Atomic charges, dielectric constant

Different charge models (atomic charges, dielectric constant, molecular surface) can be used. 

To evaluate electrostatic oiergies of molecular systems faithfully, the values onployed for atomic charges, dielectric constant of the solute and van der Waals raii of the atoms used for the definition of the dielectric boundaries should be detaining consistoitly. 

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... 

In this model of electrostatic in teraction s, two atoms (i and j) have poin t charges tq and qj. The magnitude of the electrostatic energy (V[. , [ ) varies inversely with the distance between the atoms, Rjj. fh e effective dielectric constant is . For in vacuo simulations or simulation s with explicit water rn olecules, the den om in a tor equals uRjj, In some force fields, a distance-dependent dielectric, where the denominator is uRjj Rjj, represen is solvent implicitly. 

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 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 dielectric constant is a measure of the ease with which charged species in a material can be displaced to form dipoles. There are four primary mechanisms of polarization in glasses (13) electronic, atomic, orientational, and interfacial polarization. Electronic polarization arises from the displacement of electron clouds and is important at optical (ultraviolet) frequencies. At optical frequencies, the dielectric constant of a glass is related to the refractive index k =. Atomic polarization occurs at infrared frequencies and involves the displacement of positive and negative ions. 

As for the dielectric constant, when explicit solvent molecules are included in the calculations, a value of 1, as in vacuum, should be used because the solvent molecules themselves will perform the charge screening. The omission of explicit solvent molecules can be partially accounted for by the use of an / -dependent dielectric, where the dielectric constant increases as the distance between the atoms, increases (e.g., at a separation of 1 A the dielectric constant equals 1 at a 3 A separation the dielectric equals 3 and so on). Alternatives include sigmoidal dielectrics [80] however, their use has not been widespread. In any case, it is important that the dielectric constant used for a computation correspond to that for which the force field being used was designed use of alternative dielectric constants will lead to improper weighting of the different electrostatic interactions, which may lead to significant errors in the computations. 

Althongh van der Waals forces are present in every system, they dominate the disjoining pressnre in only a few simple cases, such as interactions of nonpolar and inert atoms and molecnles. It is common for surfaces to be charged, particularly when exposed to water or a liquid with a high dielectric constant, due to the dissociation of surface ionic groups or adsorption of ions from solution, hi these cases, repulsive double-layer forces originating from electrostatic and entropic interactions may dominate the disjoining pressure. These forces decay exponentially [5,6] ... 

Water, however, is a wonderful solvent for ionic-bonded substances such as salt. The secret to its success lies in the electric dipoles created by the polar covalent bonds between the hydrogen and oxygen atoms. In water, the polar bonds are asymmetric. The hydrogen side is positive the oxygen side is negative. One measure of the amount of charge separation in a molecule is its dielectric constant. Water has a dielectric constant that is considerably higher than that of any other common liquid. 

A crucial parameter in these calculations is the dielectric constant e of the solutes, assumed to be the same for all solutes and all states. It is difficult [117], though not impossible [58, 115, 118] to evaluate the dielectric constant of a protein in fact it does not have to be spatially constant [118], and its effective value may depend strongly on the set of atomic charges used (the force field) and the process considered [58], Therefore, an empirical approach is usually preferred. The strategy used by Archontis et al. [109] was to adjust e to reproduce with PBFE the AAA obtained from MDFE for Asp/Asn binding to native AspRS (15 kcalmol-1). This led to e 4,... 

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