Electron density bond path

Figure 9.4 Electron density gradient paths in a plane containing the atoms of the HCN molecule. The solid lines are the intersections of the zero-flux surfaces with the plane. The large black dots are the bond critical points...

Type II trajectories start at a point p in the internuclear region between two bonded atoms and end at one of the two nuclei in question. There are just two trajectories per bond, which together define a path of maximum electron density (MED path) that is visible in the perspective drawing of p r) shown in Figure 9. Each lateral displacement from the MED path leads to a decrease of p(r). The point p corresponds to the minimum of p(r) along the path and to a saddle point of p(r) in three dimensions. 

Vector quantities, such as a magnetic field or the gradient of electron density, can be plotted as a series of arrows. Another technique is to create an animation showing how the path is followed by a hypothetical test particle. A third technique is to show flow lines, which are the path of steepest descent starting from one point. The flow lines from the bond critical points are used to partition regions of the molecule in the AIM population analysis scheme. 

Pd(II) compounds coordinate to alkenes to form rr-complexes. Roughly, a decrease in the electron density of alkenes by coordination to electrophilic Pd(II) permits attack by various nucleophiles on the coordinated alkenes. In contrast, electrophilic attack is commonly observed with uncomplexed alkenes. The attack of nucleophiles with concomitant formation of a carbon-palladium r-bond 1 is called the palladation of alkenes. This reaction is similar to the mercuration reaction. However, unlike the mercuration products, which are stable and isolable, the product 1 of the palladation is usually unstable and undergoes rapid decomposition. The palladation reaction is followed by two reactions. The elimination of H—Pd—Cl from 1 to form vinyl compounds 2 is one reaction path, resulting in nucleophilic substitution of the olefinic proton. When the displacement of the Pd in 1 with another nucleophile takes place, the nucleophilic addition of alkenes occurs to give 3. Depending on the reactants and conditions, either nucleophilic substitution of alkenes or nucleophilic addition to alkenes takes place. 

Fig. 1.32. (a) Molecular graphs and electron density contours for pentane and hexane. Dots on bond paths represent critical points, (b) Comparison of molecular graphs for bicycloalkanes and corresponding propellanes. (Reproduced from Chem. Rev. 91 893 (1991) with permission of the American Chemical Society.)... 

Figure 6.13 Relief map of the electron density for methanal (formaldehyde) in the molecular plane. There is a bond critical point between the carbon and the oxygen nuclei, as well as between the carbon nucleus and each hydrogen nucleus. No gradient path or bond critical point can be seen between the two hydrogen nuclei because there is no point at which the gradient of the electron density vanishes. There is no bond between the hydrogen atoms consistent with the conventional picture of the bonding in this molecule.

The many higher boranes such as B5H9 and BgH 2 are similarly electron deficient and cannot be described by a single Lewis structure. They can often be described in terms of a combination of two- and three-center bonds. Alternatively, their structures can be rationalized by electron-counting schemes such as those proposed by Wade. Analysis of the electron density of these molecules by the AIM method shows that there are bond paths between all adjacent pairs of atoms. So from the point of view of the AIM theory there are bonds between each adjacent pair of atoms, but these cannot all be regarded as Lewis two-center, two-electron bonds as is the case in B2H6. 

Figure 2. Contour maps of the electron density of (a) SCI2 and (b) H2O. The density increases from the outermost 0.001 au isodensily contour in steps of 2 x 10", 4 x 10", and 8 x 10" au with n starting at 3 and increasing in steps of unity. The lines connecting the nuclei are the bond paths, and the lines delimiting each atom are the intersection of the respective interatomic surface with the plane of the drawing. The same values for the contours apply to subsequent contour plots in this paper.

Figure 14. Contour plot of the electron density of B2H6 in the plane of the bridging hydrogen. Each hydrogen is connected to the two boron atoms by a bond path to each. In contrast, the boron atoms do not share a bond path linking them to one another. (See legend to Fig. 2 for contour values.)...

Bond paths are observed between bonded atoms in a molecule and only between these atoms. They are usually consistent with the bonds as defined by the Lewis structure and by experiment. There are, however, differences. There is only a single bond path between atoms that are multiply bonded in a Lewis structure because the electron density is always a maximum along the internuclear axis even in a Lewis multiple bond. The value of pb does, however, increase with increasing Lewis bond order, as is shown by the values for ethane (0.249 au), ethene (0.356 au), and ethyne (0.427 au), which indicate, as expected, an increasing amount of electron density in the bonding region. 

Fig. 7.1 The electron density p(t) is displayed in the and

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. 

These definitions apply to any atomic system, molecule or crystal. Fig. 7.3 a illustrates their application to the charge distribution of the guanine-cytosine base-pair. Fig. 7.3 b shows the molecular structure defined by the bond paths and the associated CPs that clearly and uniquely define the three hydrogen bonds that link the two bases. Fig. 7.3 c shows the atomic boundaries and bond paths overlaid on the electron density in the plane of the nuclei. All properties of the atoms can be determined, enabling one, for example, to determine separately the energy of formation of each of the three hydrogen bonds. 

This equation means that the normal to the surface S, n(r), is orthogonal to the gradient of the electron density. In other words, the surface is parallel to Vp, or rephrased again, the surface consists of gradient paths. The interatomic surface is a bundle of gradient paths that terminate at the bond critical point at the center of the surface. 

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