Clathrate structure of water

See also Hydrogen Bonds, Dielectric Constant, Covalent Bonds vs Non-Covalent Forces, Clathrate Structure of Water... 

The Hydrophobic Effect - interactions between hydrophobic regions of a protein, which actually increase entropy by destroying the ordered clathrate structures of water around these residues in the unfolded state. The hydrophobic effect is sometimes incorrectly called hydrophobic bonding. Table 6.4 shows numerical values assigned to the relative hydrophobicities of the amino acids. In Table 6.3, the hydrophobic effect can be seen by the more positive AS values for cytochrome c and myoglobin. 

See also Secondary Structure (General), Globular Proteins, Factors Determining Secondary and Tertiary Structure, Clathrate Structure of Water, Enthalpy, Entropy, Interplay of Enthalpy and Entropy... 

FIGURE 2.5 Formation of a clathrate structure by water molecules surrouudiug a hydrophobic solute. 

Thermal fluctuations cause a group of guest (CO2) molecules to be arranged in a configuration similar to that in the clathrate hydrate phase. The structure of water molecules around locally ordered guest molecules is perturbed compared to that in the bulk. The thermodynamic perturbation of the liquid phase is due to the finite temperature of the system. This process is stochastic. 

Fig. 17. Model of the clathrate structure of the water in clathrates I. The centre of the hole is occupied by hydrophobic guest molecules in gas-hydrates (model of the iceberg formation in aqueous solution )...

The structure of water and the ices have been a subject of intense research since the last century and the literature on the subject is voluminous [31, 32, 423]. It is surprising, however, that the classical work on the high-pressure ices and the clathrate hydrates has not been carried to more precise conclusions with regard to the hydrogen atom positions now that the experimental tools are more readily available to do so. 

Simulations of solutions have been used to study hydrophobic effects. Thus, Rossky andZicki (1994) found that hydration shells of methane and neon remain intact in mixed solvents this is understandable in terms of clathrate formation—an example of an unusual degree of disordering from the normal structure of water. 

Figure 20.2. Structure of water clathrates. When water molecules interact with non-water substances, water molecules form acage-like structure to surround them. Depending on the size of the substance, water molecules pack in different ways to solubilize or to form an interface with the materials.

Fig. 12.15. Clinographic projection showing the arrangement of some of the water molecules in the clathrate structure of chlorine hydrate, Cl2.7fH20.

Of particular interest is the effect of noble gases in biological systems. For example, xenon has an anesthetic effect. This is somewhat surprising in that the conditions present in biological systems are obviously not sufficiently severe to effect chemical combination of the noble gas (in the ordinary sense of that word). It has been proposed that the structure of water might be altered via a clathrate-type interaction. 

There are two ways to approach the hydration nature the thermodynamic and kinetic. The thermodynamic approach treats hydration as a reversible process of joining H O dipoles with the formation of peculiar aquatic complexes with a set coordination number. Such an approach is handy when studying the thermodynamics of chemical processes, in particular complex formation, and will be used in the sections dealing with these processes. The kinetic approach was introduced by O.Ya. Samoylov (1921-1980), who proposed a first model of clathrate type of water structure as early as 1946. 

CLATHRATE-LIKE STRUCTURE OF WATER AROUND SOME NONELECTROLYTES IN DILUTE SOLUTION AS REVEALED BY COMPUTER SIMULATION AND X-RAY DIFFRACTION STUDIES... 

ABSTRACT. An X-ray diffraction measurement has been carried out for a 3.9 mol% aqueous solution of TBA (tertiary butylalcohol) with an energy-dispersive diffractometer. Constant temperature molecular dynamics calculation has also been made for an aqueous solution model simulating the above-mentioned mixture. Both results suggest the formation of a fairly stable clathrate-like structure of water around TBA molecules. 

On the basis of such experimental evidence, it has been suggested that there should be the formation of clathrate-like structure of water around TBA and some other hydrophobic solutes in dilute solution. The purpose of the present study is to examine whether or not the structure of water in the solution is different from that of pure water and whether the difference, if any, can be accounted for by the clathrate-like structure. The internal structure of a liquid can be investigated both by diffraction measurements using X-ray or neutron radiation and... 

CLATHRATE-LIKE STRUCTURE OF WATER AROUND SOME NONELECTROLYTES... 

There are also large reservoirs of CH4 stored as methane clathrate methane hydrate), a crystalline ice-like structure of water and CH4 that can exist at high pressures and low temperatures, such as may occur in areas of permafrost and beneath certain ocean sediments. Figure 4.51 shows the stability diagram of methane clathrate. Approximately 2 X10 Tg CH4 are estimated to be stored as methane clathrate in the ocean floor (Archer et al., 2009). 

The clathrate cage model states that the structure of water is strengthened around a hydrophobic solute, thus causing a large unfavorable entropic effect. The surrounding water molecules adopt only a few orientations (low entropy) to avoid wasting hydrogen... 

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