Atoms, overlaid positions

Figure 4 Overlaid positions of Mn, B, and H atoms from the crystal structures of 28-30. Adapted with permission from J. Am. Chem. Soc. 122 (2000) 9435-9443. Copyright (2000) American Chemical Society.

The density is a maximum in all directions perpendicular to the bond path at the position of a bond CP, and it thus serves as the terminus for an infinite set of trajectories, as illustrated by arrows for the pair of such trajectories that lie in the symmetry plane shown in Fig. 7.2. The set of trajectories that terminate at a bond-critical point define the interatomic surface that separates the basins of the neighboring atoms. Because the surface is defined by trajectories of Vp that terminate at a point, and because trajectories never cross, an interatomic surface is endowed with the property of zero-flux - a surface that is not crossed by any trajectories of Vp, a property made clear in Fig. 7.2. The final set of diagrams in Fig. 7.1 depict contour maps of the electron density overlaid with trajectories that define the interatomic surfaces and the bond paths to obtain a display of the atomic boundaries and the molecular structure. 

A solvent-accessible surface of HRV14 (from the 61605 bound structure, dot surface) overlaid with WIN 61605 (ball and stick), 51711, 56826, and 56291 (a). The atoms closest to the toe pocket wall (top) for each compound are in approximately the same position, while the isoxazole ring (C ring) positions vary significantly. The atom closest to the toe pocket wall is quite different in (b), which compares WIN 61605 (ball and stick) to R61837 (tubes) and... 

Fig. 3a-c. Schematic representation of the three residues involved in the formation of the catalytic triad of chymotrypsin [82] with the pseudo-atom vectors (arrows) overlaid a the positions of real non-hydrogen atoms in the sidechains, residues b the S and E pseudo-atom positions with the associated distances between them (dotted lines) (for clarity the MM distances are not shown) c the search matrix for this grouping of sidechains, the distances, all of which are in A, being for the SS, SE, ES and EE distances respectively... 

Figure 10.9. A pharmacophore model for the active site of P450 2D6 (ref [527]). Inhibitors are overlaid to keep the nitrogen atoms (marked with arrow) in a fixed position.

Figure 23.15 Product images of HCL(v = 0, J = 1 and J = 5) from the reaction of Cl with n-butane. The Newton diagram for the reaction is overlaid on the image of the Cl atom reactant. CM indicates the position of the centre of mass, the vectors VcLj and Vrh represent the CL2 and RH molecular beam velocities respectively Vci and i/q are the velocities of the Cl atoms in the Laboratory and centre-of-mass frame respectively Hciis the velocity of the product HCl in the centre-of-mass frame and 6 is the scattering angle. Reproduced from Toomes and KitsopouLos, Phys. Chem. Chem. Phys., 2003, 5 2A81, with permission of the PCCP Owner Societies...

Thermal ellipsoids are indicative not only of the extent of atom or group motion but also of their directionality. These ellipsoids can be overlaid on the average positions of ions and of backbone atoms to promote an understanding of the extent and cooperativity of backbone—counterion motions. Figure 10 shows the motion of counterions around DNA successive locations of ions along the trajectory are connected, the initial ion positions are indicated by means of small spheres, and the average structure df DNA is displayed for... 

Figure 1 Relief and contour maps of the electron density for diborane in the plane of the terminal hydrogen atoms. The density value is arbitrarily terminated at the positions of the boron nuclei. The lower maps illustrate the trajectories traced out by Vp, the gradient vectors of the density. The contour map is overlaid with the trajectories of Vp associated with the bond cps that define the bond paths and the intersection of the interatomic surfaces with the plane of the diagram. (Reproduced with permission of the American Chemical Society from J. Am. Chern. Soc., 1979, 101, 1389)...

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