Hydrophobic effect separation from other effects

Because of the complex nature of most biological samples, a single fractionation technique may not be adequate for the separation of the wide range of molecules present. Better resolution of some molecules is obtainal when properties other than differences in size are exploited. These include differences in ionic characteristics, affinity for other molecules and hydrophobicity. In separations that involve any one or more of these properties, the sample constituents interact with the column material and are then eluted with a suitable eluant. As a consequence of this interaction, and the use of eluants, whose properties may not closely resemble those of the medium found in vivo, the metal may dissociate from the ligand. In addition, as the complexity of the sample increases it is difficult to predict the behaviour of the various constituents. Undesirable effects leading to irreversible interaction between some molecules in the sample and the column packing material, degradation and decomposition of some constituents may result. Furthermore, it may be difficult to rid the column of certain trace metal contamination. 

With the hydrophobic effect defined as the contribution to the thermodynamics that is proportional to the exposure of apolar surface area, it is then possible for a set of homologous compounds to separate the hydrophobic contribution from all other effects by plotting any thermodynamic function (for instance, AH0) versus the number of apolar hydrogens (or the apolar surface area) that become exposed to the solvent on transfer. To the extent that the other interactions make a constant contribution to the thermodynamics,... 

The maintenance of tertiary and quartemary structure of polypeptides and proteins, as well as their mechanisms of association with other cellular components, is known to be, in part, mediated by hydrophobic interactions. In fact, the most important single factor in the organization of the constituent molecules of living matter into complex structural entities and the subsequent transmission of the encoded information from one structure to another is probably the hydrophobic effect. Consequently, it is not surprising that separative methods should have been developed which exploit this phenomenon. 

None of these five categories of noncovalent forces can be completely separated out from all of the others. Van der Waals interactions continue to play a part in each of the other four phenomena. Hydrogen bonds can be considered as a special case of ionic interactions, and the hydrophobic effect tends to reflect hydrogen bonding in the solvent. Therefore, it is informative to discuss each of these categories separately so as to focus on their unique properties. 

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