Electrostatic interactions hydrogen bonds

As we have just seen, the initial encounter complex between an enzyme and its substrate is characterized by a reversible equilibrium between the binary complex and the free forms of enzyme and substrate. Hence the binary complex is stabilized through a variety of noncovalent interactions between the substrate and enzyme molecules. Likewise the majority of pharmacologically relevant enzyme inhibitors, which we will encounter in subsequent chapters, bind to their enzyme targets through a combination of noncovalent interactions. Some of the more important of these noncovalent forces for interactions between proteins (e.g., enzymes) and ligands (e.g., substrates, cofactors, and reversible inhibitors) include electrostatic interactions, hydrogen bonds, hydrophobic forces, and van der Waals forces (Copeland, 2000). 

One of the most popular applications of molecular rotors is the quantitative determination of solvent viscosity (for some examples, see references [18, 23-27] and Sect. 5). Viscosity refers to a bulk property, but molecular rotors change their behavior under the influence of the solvent on the molecular scale. Most commonly, the diffusivity of a fluorophore is related to bulk viscosity through the Debye-Stokes-Einstein relationship where the diffusion constant D is inversely proportional to bulk viscosity rj. Established techniques such as fluorescent recovery after photobleaching (FRAP) and fluorescence anisotropy build on the diffusivity of a fluorophore. However, the relationship between diffusivity on a molecular scale and bulk viscosity is always an approximation, because it does not consider molecular-scale effects such as size differences between fluorophore and solvent, electrostatic interactions, hydrogen bond formation, or a possible anisotropy of the environment. Nonetheless, approaches exist to resolve this conflict between bulk viscosity and apparent microviscosity at the molecular scale. Forster and Hoffmann examined some triphenylamine dyes with TICT characteristics. These dyes are characterized by radiationless relaxation from the TICT state. Forster and Hoffmann found a power-law relationship between quantum yield and solvent viscosity both analytically and experimentally [28]. For a quantitative derivation of the power-law relationship, Forster and Hoffmann define the solvent s microfriction k by applying the Debye-Stokes-Einstein diffusion model (2)... 

It is possible that the interaction between apo(a) and apo-Bl00 involves more than a simple covalent disulfide bond, such as electrostatic interactions, hydrogen bonds, and van der Waals interactions between specific amino acids and kringle-ligand complex forms (F9, G29). 

Many pharmaceutical preparations contain multiple components with a wide array of physico-chemical properties. Although CZE is a very effective means of separation for ionic species, an additional selectivity factor is required to discriminate neutral analytes in CE. Terabe first introduced the concept of micellar electrokinetic capillary chromatography (MEKC) in which ionic surfactants were included in the running buffer at a concentration above the critical micelle concentration (CMC) [17], Micelles, which have hydrophobic interiors and anionic exteriors, serve as a pseudostation-ary phase, which is pumped electrophoretically. Separations are based on the differential association of analytes with the micelle. Interactions between the analyte and micelles may be due to any one or a combination of the following electrostatic interactions, hydrogen bonding, and/or hydro-phobic interactions. The applicability of MEKC is limited in some cases to small molecules and peptides due to the physical size of macromolecules... 

The photoinduced electron transfer (PET) is especially important in the case of large or giant molecules (supermolecules), ie systems made up of molecular components in the same way as molecules are made up of atoms [11-19], As the systems are made up of a number of discrete components held together by different but not always exactly specified forces (covalent bonds, electrostatic interactions, hydrogen bonds, or other intermolecular interactions), the photoinduced electron transfer or energy transfer in these systems may be formally treated as intermolecular [20],... 

Specific interactions between the template and the substrate which have been described include covalent bonds, ligand-metal binding complexation, electrostatic interactions, hydrogen bonds, charge-transfer- and hydrophilic interactions. The most selective sites were obtained by means of ionic interactions, covalent- and hydrogen bonds [444,486]. 

Fig. 7. Schematic diagram of the contributions of various types of interactions to the free energy of the native conformations of a hypothetical protein or a DNA molecule in aqueous solution. Fs, Fb, Fi/b, and Fm represent the free energy contributions of conformational entropy, electrostatic interactions, hydrogen bonding, and hydrophobic interactions, respectively. The magnitude oi Fg may vary considerably with the pH and ionic strength of the aqueous solution.

Figure 2-11. Interactions between amino acid residues in a polypeptide chain. Electrostatic interactions hydrogen bonds hydrophobic interactions disulfide bonds.

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