions by including a dielectric constant k, as in the following Coulombic interaction equation ... 

This modification of the charge interaction is responsible for shifts in the electron density as permitted by the polarizability of the molecule. 

The above potential describes the monopole-monopole interactions of atomic charges Q and Qj a distance Ry apart. Normally these charge interactions are computed only for nonbonded atoms and once again the interactions might be treated differently from the more normal nonbonded interactions (1-5 relationship or more). The dielectric constant 8 used in the calculation is sometimes scaled or made distance-dependent, as described in the next section. 

The OPLS form of electrostatic interactions is that of equation (26) on page 179. That is, it uses a charge-charge interaction just like AMBER. However, since the nonbonded potentials were developed... 

E causes a particle of charge q to experience a force and hence a displacement. Both the force and the displacement are proportional to E therefore the energy of the field-charge interaction-the product of the force and the displacement-is proportional to E. ... 

Figure 10.18 Side-chain interactions in the leucine zipper structure, (a) The hydrophobic side chains in spikes a and d (see Figure 10.17) form a hydrophobic core between the two coiled a helices, (b) Charged side chains in spikes and g can promote dimer formation by forming complementary charge interactions between the two a helices.

As discussed already in Chapter 2 the work function, , of a solid surface is one of the most important parameters dictating its chemisorptive and catalytic properties. The work function, (eV/atom) of a surface is the minimum energy which an electron must have to escape from the surface when the surface is electrically neutral. More precisely is defined as the energy to bring an electron from the Fermi level, EF, of the solid at a distance of a few pm outside of the surface under consideration so that image charge interactions are negligible. 

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