Electrostatic errors

The AMSOL model and the related SMx methods [22] are based on semi-empirical quantum chemical calculations. Normally these models use a GB approximation for the dielectric contribution of AG of solvation, but COSMO has also been used for one parameterization. In order to overcome the large electrostatic errors of bare semi-empirical methods, charge models have been developed, which improve the electrostatic... 

Gilson, M. K., Sharp, K. A., Honig, B. H. Calculating the electrostatic potential of molecules in solution Method and error assessment. J. Comp. Chem. 9 (1988) 327-335. 

By using an effective, distance-dependent dielectric constant, the ability of bulk water to reduce electrostatic interactions can be mimicked without the presence of explicit solvent molecules. One disadvantage of aU vacuum simulations, corrected for shielding effects or not, is the fact that they cannot account for the ability of water molecules to form hydrogen bonds with charged and polar surface residues of a protein. As a result, adjacent polar side chains interact with each other and not with the solvent, thus introducing additional errors. 

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... 

There are several variations of this method. The PRDDO/M method is parameterized to reproduce electrostatic potentials. The PRDDO/M/FCP method uses frozen core potentials. PRDDO/M/NQ uses an approximation called not quite orthogonal orbitals in order to give efficient calculations on very large molecules. The results of these methods are fairly good overall, although bond lengths involving alkali metals tend to be somewhat in error. 

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. 

Since empirical force fields do not accurately estimate the true interatomic forces, it is difficult a priori to say how accurate the fast multipole approximation to the exact Coulomb potential and forces (exact in terms of the sum over partial charges) should be. Probably a good rule is to make sure that at each atom the approximate electrostatic force is within a few percent relative error of the true electrostatic force, obtained by explicitly summing over all atom pairs, i.e., IF — FJ < 0.05 F , for all atoms i, where F is the... 

Figure 14-1. Left Relative errors (RELE) in the force as a function of radial distance from the center of the active dynamical region for the VEP-RVM charge-scaling method [80] for the solvated hammerhead ribozyme at different discretization levels [151] of die co surface. Right The projected total electrostatic potential due to the fully solvated hammerhead ribozyme projected onto die YEP surface [80]...

How does a rigorously calculated electrostatic potential depend upon the computational level at which was obtained p(r) Most ab initio calculations of V(r) for reasonably sized molecules are based on self-consistent field (SCF) or near Hartree-Fock wavefunctions and therefore do not reflect electron correlation in the computation of p(r). It is true that the availability of supercomputers and high-powered work stations has made post-Hartree-Fock calculations of V(r) (which include electron correlation) a realistic possibility even for molecules with 5 to 10 first-row atoms however, there is reason to believe that such computational levels are usually not necessary and not warranted. The Mpller-Plesset theorem states that properties computed from Hartree-Fock wave functions using one-electron operators, as is T(r), are correct through first order (Mpller and Plesset 1934) any errors are no more than second-order effects. 

Fig. 2.2. Average electrostatic potential mc at the position of the methane-like Lennard-Jones particle Me as a function of its charge q. mc contains corrections for the finite system size. Results are shown from Monte Carlo simulations using Ewald summation with N = 256 (plus) and N = 128 (cross) as well as GRF calculations with N = 256 water molecules (square). Statistical errors are smaller than the size of the symbols. Also included are linear tits to the data with q < 0 and q > 0 (solid lines). The fit to the tanh-weighted model of two Gaussian distributions is shown with a dashed line. Reproduced with permission of the American Chemical Society...

The second necessary ingredient in the primitive quasichemical formulation is the excess chemical potential of the metal-water clusters and of water by itself. These quantities p Wm — can typically be obtained from widely available computational packages for molecular simulation [52], In hydration problems where electrostatic interactions dominate, dielectric models of those hydration free energies are usually satisfactory. The combination /t xWm — m//, wx is typically insensitive to computational approximations because the water molecules coat the surface of the awm complex, and computational errors can compensate between the bound and free ligands. 

Procedure of pollen preparation Pollen can be washed off stigmas with an acetone solution as water or other polar solutions often fail to sufficiently break electrostatic bonds holding heterospecific pollen to stigma. However, this means the acetone must be evaporated in an air drying oven (48 h) because a Coulter Counter requires a saline solution of standard volume (usually 10-20 ml) be used to prepare pollen samples. If the solutions are mixed and the volumes are inconsistent, there is a risk that differences in conductivity will create errors. 

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