Explicit water molecules

A til Stan cc-dcpM don 1 diolacLric con sLtiii L is com in on ly used to mimic ihe effect of solvent in moleciiltir mechanics ctilciikilioiis, in the absence ol explicit water molecules. 

In this model of electrostatic interactions, two atoms (i and j) have point charges q and qj. The magnitude of the electrostatic energy (Veel) varies inversely with the distance between the atoms, Ry. The effective dielectric constant is 8. For in vacuo simulations or simulations with explicit water molecules, the denominator equals eRij. In some force fields, a distance-dependent dielectric, where the denominator is eRy Rjj, represents solvent implicitly. 

A distance-dependent dielectric constant is commonly used to mimic the effect of solvent in molecular mechanics calculations, in the absence of explicit water molecules. 

There are cases in which one is interested in the motion of a biomolecule but wishes also to study the effect of different solvent environments on this motion. In other cases, one may be interested in studying the motion of one part of the protein (e.g., a side chain or a loop) as moving in a solvent bath provided by the remainder of the protein. One way to deal with these issues is, of course, to explicitly include all the additional components in the simulation (explicit water molecules, the whole protein, etc.). This solution is computationally very expensive, because much work is done on parts of the system that are of no direct interest to the study. 

Figure 1 Schematic representation of an atomic model of a biomolecular solute surrounded by explicit water molecules.

Consider an alchemical transformation of a particle in water, where the particle s charge is changed from 0 to i) (e.g., neon sodium q = ). Let the transformation be performed first with the particle in a spherical water droplet of radius R (formed of explicit water molecules), and let the droplet then be transferred into bulk continuum water. From dielectric continuum theory, the transfer free energy is just the Born free energy to transfer a spherical ion of charge q and radius R into a continuum with the dielectric constant e of water ... 

The idea of a finite simulation model subsequently transferred into bulk solvent can be applied to a macromolecule, as shown in Figure 5a. The alchemical transformation is introduced with a molecular dynamics or Monte Carlo simulation for the macromolecule, which is solvated by a limited number of explicit water molecules and otherwise surrounded by vacuum. Then the finite model is transferred into a bulk solvent continuum... 

Basis Set Choice The most relevant geometrical parameters of several stationary points, with and without an explicit water molecule, located using several... 

The effect of solvation on uracil and thymine photophysics has been studied by Gustavvson and coworkers, who have studied uracil with four explicit water molecules and PCM to study distorted geometries [92,93,149], The conical intersection connecting Si to the ground state that was found in the gas phase is also present in solution. The barrier connecting the Si minimum to the conical intersection is lower in solution, however, causing much shorter lifetimes. So the nanosecond lifetime which is observed in the gas phase is not observed in solution but a picosecond lifetime is observed. 

The introduction of the external potential Vex, in Equation 4 is designed to mimic the effect of the surrounding (implicit) bulk solvent on the system by restricting the movement of any explicit water molecules.49 Thus, Vex[ is interpreted as arising from the force exerted on the explicit atoms by the implicit surrounding bulk solvent. This restraining potential has the simple harmonic form,49... 

The elucidation of actinide chemistry in solution is important for understanding actinide separation and for predicting actinide transport in the environment, particularly with respect to the safety of nuclear waste disposal.72,73 The uranyl CO + ion, for example, has received considerable interest because of its importance for environmental issues and its role as a computational benchmark system for higher actinides. Direct structural information on the coordination of uranyl in aqueous solution has been obtained mainly by extended X-ray absorption fine structure (EXAFS) measurements,74-76 whereas X-ray scattering studies of uranium and actinide solutions are more rare.77 Various ab initio studies of uranyl and related molecules, with a polarizable continuum model to mimic the solvent environment and/or a number of explicit water molecules, have been performed.78-82 We have performed a structural investigation of the carbonate system of dioxouranyl (VI) and (V), [U02(C03)3]4- and [U02(C03)3]5- in water.83 This study showed that only minor geometrical rearrangements occur upon the one-electron reduction of [U02(C03)3]4- to [U02(C03)3]5-, which supports the reversibility of this reduction. 

We have also studied the coordination of the monocarbonate, bicarbonate, and tricarbonate complexes of neptunyl in water, by using both explicit water molecules and a continuum solvent model.84 The monocarbonate complex was shown to have a pentacoordinated structure, with three water molecules in the first coordination shell, and the bicarbonate complex has a hexacoordinated structure, with two water molecules in the first coordination shell. Overall good agreement with experimental results was obtained. 

Fig. 3. Thermodynamic cycle used to analyse relative binding of ligands Sj and S2 to an enzyme, E. Each state is solvated by a box of explicit water molecules.

Mancera, R. L. (2002) De novo ligand design with explicit water molecules an application to bacterial neuraminidase. J. Comput. Aided Mol. Des. 16,479-499. 

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