hydrogen bonds. The formic acid dimer (Fig. 18.4f) reveals stronger HBs than in
the water dimer, and also weak van der Waals interactions between the two
closely-interacting acidic hydrogens.
Finally, in the benzene dimer (Fig. 18.4c), there is an area of non-bonded
overlap located at the center of each benzene ring, resembling the isosurface for
bicyclo[2,2,2]octene. There is another lower-density surface between the overlapping portions of the benzenes, where π-stacking is expected. It is important to
compare this image to the ones displayed in Table 18.1. The intermolecular
interaction in benzene dimer appears very clearly with NCI as a surface that
highlights the benzene to benzene stacking interaction, well beyond the pair
interactions found with AIM.
18.5 Solids
As we saw in the Introduction, non-covalent interactions in solid state have raised a
great deal of interest lately, due to their relevance for self-assembly [36] and
crystallization [37] processes.
Indeed, crystalline solids exhibit rich and challenging bonding patterns. We
consider the prototypical examples of carbon in the diamond (Fig. 18.4g) and
graphite (Fig. 18.4h) phases at their equilibrium geometries. In diamond, the carbon
atoms are sp
3 hybridized and are connected by strong covalent bonds that form a
tridimensional, tetrahedral network. Figure 18.4g shows an NCI isosurface for a
cuboid section of the diamond crystal. The non-covalent surface extends through
the voids of the structure, creating a network similar to that of the covalent bonds.
Graphite in its α form (Fig. 18.4h) has a bidimensional, hexagonal lattice, with
the carbon atoms sp
2 hybridized and covalently bonded to their three nearest
neighbors. The NCI isosurface shows areas of non-bonded overlap at the center of
the hexagonal rings, as seen previously in benzene. π–π stacking interactions
between the graphene sheets are clearly manifested by the isosurfaces filling the
interlayer spaces.
18.6 Biological Systems
Understanding of non-covalent interactions is crucial for the comprehension of the
3D structure and, thus, of the activity of biosystems [65, 66]. However, the calculation of the electron density in these systems is totally unbearable.
Approximations need thus to be sought.
18 A Complete NCI Perspective: From New Bonds to Reactivity
505
the water dimer, and also weak van der Waals interactions between the two
closely-interacting acidic hydrogens.
Finally, in the benzene dimer (Fig. 18.4c), there is an area of non-bonded
overlap located at the center of each benzene ring, resembling the isosurface for
bicyclo[2,2,2]octene. There is another lower-density surface between the overlapping portions of the benzenes, where π-stacking is expected. It is important to
compare this image to the ones displayed in Table 18.1. The intermolecular
interaction in benzene dimer appears very clearly with NCI as a surface that
highlights the benzene to benzene stacking interaction, well beyond the pair
interactions found with AIM.
18.5 Solids
As we saw in the Introduction, non-covalent interactions in solid state have raised a
great deal of interest lately, due to their relevance for self-assembly [36] and
crystallization [37] processes.
Indeed, crystalline solids exhibit rich and challenging bonding patterns. We
consider the prototypical examples of carbon in the diamond (Fig. 18.4g) and
graphite (Fig. 18.4h) phases at their equilibrium geometries. In diamond, the carbon
atoms are sp
3 hybridized and are connected by strong covalent bonds that form a
tridimensional, tetrahedral network. Figure 18.4g shows an NCI isosurface for a
cuboid section of the diamond crystal. The non-covalent surface extends through
the voids of the structure, creating a network similar to that of the covalent bonds.
Graphite in its α form (Fig. 18.4h) has a bidimensional, hexagonal lattice, with
the carbon atoms sp
2 hybridized and covalently bonded to their three nearest
neighbors. The NCI isosurface shows areas of non-bonded overlap at the center of
the hexagonal rings, as seen previously in benzene. π–π stacking interactions
between the graphene sheets are clearly manifested by the isosurfaces filling the
interlayer spaces.
18.6 Biological Systems
Understanding of non-covalent interactions is crucial for the comprehension of the
3D structure and, thus, of the activity of biosystems [65, 66]. However, the calculation of the electron density in these systems is totally unbearable.
Approximations need thus to be sought.
18 A Complete NCI Perspective: From New Bonds to Reactivity
505