Electrostatic interaction factor

The expected value of the electrostatic interaction factor w is given by Eq. (4). To estimate the radius R of the sphere representing the protein molecule, we can use an experimental value of the partial specific volume V and a reasonable estimate for the bound water, 5i grams per gram of protein (usually 6i 0.2 is chosen). The volume per protein molecule becomes (Tanford, 1961b)... 

Theoretical Effect of Swelling, Dissociation, and Aggregation on the Electrostatic Interaction Factor w at SS C... 

If Ml is the true molecular weight of the protein, Wi the corresponding value of the electrostatic interaction factor, and Zi the corresponding charge at any pH, then, for any titratable group with given pKint,... 

The preceding section has considered the electrostatic interaction factor w of the Linderstr0m-Lang equation. We consider now the value of the intrinsic pK, which is obtained formally as the value of pH — logla /-(1 — a )], for any given kind of titratable group, at the point Z = 0. 

W is the so-called electrostatic interaction factor, and it depends primarily on the dielectric constant and the ionic strength of the medium. In differential form. Equation 9.8, in combination with Equation 9.7, can be written as... 

Although in teraetion s between vicinal I 4 atom s arc n om in ally treated as non bonded interactions, triost of the force fields treat these somewhat differently from normal 1 5 and greater non-bonded interactions. HyperCbern allows each of these 1 4 non-bonded interactions to be scaled down by a scale factor < 1.0 with AMBHR or OPI-S. bor HIO+ the electrostatic may be scaled and different param eters rn ay be ti sed for I 4 van dcr Waals interactions, fh e. AMBHR force field, for exam pie, n orrn a lly uses a seal in g factor of 0.5 for both van der Waals an d electrostatic interactions. 

Fhe van der Waals and electrostatic interactions between atoms separated by three bonds (i.c. the 1,4 atoms) are often treated differently from other non-bonded interactions. The interaction between such atoms contributes to the rotational barrier about the central bond, in conjunction with the torsional potential. These 1,4 non-bonded interactions are often scaled down by an empirical factor for example, a factor of 2.0 is suggested for both the electrostatic and van der Waals terms in the 1984 AMBER force field (a scale factor of 1/1.2 is used for the electrostatic terms in the 1995 AMBER force field). There are several reasons why one would wish to scale the 1,4 interactions. The error associated wilh the use of an repulsion term (which is too steep compared with the more correct exponential term) would be most significant for 1,4 atoms. In addition, when two 1,4... 

Molecular mechanics methods may work well or poorly for compounds containing alkali metals. The crucial factor is often how the force field computes charges for electrostatic interactions. 

AMBER, BIO-h and OPLS scale 1 van der Waals and 1 electrostatic interactions. Although the value of the 1 nonbonded scale factors is an option in HyperChem, you should generally use recommended values. This is because during parameterization, the force field developers used particular values for the 1 nonbonded scale factors, and their parameters may not be correct for other scale factors. 

The van der Waals scale factors used during force field parameterization are 0.5 for AMBER, 1.0 for BlO-t, and 0.125 for OPLS. Eor 1-4 electrostatic interactions, use 0.5 for AMBER, BlO-t, and OPLS. 

Other reactions are controlled kinetically, and the most stable product is not the major one observed. In these cases, you must look at the reactant side of the reaction coordinate to discover factors determining the outcome. Klopman and Salem developed an analysis of reactivity in terms of two factors an electrostatic interaction approximated by atomic charges and a Frontier orbital interaction. Fleming s book provides an excellent introduction to these ideas. 

The first modification is to simply scale the dielectric permittivity of free space (8 ) by a scale factor D to mediate or dampen the long range electrostatic interactions. Its value was often set to be between 1.0 and 78.0, the macroscopic value for water. A value of D=2.5, so that 8 =2.58q, was often used in early CHARMM calculations. 

Other factors that can stabili2e such a forming complex are hydrophobic bonding by a variety of mechanisms (Van der Waals, Debye, ion-dipole, charge-transfer, etc). Such forces complement the stronger hydrogen-bonding and electrostatic interactions. 

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