Fully solvated model

Figure 3.6 Schematic of (a) vacuum slab model, (b) partially solvated model, and (c) fully solvated model. In the vacuum model, A represents a surface adsorbate in the solvated models, a water molecule is shown as the adsorbate.

Figure 3.7 Optimized adsorption configurations of sulfate over the Pt(lll) surface using (a) a vacuum model, (b) a partially solvated model used in the electric field model, and (c) a fully solvated model used in double reference method.

The fully solvated model cannot easily be used with the dipole-correction or applied field methods discussed above. The absence of a vacuum layer in the fully solvated model makes dipole moment evaluation and field application impossible within the periodic model. Hybrid approaches, in which the dipole is measured in an unsolvated model and solvation approximated in the fully solvated model, might be considered. However, the advantage of the fully solvated model is its integration within the direct charging of the electrochemical interface. 

The influence of solvation on the reaction was evaluated using the fully solvated model. The reaction free energy of O2 is equal to... 

From the starting structures (PDB file), the full complement of hydrogens is added using a utility within CHARMM. The entire protein is then solvated within a sphere of TIP3P model waters, with radius such that all parts of the protein were solvated to a depth of at least 5 A. A quartic confining potential localized on the surface of the spherical droplet prevented evaporation of any of the waters during the course of the trajectory. The fully solvated protein structure is energy minimized and equilibrated before the production simulation. 

As discussed in Section 2, one key assumption of reaction field models is that the polarization field of the solvent is fully equilibrated with the solute. Such a situation is most likely to occur when the solute is a long-lived, stable molecular structure, e g., the electronic ground state for some local minimum on a Bom-Oppenheimer potential energy surface. As a result, continuum solvation models... 

Figure 2.13 illustrates what is currently a widely accepted model of the electrode-solution interphase. This model has evolved from simpler models, which first considered the interphase as a simple capacitor (Helmholtz), then as a Boltzmann distribution of ions (Gouy-Chapman). The electrode is covered by a sheath of oriented solvent molecules (water molecules are illustrated). Adsorbed anions or molecules, A, contact the electrode directly and are not fully solvated. The plane that passes through the center of these molecules is called the inner Helmholtz plane (IHP). Such molecules or ions are said to be specifically adsorbed or contact adsorbed. The molecules in the next layer carry their primary (hydration) shell and are separated from the electrode by the monolayer of oriented solvent (water) molecules adsorbed on the electrode. The plane passing through the center of these solvated molecules or ions is referred to as the outer Helmholtz plane (OHP). Beyond the compact layer defined by the OHP is a Boltzmann distribution of ions determined by electrostatic interaction between the ions and the potential at the OHP and the random jostling of ions and... 

C. J. Cramer, private communication, 1993. AMSOL is based on AMPAC, with the inclusion of solvation effects. A fully parallel version of this code is under development by Cray Research Inc. See also, C. J. Cramer and D. G. Truhlar, Chapter 1, this volume. Continuum Solvation Models Classical and Quantum Mechanical Methods. 

Environmental effects, such as solvation and long-range electrostatic interactions, can be included approximately in a calculation on a an active site cluster model by the use of continuum solvation models, but these cannot fully represent the heterogeneous electrostatic environment in an enzyme.74 An... 

Fundamental advances in theory and computation will radically change the way we do science. Simulation science will become even more multidisciplinary. Simulation and computation will fully come of age as the third branch of science, fulfilling the promise of the past 20 years. Simulation will be key to coupling multiple temporal and spatial scales while maintaining accuracy. New models will emerge that will completely replace the techniques that have been used so far. For example, new, fast methods will replace 50 years of traditional quantum chemistry approaches and we will have new solvation models. 

It should be stressed that the SMC parameterization procedure is very different from standard Born model analysis where an ion of assigned radius is embedded in a uniform continuum dielectric with bulk permittivity. Here, the ion is fully solvated by the model water, and the dielectric constant refiects the solvent s electronic properties. The structural component of dielectric reorganization is treated explicitly. 

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