Generalized solvent boundary potential using

Variational electrostatic projection method. In some instances, the calculation of PMF profiles in multiple dimensions for complex chemical reactions might not be feasible using full periodic simulation with explicit waters and ions even with the linear-scaling QM/MM-Ewald method [67], To remedy this, we have developed a variational electrostatic projection (VEP) method [75] to use as a generalized solvent boundary potential in QM/MM simulations with stochastic boundaries. The method is similar in spirit to that of Roux and co-workers [76-78], which has been recently... 

Banavali, N.K. Im, W. Roux, B., Electrostatic free energy calculations using the generalized solvent boundary potential method, J. Chem. Phys. 2002,117,7381-7388. 

The energetics of proton transfer along the water chains can be evaluated using methods that combine QM for a system, MM (or MD) for the protein (including internal water), and continuum electrostatics for external solvent and the membrane. (The latter can treated via generalized solvent boundary potential (GSBP) [139]). The methods of such calculations are currently well developed [32,140, 141-151], and have been reviewed recently [152], At the time of this writing, such... 

QM and MM region, //mm represents the potential energy of the MM region, and i/b is an appropriate boundary potential taking into account the effect from the bulk solvent. The Hamiltonian //qm is identical to that used in QM calculations for an isolated molecule in the gas phase (see Density Functional Theory (DFT), Hartree-Fock (HF), and the Self-consistent Field), whereas //mm takes the same form of empirical potential energy expressions as those used in MM force fields (see Force Fields A General Discussion). 

Half-Cells. The concept of a supported electrolyte has proven quite valuable in solution electrochemistry by allowing great theoretical simplification at (usually) only a small cost in accuracy. The several (often implicit) assumptions made in treating the electrolyte in a given cell as supported, however, deserve careful attention as they generally do not apply in the case of solid state electrochemical systems. It should also be noted that it is usually possible in solution electrochemistry to use a large, essentially kineticaUy reversible counterelectrode so that aU but a negligible fraction of the applied potential difference falls across the electrode-electrolyte interface of interest. In its simplest form, the supported approach assumes that all the potential difference in the system falls across the compact double layer—approximately one solvent molecule diameter in thickness— at this electrode, and the approach of the electroactive species to the boundary of the compact layer, the outer Helmholtz plane, occurs purely by diffusion. Corrections for the buildup of space... 

Eventually, an implicit solvation model can be used for the external outer layer, either for an average treatment of the bulk solvent, in order to sensibly reduce the number of the FX molecules explicitly considered, or for the inclusion of non-periodic boundary conditions [21-24]. In the following we will treat the implicit layer within the MF formalism, and all the relevant aspect emphasised with this model can be easily generalised to the case of a general potential defined on a regular surface. 

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