Dielectric potential

Use a shifted function only to reproduce reported results. Since a shifted dielectric potential affects the entire potential energy surface, it is not recommended. 

Each fractional charge Q, contributes to a dielectric potential A3>, = Qt AV /r, in a volume element AV = 5,. Ars of the solvent cage in the distance r, = r1 from center i. The mean potential (< >,) inside the cage increment AV( around the /th subgroup is given by summation over all centers j (distance rJ from 5, ),... 

Flere u. j(r,T,P) is the short-range potential for ions, and e is the dielectric constant of the solvent. The solvent averaged potentials are thus actually free energies that are fimctions of temperature and pressure. The... 

The are essentially adjustable parameters and, clearly, unless some of the parameters in A2.4.70 are fixed by physical argument, then calculations using this model will show an improved fit for purely algebraic reasons. In principle, the radii can be fixed by using tables of ionic radii calculations of this type, in which just the A are adjustable, have been carried out by Friedman and co-workers using the HNC approach [12]. Further rermements were also discussed by Friedman [F3], who pointed out that an additional temi is required to account for the fact that each ion is actually m a cavity of low dielectric constant, e, compared to that of the bulk solvent, e. A real difficulty discussed by Friedman is that of making the potential continuous, since the discontinuous potentials above may lead to artefacts. Friedman [F3] addressed this issue and derived... 

Colloidal particles can be seen as large, model atoms . In what follows we assume that particles with a typical radius <3 = lOO nm are studied, about lO times as large as atoms. Usually, the solvent is considered to be a homogeneous medium, characterized by bulk properties such as the density p and dielectric constant t. A full statistical mechanical description of the system would involve all colloid and solvent degrees of freedom, which tend to be intractable. Instead, the potential of mean force, V, is used, in which the interactions between colloidal particles are averaged over... 

Highly protective layers can also fonn in gaseous environments at ambient temperatures by a redox reaction similar to that in an aqueous electrolyte, i.e. by oxygen reduction combined with metal oxidation. The thickness of spontaneously fonned oxide films is typically in the range of 1-3 nm, i.e., of similar thickness to electrochemical passive films. Substantially thicker anodic films can be fonned on so-called valve metals (Ti, Ta, Zr,. ..), which allow the application of anodizing potentials (high electric fields) without dielectric breakdown. 

The first term represents the forces due to the electrostatic field, the second describes forces that occur at the boundary between solute and solvent regime due to the change of dielectric constant, and the third term describes ionic forces due to the tendency of the ions in solution to move into regions of lower dielectric. Applications of the so-called PBSD method on small model systems and for the interaction of a stretch of DNA with a protein model have been discussed recently ([Elcock et al. 1997]). This simulation technique guarantees equilibrated solvent at each state of the simulation and may therefore avoid some of the problems mentioned in the previous section. Due to the smaller number of particles, the method may also speed up simulations potentially. Still, to be able to simulate long time scale protein motion, the method might ideally be combined with non-equilibrium techniques to enforce conformational transitions. 

The Poisson equation relates spatial variation of the potential 4> at position r to the density of the charge distribution, p, in a medium with a dielectric constant e... 

N is the number of point charges within the molecule and Sq is the dielectric permittivity of the vacuum. This form is used especially in force fields like AMBER and CHARMM for proteins. As already mentioned, Coulombic 1,4-non-bonded interactions interfere with 1,4-torsional potentials and are therefore scaled (e.g., by 1 1.2 in AMBER). Please be aware that Coulombic interactions, unlike the bonded contributions to the PEF presented above, are not limited to a single molecule. If the system under consideration contains more than one molecule (like a peptide in a box of water), non-bonded interactions have to be calculated between the molecules, too. This principle also holds for the non-bonded van der Waals interactions, which are discussed in Section 7.2.3.6. 

Another way of calculating the electrostatic component of solvation uses the Poisson-Boltzmann equations [22, 23]. This formalism, which is also frequently applied to biological macromolecules, treats the solvent as a high-dielectric continuum, whereas the solute is considered as an array of point charges in a constant, low-dielectric medium. Changes of the potential within a medium with the dielectric constant e can be related to the charge density p according to the Poisson equation (Eq. (41)). 

Alper H E and R M Levy 1989. Computer Simulations of the Dielectric Properties of Water - Studies of the Simple Point-Charge and Transferable Intermolecular Potential Models. Journal of Chemical Physics 91 1242-1251. 

The final class of methods that we shall consider for calculating the electrostatic compone of the solvation free energy are based upon the Poisson or the Poisson-Boltzmann equatior Ihese methods have been particularly useful for investigating the electrostatic properties biological macromolecules such as proteins and DNA. The solute is treated as a body of co stant low dielectric (usually between 2 and 4), and the solvent is modelled as a continuum high dielectric. The Poisson equation relates the variation in the potential (f> within a mediu of uniform dielectric constant e to the charge density p ... 

A cubic lattice is superimposed onto the solute(s) and the surrounding solvent. Values of the electrostatic potential, charge density, dielectric constant and ionic strength are assigned to each grid point. The atomic charges do not usually coincide with a grid point and so the... 

The Poisson equation describes the electrostatic interaction between an arbitrary charge density p(r) and a continuum dielectric. It states that the electrostatic potential ([) is related to the charge density and the dielectric permitivity z by... 

Example For two atoms having point charges of 0.616 and -0.504 e and a constant dielectric function, the energy curve shows a switching function turned on (Ron) at a nonbonded distance of 10 A and off (Roff) at a distance of 14 A. Compare the switched potential with the abruptly truncated potential. 

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