Bulk solvent region

An excellent summary of work reported up to 1997 was presented by Dunn and Zink (22), who put forth a simple model for the interior of a sol-gel, which is very useful in considering interactions of molecules with the sol-gel environment. The pore structure was considered as a collection of small test tubes whose walls are made up of component silica particles, and which contain a bulk solvent region. This model of the sihca interior is represented in Figure 6,... 

An alternative approach is to employ stochastic boundary conditions where the finite molecular system employed in the simulation is not duplicated, but rather, a boundary force is applied to interact with atoms of the sys-tem. 2-67 Yhe boundary force is chosen to mimic the bulk solvent regions that have been neglected. However, a difficulty with the use of this method is due to the ambiguity associated with the definition and parameterization of the boundary forces. Thus, there is sometimes the impression that the method is not rigorous. Recently, Beglov and Roux provided a formal definition and suggested a useful implementation of the boundary forces. Their results are very promising. 

It is sometimes desirable to include the effect of the rest of the system, outside of the QM and MM regions. One way to do this is using periodic boundary conditions, as is done in liquid-state simulations. Some researchers have defined a potential that is intended to reproduce the effect of the bulk solvent. This solvent potential may be defined just for this type of calculation, or it may be a continuum solvation model as described in the next chapter. For solids, a set of point charges, called a Madelung potential, is often used. 

Another variant that may mrn out to be the method of choice performs the alchemical free energy simulation with a spherical model surrounded by continuum solvent, neglecting portions of the macromolecule that lie outside the spherical region. The reaction field due to the outer continuum is easily included, because the model is spherical. Additional steps are used to change the dielectric constant of that portion of the macromolecule that lies in the outer region from its usual low value to the bulk solvent value (before the alchemical simulation) and back to its usual low value (after the alchemical simulation) the free energy for these steps can be obtained from continuum electrostatics [58]. 

The main peculiarity of solutions of reversed micelles is their ability to solubilize a wide class of ionic, polar, apolar, and amphiphilic substances. This is because in these systems a multiplicity of domains coexist apolar bulk solvent, the oriented alkyl chains of the surfactant, and the hydrophilic head group region of the reversed micelles. Ionic and polar substances are hosted in the micellar core, apolar substances are solubilized in the bulk apolar solvent, whereas amphiphilic substances are partitioned between the bulk apolar solvent and the domain comprising the alkyl chains and the surfactant polar heads, i.e., the so-called palisade layer [24],... 

The solubility-diffusion theory assumes that solute partitioning from water into and diffusion through the membrane lipid region resembles that which would occur within a homogeneous bulk solvent. Thus, the permeability coefficient, P, can be expressed as... 

Geometry-based approach from a geometrical point of view, a cavity is a concave empty space that can be described using 2D (surface) or 3D shape descriptors (19-21). We consider three regions in the protein environment the protein bulk, the bulk solvent and the cavity space. The protein bulk is the space filled by the protein atoms. The bulk solvent is the space outside the protein which differentiates from the space inside the protein which defines the cavity where the drug-like molecule is supposed to bind. The identification of protein pockets by numerical methods suppose the capacity to discriminate first the protein bulk from the rest... 

A Primary solvation shell B Secondary solvation shell C Disordered region D Bulk solvent... 

Some enzymes are parts of multienzyme complexes in which reactants are channeled from one enzyme to another without ever entering the bulk solvent. Diffusion is hindered in the gel-like cytosol, and the cytosolic composition varies in different regions of the cell. In short, a given molecule may function quite differently in the cell than in vitro. A central challenge of biochemistry is to understand the influences of cellular organization and macromolecular associations on the function of individual enzymes and other biomolecules—to understand function in vivo as well as in vitro. 

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