Physical chemistry

Adsorption is accumulation of a substance at an interface. Binding a solute to a packing surface can delay its passage through a chromatography column. Ideal size-exclusion chromatography separates through SEC pore access without such binding; extra retention from adsorption requires a different interpretation.

Chemical polarity concerns unequal distribution of electron density in a chemical bond or molecule. A polar molecule has a permanent electric dipole moment; the effects of individual bonds must be combined with their spatial arrangement. In a symmetric linear carbon dioxide molecule, opposing bond-dipole contributions cancel. In water, its bent molecular geometry prevents that cancellation, giving a permanent electric dipole moment.^[ref]

A polar molecule has a nonzero permanent electric dipole moment because of its internal electric charge distribution. It can still have zero total electric charge. Water is polar; a nonpolar molecule has no permanent electric dipole moment.

A nonpolar molecule has no permanent electric dipole moment. This distinguishes its charge distribution from the separated partial charges of a polar molecule.

Hydrophilicity describes affinity for water. Regions with chemical polarity or electric charge can interact favorably with water, including through hydrogen bonds where suitable groups are present. Hydrophilic regions of membrane-forming phospholipids face the water on either side of a lipid bilayer. Such affinity does not mean forming covalent bonds with every neighboring substance, nor does it require a net negative electric charge. See Alberts et al.: the chemical components of a cell.

An amphiphile is a molecule containing distinct hydrophilic and hydrophobic regions. Amphiphilic and amphipathic describe this combination. Membrane-forming phospholipids are examples; their two regions give different parts of one molecule different affinities for water. The word describes a structure, not a guarantee of a particular aggregate shape. See IUPAC Gold Book: amphiphilic.

Hydrophobicity describes unfavorable mixing with water, as illustrated by long hydrocarbon regions. The hydrophobic regions of membrane-forming phospholipids face the interior of a lipid bilayer. This organization is explained by the hydrophobic effect, rather than by imagining that chains actively repel water. See IUPAC Gold Book: hydrophobic interaction.

The hydrophobic effect is the solvent-mediated tendency of nonpolar regions to associate in water. Exposing a hydrocarbon region changes how surrounding water molecules can arrange and interact; reducing that exposure can lower the total free energy. Both water and lipids enter the accounting. The effect is not an additional covalent bond between chains. See IUPAC Gold Book: hydrophobic interaction.

At fixed temperature and pressure, compare two candidate organizations by the change in Gibbs free energy, $\Delta G=\Delta H-T\Delta S$, where $H$ is enthalpy, $T$ is absolute temperature, and $S$ is entropy. An organization with lower $G$ is favored in this comparison. Reducing exposed hydrocarbon area is one contribution; changes in chain packing and the entropy of the lipids also matter. This explains why hydrophobicity alone cannot predict every aggregate shape. See 16.4 Free Energy.

Absorbance is the dimensionless quantity $A={\log }_{10}(P_0/P)$, where $P_0$ and $P$ are reference and transmitted radiant powers at the chosen wavelength. For example, $A=1$ means one tenth of the reference power is transmitted. Under the Beer-Lambert law, absorbance can determine an absorbing species' concentration; attenuation by cloudiness or unrelated colored solutes needs separate controls. ^[ref]

The Beer-Lambert law relates absorbance $A$ to an absorbing species' concentration $c$ and path length $l$ by $A=\epsilon lc$ in a homogeneous medium using sufficiently narrow-band light. The coefficient $\epsilon$ depends on the species, wavelength and chemical solution conditions. This makes Ellman's reagent useful for quantitative thiol assays once its released colored species has been calibrated. ^[ref]