Surface, solvent-exposed

In polar solvents, the structure of the acridine 13 involves some zwitterionic character 13 a [Eq. (7)] and the interior of the cleft becomes an intensely polar microenvironment. On the periphery of the molecule a heavy lipophilic coating is provided by the hydrocarbon skeleton and methyl groups. A third domain, the large, flat aromatic surface is exposed by the acridine spacer unit. This unusual combination of ionic, hydrophobic and stacking opportunities endows these molecules with the ability to interact with the zwitterionic forms of amino acids which exist at neutral pH 24). For example, the acridine diacids can extract zwitterionic phenylalanine from water into chloroform, andNMR evidence indicates the formation of 2 1 complexes 39 such as were previously described for other P-phenyl-ethylammonium salts. Similar behavior is seen with tryptophan 40 and tyrosine methyl ether 41. The structures lacking well-placed aromatics such as leucine or methionine are not extracted to measureable degrees under these conditions. 

These researchers also described [93] the design and synthesis of iron(II) porphyrin dendrimers with triethylene glycol monomethyl, ether surface groups (e.g., 31) which render them soluble in a wide range of organic solvents and water. The potential difference between the first (1 FeCl) and second generation (2 FeCl) Fe-porphryin dendrimers was found to increase more in water than in dichloromethane (0.42 vs 0.08 V). This remarkable potential difference between 2 FeCl and 1 FeCl in water was comparable with that found between cytochrome c and a similarly ligated, more solvent-exposed cytochrome c heme model compound. 

SPT provides a conceptual basis relating the nonpolar free energy contribution to the solvent-exposed surface area. An attractive approximation is to ignore curvature effects and write... 

However, just considering the individual properties of each amino acid type is not enough to determine its accessibility to the surrounding aqueous environment. There have been many attempts at developing analytical models with predictive value for determining buried or surface accessible amino acids in a folded polypeptide chain. These studies have concluded fractional assignments for each residue that relate to its accessible surface area (ASA) or its solvent exposed area (SEA). 

Figure 1.21 Comparison of the solvent exposed surface area of amino acids in proteins. Data are plotted as a percentage of each amino acid in a protein having greater than a 30 A2 exposure to the aqueous environment. Charged and polar amino acids are seen to have the most solvent exposure, while uncharged, aromatic, or aliphatic amino acids have the least exposure.

Reduction of particle size increases the total specific surface area exposed to the solvent, allowing a greater number of particles to dissolve more rapidly. Furthermore, smaller particles have a small diffusion boundary layer, allowing faster transport of dissolved material from the particle surface [58]. These effects become extremely important when dealing with poorly water-soluble drugs, where dissolution is the rate-limiting step in absorption. There are numerous examples where reduction of particle size in such drugs leads to a faster dissolution rate [59-61], In some cases, these in vitro results have been shown to correlate with improved absorption in vivo [62-64]. 

Another property specific to /l-solenoids is the existence of a well-defined boundary between the interior side chains that form the hydrophobic core and the side chains at solvent-exposed surfaces. This boundary is formed by a tighdy packed layer of H-bonded polypeptide backbones wrapping around the hydrophobic core. 

We have to take into account these effects when the dyes are located in structurally inhomogeneous environments, for instance, in the core and on the surface of a nanoparticle. If their core is low-polar and the surface is exposed to an aqueous solvent, we will observe that the energy flow is directed to the dyes located at the surface. It is because their absorption and emission spectra are shifted to the red due to the fact that they are more efficient as FRET acceptors. 

Structural and energetic properties of studied molecules strongly depend on the solvent membrane-mimetic media significantly promote formation of a-helices capable of traversing the bilayer, whereas a polar environment destabilizes a-helical conformation via reduction of solvent-exposed surface area and packing. 

Given the somewhat ad hoc nature of most specific schemes for evaluating the non-electrostatic components of the solvation free energy, a reliance on a simpler, if somewhat more empirical, scheme has become widely accepted within available continuum models. In essence, the more empirical approach assumes that the free energy associated with the non-electrostatic solvation of any atom will be characteristic for that atom (or group) and proportional to its solvent-exposed surface area. Thus, the molecular Geos may be computed simply as... 

In both subunits the RNA molecules form the internal core. Proteins are largely found on the solvent-exposed surfaces. Some of them form the stalk and other features.17 They often have globular domains with extended tails that interact with the ribosomal RNA. 

The magnitude of the classical hydrophobic effect is proportional to the amount of hydrophobic surface area buried on formation of the hydrophobic interaction, A A hp (Chapter 11). Changes in energy on mutation of Ala — Gly in the solvent exposed surfaces of a helixes are proportional to AAHP, and so these energetics are presumably driven by hydrophobicity.34,35 On the other hand, the correlation of energy changes in the core with packing density indicates that the interactions are dominated by the van der Waals term, because van der Waals interactions are... 

The complex with ADP and aluminium fluoride is thought to resemble the early ADP.Pi state immediately after hydrolysis, whereas the complex with ADP and vanadate may represent a late state in which the phosphate (mimicked by vanadate) has moved quite a long distance (15 A) from the active center to the surface of the motor domain. There it is fixed by two hydrogen bonds to the solvent exposed tips of the switch-1 loop region (L9) at one side and the switch-2 loop (Lll) at the other side. 

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