Electrostatic calculations

Procacci P, March M and Martyna G J 1998 Electrostatic calculations and multiple time scales in molecular dynamics simulation of flexible molecular systems J. Chem. Phys. 108 8799-803... 

Madura J D, Davis M E, Gilson, M K, Wade R C, Luty B A and McCammon J A 1994 Biological applications of electrostatic calculations and Brownian dynamics simulations Rev. Comput. Chem. 5 229-67... 

If the MM+ option to n sc bond dipoles for nonbonded electrostatic calculation s is set, then MM-t-ignores atomic charges but uses dipole m om en ts supplied in its parameter set (in themmpstr. files ). 

In Section III we described an approximation to the nonpolar free energy contribution based on the concept of the solvent-accessible surface area (SASA) [see Eq. (15)]. In the SASA/PB implicit solvent model, the nonpolar free energy contribution is complemented by a macroscopic continuum electrostatic calculation based on the PB equation, thus yielding an approximation to the total free energy, AVP = A different implicit... 

R Abagyan, M Totrov. Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. I Mol Biol 235 983-1002, 1994. 

Computer simulations of electron transfer proteins often entail a variety of calculation techniques electronic structure calculations, molecular mechanics, and electrostatic calculations. In this section, general considerations for calculations of metalloproteins are outlined in subsequent sections, details for studying specific redox properties are given. Quantum chemistry electronic structure calculations of the redox site are important in the calculation of the energetics of the redox site and in obtaining parameters and are discussed in Sections III.A and III.B. Both molecular mechanics and electrostatic calculations of the protein are important in understanding the outer shell energetics and are discussed in Section III.C, with a focus on molecular mechanics. 

Molecular mechanics and electrostatics calculations have both played an important role in studying electron transfer proteins. Molecular mechanics calculations of these proteins use the same techniques (molecular dynamics, energy minimization) as for other proteins, although special consideration must be made in simulation conditions. 

CL Eisher, J-L Chen, J Li, D Bashford, L Noodleman. Density-functional and electrostatic calculations for a model of a manganese superoxide dismutase active site in aqueous solution. J Phys Chem 100 13498-13505, 1996. 

Hurley, A. C., Proc. Roy. Soc. London) A226, 170, 179, The electrostatic calculation of molecular energies. I. Methods of calculating molecular energies. II. Approximate wave functions and the electrostatic model/ ... 

Bashford D, Gerwert K (1992) Electrostatic calculations of the pKa values of ionizable groups in bacteriorhodopsin. J Mol Biol 224 473 186. 

Schamagl C, Raupp-Kossmann R, Fischer SF (1999) Molecular basis for pH sensitivity and proton transfer in green fluorescent protein protonation and conformational substates from electrostatic calculations. Biophys J 77 1839-1857... 

Nina, M. Beglov, D. Roux, B., Atomic radii for continuum electrostatics calculations based on molecular dynamics free energy simulations, J. Phys. Chem. B 1997, 101, 5239-5248... 

In addition, mention may be made of more recent electrostatic calculations due to Voitlander and his coworkers 110,177). Qualitatively the results are very similar to those of Robertson and McConnell 30), although the latter contain erroneous numerical values (177), but the choice of R as the metal to ring centroid distance, rather than the metal to carbon distance, leads to much better agreement with experiment. Thus, for Fe(Cp)2, the latter choice predicts 6 < n < o, but the former yields 5 o < ir, with a total splitting of some 18000 cm-1, in quite good agreement with experiment. 

An alternative to the GB, COSMO, and Poisson electrostatic calculations is to model the solution to the Poisson equation in terms of pair potentials between solute atoms this procedure is based on the physical picture that the solvent screens the intra-solute Coulombic interactions of the solute, except for the critical descreening of one part of the solute from the solvent by another part of this solute. This descreening can be modeled in an average way to a certain level of accuracy by pairwise functions of atomic positions.18, M 65 One can obtain quite accurate solvation energies in this way, and it has recently been shown that this algorithm provides a satisfactory alternative to more expensive explicit-solvent simulations even for the demanding cases of 10-base-pair duplexes of DNA and RNA in water.66... 

Perhaps the most widely discussed source of uncertainty in electrostatic calculations is the location of the solute/solvent boundary. The most common treatment is to place the boundary at the surface of a set of overlapping spheres centered at the nuclei. But what radius should one use for those spheres One common answer is van der Waals radii times I.2.46 In our own quantum mechanical solvation models,12 27 and those of several others59, 69, these radii are empirical parameters. Recently Barone et al.70 have modified the PCM to use charge-dependent united-atom spheres instead of all-atom spheres, and they optimized the electrostatic radii for a... 

Charges also accumulate when solids are transported. The buildup results from the separation of solid particle surfaces. Because solid geometries are almost always ill-defined, electrostatic calculations for solids are handled empirically. 

Some generally accepted guidelines for electrostatic calculations are shown in Table 7-4. 

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