Solvent-accessible area

The football-shaped hexamer is made up of two identical trimers. The two NCI trimers are related by a two-fold noncrystallographic symmetry axis lying in the equatorial plane and perpendicular to the pseudo-three-fold axis (Figure 20). The interface, which covers about 4400 A of solvent-accessible area per trimer, is formed by the nearly flat surfaces of the two trimers. The polar (45.5%) and nonpolar atoms (54.5%) in the interface are in almost equal proportions, underscoring the importance of both types of interactions in the hexamer stabilization. ... 

Planet offers a 2-D representation (similar to that used in LIGPLOT [36]) of the protein-ligand interaction called a PLAID (Protein-Ligand Accessibility and Interaction Diagram, Figure 10.3). It is automatically calculated from the PDB data and shows van der Waals interactions, hydrogen bonds and solvent accessible areas. The interaction can be also viewed in 3 D or as the original PDB entry. 

The surface traced out by the center of a solvent probe molecule as it is rolled over the surface of a protein whose three-dimensional structure has been determined at the atomic level. Solvent-accessible surface areas can be calculated by various computer algorithms, and differences in solvent-accessible areas can be used to characterize the energetics of surface hydration as a function of changes in protein conformation, oligomerization, and complexation. 

Calculation of Crystal Habit and Solvent-Accessible Areas of Sucrose and Adipic Acid... 

The ciystal habit of sucrose and adipic add crystals were calculated from their intern structure and from the attachment energies of the various crystal faces. As a first attempt to indude the role of the solvent on the crystal habit, the solvent accessible areas of the faces of sucrose and adipic add and were calculated for spherical solvent probes of difierent sizes. In the sucrose system the results show that this type of calculation can qualitatively account for differences in solvent (water) adsorption hence fast growing and slow growing faces. In the adipic add system results show the presence of solvent sized receptacles that might enhance solvent interadions on various fares. The quantitative use of this type of data in crystal shape calculations could prove to be a reasonable method for incorporation of solvent effeds on calculated crystal shapes. 

It is the purpose of this work to employ calculations of the solvent accessible area (SAA) of sucrose and adipic acid crystals as a first attempt to quantify the effect of solvent on the crystal morphology. 

Figure 5. The relative solvent accessible areas (SAA) of the five most common faces on the sucrose crystal. Solvent radius 0 A.

Figure 8. The solvent accessible areas (SAA) of five sucrose ciystal faces in angstroms per unit cell and their mesh areas (same units). Solvent radius 15 A.

Figure 10. Solvent accessible area of three faces of Adipic acid solvent radius 1.5 A.

Fig. 5. Various parameters of accessibility, twist, and bend plotted vs. sequence number. Part 1 (a) Solvent-accessible area of side chains, (b) Fractional accessibility (referred to full sphere) of backbone carbonyl oxygen and peptide nitrogen. The separate plot for values less than 1% is meant to show that no accessibility was detected for many atoms. The actual nonzero values are not to be taken too literally. Part 2 (c) Backbone angles as normally defined, (d) Angles between sequentially adjacent carbonyl vectors in the backbone plotted between the sequence numbers of the two residues involved. Part 3 (e) Distance in A between the tips, T, of adjacent residues as defined in the text, (f) Distances in A between peptide center, M, and the third sequential peptide center (open circles), and between carbon a and the sixth sequential a-carbon (crosses) plotted opposite the central carbon atom in each case, (g) Angles between lines joining the centers of successive peptide bonds plotted between the residues defining the central bond, (h) Angles between lines joining successive a carbons plotted opposite the central carbon, (Note that the accessibilities were calculated with coordinate set 4 and the other parameters with set 6 see text.)...

Fig. 41 Energy-minimized structure of the complex between a trisphosphonate salt and its analogous triammonium salt showing (from left to right) the Lewis structure, a front view of the CPK model and the solvent-accessible area around the complex with an internal cavity. Reprinted with permission from [119]. Copyright 2002 American Chemical Society...

It is a hydrogen-bonding descriptor based on solvent-accessible area of hydrogen-bond donor atoms and corresponding partial charges proposed as variant of FHDCA index [Katritzky et al, 1996b] ... 

The coefficients D0 and Di are determined from experimental solvation free energies of linear hydrocarbons. The solvent accessible area is the area formed from overlapping spheres centered at the atom positions with radii equal to vdW radii increased by a probe radius. This surface area definition is usually used in Eq. (35). Depending on the set of vdW radii used and the probe radii (usually 1.4 A), the coefficients D0 and Di are approximately equal to 0.85 kcal/mol and 0.005 kcal/mol/A2, respectively. 

Apart from methods based on continuum approaches, methods based on the division of the total solvation energy by atom or group contributions that are independent from each other are quite popular. The solvation free energy in these methods is computed as a sum of products of an empirical constant depending on the nature of atom or group (wy), and a solvent accessible area of this atom or group (Si) ... 

Conformationally averaged surface descriptors, such as solvent-accessible areas, provide a realistic descriptor of the space spanned by a flexible molecule or a weakly bound complex. Simulations indicate correlations between the stability of a diastereomeric complex and its accessible dynamic... 

In addition, calculations of the void volumes of pure a-crystals indicate no solvent accessible areas. These calculations axe carried out with the program Platon [58], using a 1.2 A probe to scan the van der Waals surface of the polymer. The used van der Waals radii for C, N and O are 1.70A, 1.55 A and 1.52A respectively. Since no solvent accessible areas were found and no shift (within the experimental error) of the WAXD peak (200) was observed, we conclude that no water is located inside the crystallites of the Q-form. 

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