Solvents Space filling” model

Figure 3. a) Space-filling model of the sucrose molecule with undersized oxygens and hydrogens to expose the carbon backbone, b) Space-filling model of the sucrose molecule (same orientation as in a) with van der Waals - sized atoms. RC = 1.6 A, RO = 1.4A, RH = 12 A. The carbon backbone is almost completely obscured by the oiQrgens and l drogens and thus shielded from the solvent molecules. 

Figure 4. A nine-molecule space-filling model of the (100) sucrose crystal. Atoms of one of the molecules are labeled. The sub-layer of the screw-axis related molecules is completely shielded from possible solvent effects.

Fig. 16 X-ray structure of (j tiiitaa)CrCl complex with a solvent molecule (Me2SO) bound to chromium (left), along with its space-filling model (right)...

Figure 1.4. Space-filling models of cyclosporin A. (a) Solid-state conformation (X-ray analysis) (b) computer-generated conformation in apolar solvents (NMR measurements).

Fig. 26 Crystallographic packing in PhBABI (left), including solvated voids (right, solvent hexane and benzene shown as space-filling models).

Fig. 4. (A) Space-filling model of the PapD chaperone. The solvent-exposed conserved...

Figure 11.3 Computer-generated space-filling model of a spherical micelle of dodecanale, which is in good agreement with low-angle neutronscattering measurements. Black head groups while hydrocarbon chains stippled terminal methyl groups. A substantial proportion of the outer surface is occupied by hydrocarbon groups in contact with the solvent.

Fig. 3.1. Visualization of a drug molecule N-(4-hydroxy-phenyl)-acetamide (Tylenol or acetaminophen) computerized with different levels of graphic representations. (A) Molecular structure of the drug Tylenol. (B) Ball-stick model showing atomic positions and types. (C) Ball-stick model with van der Waals dot surfaces. (D) Space-filled model showing van der Walls radii of the oxygen, nitrogen, and carbon atoms. (E) Solvent accessible surface model (solid) (solvent radius, 1.4A). (See black and white image.)...

The interior of the iPamino acid side chains, as shown in Figure 29. Solvent accessibility calculations show that water is excluded from the barrel center, although a large proportion of the rest of the barrel interior is exposed to solvent. When a space-filling model of the protein is sliced at 1 A intervals, it is evident that the density of amino acid residues in the interior of the barrel is that normally expected for the interior of proteins. 

A realistic model of a solution requires at least several hundred solvent molecules. To prevent the outer solvent molecules from boiling off into space, and minimizing surface effects, periodic boundary conditions are normally employed. The solvent molecules are placed in a suitable box, often (but not necessarily) having a cubic geometry (it has been shown that simulation results using any of the five types of space filling polyhedra are equivalent ). This box is then duplicated in all directions, i.e. the central box is suiTounded by 26 identical cubes, which again is surrounded by 98 boxes etc. If a... 

Fig. 4 Representative membrane-active peptides that have been studied by solid-state 19F-NMR. (a) The primary sequences show which positions were substituted (filled green boxes) or which ones could in principle be substituted (dotted green lines), (b) Characteristic conformations of the peptides in the membrane-bound state. The space-filling solvent-accessibility models emphasize the amphiphilicity by colouring hydrophobic residues in yellow and cationic side-chains in blue. (c) Observed structures and alignment states of the peptides as determined by 19F-NMR...

Estimation of ligand thickness. The simplest method consists in measuring the thickness s of the ligand layer on space-filling molecular models. When X-ray structures are available, the thickness may be obtained from crystal packing data. However, ligands often have regions of different thicknesses and contain crevasses in which solvent molecules may or may not penetrate. 

It is clear that such calculation are very approximate. Nevertheless they appear to provide reasonable s values as judged from comparison with measurements on space-filling molecular models. The procedure is best suited for ligands which completely embed the cation in a tridimensional cavity. In the case of complexes having regions where the cation is accessible to solvent molecules (e. g. complexes with macrocycles of type D in figure 2, which have open top and bottom sides) one may hope that the effect of a large s in one direction and a small s in another is taken... 

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