Hydrophobicity scales
The hydrogen bonds are partially reconstructed by building a water "cage" around the hexane molecule, similar to that in clathrate hydrates formed at lower temperatures.
This leads to significant losses in translational and rotational entropy of water molecules and makes the process unfavorable in terms of free energy of the system.
However, organic solvents are slightly miscible with water and the characteristics of both phases change making it difficult to obtain pure hydrophobicity scale.
[16][17] Fendler et al. measured the partitioning of 14 radiolabeled amino acids using sodium dodecyl sulfate (SDS) micelles.
Pliska and his coworkers[27] used thin layer chromatography to relate mobility values of free amino acids to their hydrophobicities.
These parameters include the silica surface area and pore diameter, the choice and pH of aqueous buffer, temperature and the bonding density of stationary phase chains.
In his detailed site-directed mutagenesis studies, Utani and his coworkers substituted 19 amino acids at Trp49 of the tryptophan synthase and he measured the free energy of unfolding.
The main disadvantage of site-directed mutagenesis method is that not all the 20 naturally occurring amino acids can substitute a single residue in a protein.
The most popular hydrophobicity scale was developed by measuring surface tension values for the naturally occurring 20 amino acids in NaCl solution.
[30] The main drawbacks of surface tension measurements is that the broken hydrogen bonds and the neutralized charged groups remain at the solution air interface.
[34] The hydropathy plot constructed using ΔGwoct − ΔGwif shows favorable peaks on the absolute scale that correspond to the known TM helices.
[35][36][37][38] Most of the existing hydrophobicity scales are derived from the properties of amino acids in their free forms or as a part of a short peptide.
This quantitative descriptor for microenvironment was derived from the octanol-water partition coefficient, (known as Rekker's Fragmental Constants) widely used for pharmacophores.
[9] In the field of engineering, the hydrophobicity (or dewetting ability) of a flat surface (e.g., a counter top in kitchen or a cooking pan) can be measured by the contact angle of water droplet.
A University of Nebraska-Lincoln team recently devised a computational approach that can relate the molecular hydrophobicity scale of amino-acid chains to the contact angle of water nanodroplet.
[39] The team constructed planar networks composed of unified amino-acid side chains with native structure of the beta-sheet protein.
Using molecular dynamics simulation, the team is able to measure the contact angle of water nanodroplet on the planar networks (caHydrophobicity).
On the other hand, previous studies show that the minimum of excess chemical potential of a hard-sphere solute with respect to that in the bulk exhibits a linear dependence on cosine value of contact angle.
[40] Based on the computed excess chemical potentials of the purely repulsive methane-sized Weeks–Chandler–Andersen solute with respect to that in the bulk, the extrapolated values of cosine value of contact angle are calculated(ccHydrophobicity), which can be used to quantify the hydrophobicity of amino acid side chains with complete wetting behaviors.
