Solvation sphere structure

Three types of methods are used to study solvation in molecular solvents. These are primarily the methods commonly used in studying the structures of molecules. However, optical spectroscopy (IR and Raman) yields results that are difficult to interpret from the point of view of solvation and are thus not often used to measure solvation numbers. NMR is more successful, as the chemical shifts are chiefly affected by solvation. Measurement of solvation-dependent kinetic quantities is often used (<electrolytic mobility, diffusion coefficients, etc). These methods supply data on the region in the immediate vicinity of the ion, i.e. the primary solvation sphere, closely connected to the ion and moving together with it. By means of the third type of methods some static quantities entropy and compressibility as well as some non-thermodynamic quantities such as the dielectric constant) are measured. These methods also pertain to the secondary solvation-sphere, in which the solvent structure is affected by the presence of ions, but the... 

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. 

In the IPCM calculations, the molecule is contained inside a cavity within the polarizable continuum, the size of which is determined by a suitable computed isodensity surface. The size of this cavity corresponds to the molecular volume allowing a simple, yet effective evaluation of the molecular activation volume, which is not based on semi-empirical models, but also does not allow a direct comparison with experimental data as the second solvation sphere is almost completely absent. The volume difference between the precursor complex Be(H20)4(H20)]2+ and the transition structure [Be(H20)5]2+, viz., —4.5A3, represents the activation volume of the reaction. This value can be compared with the value of —6.1 A3 calculated for the corresponding water exchange reaction around Li+, for which we concluded the operation of a limiting associative mechanism. In the present case, both the nature of [Be(H20)5]2+ and the activation volume clearly indicate the operation of an associative interchange mechanism (156). 

But if we examine the localized near the donor or the acceptor crystal vibrations or intra-molecular vibrations, the electron transition may induce much larger changes in such modes. It may be the substantial shifts of the equilibrium positions, the frequencies, or at last, the change of the set of normal modes due to violation of the space structure of the centers. The local vibrations at electron transitions between the atomic centers in the polar medium are the oscillations of the rigid solvation spheres near the centers. Such vibrations are denoted by the inner-sphere vibrations in contrast to the outer-sphere vibrations of the medium. The expressions for the rate constant cited above are based on the smallness of the shift of the equilibrium position or the frequency in each mode (see Eqs. (11) and (13)). They may be useless for the case of local vibrations that are, as a rule, high-frequency ones. The general formal approach to the description of the electron transitions in such systems based on the method of density function was developed by Kubo and Toyozawa [7] within the bounds of the conception of the harmonic vibrations in the initial and final states. 

In this chapter, we present new results based on semi-empirical quantum calculations (PM3) that include solvation and charging effects simultaneously on the same model SFA.71 These calculations were carried out in HyperChem 5.0 (Hypercube, Inc.). Solvation was carried out with two approaches. In the first approach, the neutral, gas-phase SFA model was simulated, then this molecule was deprotonated at each of four carboxylic acid sites. Finally, a solvation sphere of H20 molecules was used to surround the anionic SFA and the structure obtained via molecular dynamics simulations and energy minimizations as an isolated nanodroplet. This approach has the advantage of allowing maximum flexibility of the model SFA. Larger model systems may require long simulation runs to sample all available conformations, but isolation of the SFA and water allows each component to move more freely. 

The two center structures show the complex that forms between iV,iV -bis(2-phenylethyl)-4,13-diaza-18-crown-6 and KI <2000PNAS6271>. The K+ ion is bound in the center of the macroring, as expected for any 18-crown-6 macrocycle. The twin sidearms of the bibracchial lariat ether turn inward in this complex and the arenes serve as apical donors. The top center structure shows the symmetrically bound cation and illustrates that the iodide anion is excluded from the cation s solvation sphere. The bottom center structure shows the superimposition of the two benzene rings upon each other and upon the K+ ion. Note in the bottom center structure that the iodide anion is not illustrated. The ideal sandwich of arene-cation-arene confirms the cation-pi interaction between benzene and K+. 

Type 1 or blue copper (TICu) proteins comprise a rich case where the effects of electronic OSC, structural OSC, and the solvation sphere have all been explored. 

Ions and charged surfaces can break down the ice slurry structure of water. The electric charges are stronger than dipole forces and tend to pull water molecules away from their groups by attracting the positive or negative ends of the water dipoles. Solutes and water molecules are constantly in motion, but they remain in the vicinity of each other for some period of time. If water molecules remain near an ion longer than the time required for the water molecules to dissociate from the water structure, the ion will have a sphere of water molecules (a solvation sphere or sheath) around itself. The number of water molecules in the closest solvation sphere is called the primary hydration number. 

Outside of the primary solvation sphere is a second sphere of water molecules also affected by the ion s charge. These water molecules have also been tom away from their water structure to some extent, but are not so closely associated with the ion. The orientation of water molecules in the primary solvation sphere and the more random orientation of water molecules in the secondary sphere essentially dissipate... 

A spectroscopic study of Eu -Br showed that the increase in the Br concentration causes a larger enhancement in the intensity and band area of the -> transitions than for the Fj -> transitions. These modifications in the spectra were attributed to changes in the structure and nature of the inner solvation sphere of Eu in the excited state as compared to that of the ground state (Marcantonatos et al. 1984). The differences in intensity between absorption and emission bands would, therefore, reflect formation of inner-sphere complexes by Br in the excited state while outer-sphere complexation would dominate the ground state. It was proposed (Marcantonatos et al. 1981, 1982) that excitation of Eu " ion to the state would result in an expansion of the 4f and a shrinkage of the 5p orbitals with an overall decrease in the metal ion radius. The consequent contraction of the iimer shell would be expected to produce more compact and less easily disrupted outer hydration spheres for both ( Dj) Eu(H20)g and ( Di)Eu(H20)g with a possible increase in kobs-... 

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