Bonds, spatial orientation

The representation of molecular properties on molecular surfaces is only possible with values based on scalar fields. If vector fields, such as the electric fields of molecules, or potential directions of hydrogen bridge bonding, need to be visualized, other methods of representation must be applied. Generally, directed properties are displayed by spatially oriented cones or by field lines. 

Table 4.14 Spatial Orientation of Common Hybrid Bonds Figure 4.1 Crystal Lattice Types Table 4.15 Crystal Structure...

TABLE 4.14 Spatial Orientation of Common Hybrid Bonds... 

Retention of configuration (Section 6.13) Stereochemical pathway observed when a new bond is made that has the same spatial orientation as the bond that was broken. 

Conformational isomers are represented in two ways, as shown in Figure 3.6. A sawhorse representation views the carbon-carbon bond from an oblique angle and indicates spatial orientation by showing all C-Tl bonds. A Newman projection views the carbon-carbon bond directly end-on and represents the two carbon atoms by a circle. Bonds attached to the front carbon are represented by lines to the center of the circle, and bonds attached to the rear carbon are represented by lines to the edge of the circle. 

The dependence of the j3-deuterium effect on the spatial orientation of the isotopic bond with respect to the developing -orbital, on the a-carbon atom was elegantly demonstrated by Shiner and Humphrey (1963). This work will not be discussed in detail here suffice it to say the suggestion is made that j8-deuterium effects are better correlated by the postulate of hyperconjugation and its angular dependence than by the simple steric model (Shiner and Humphrey, 1963). 

Monosaccharides can differ in their formulas, their ring sizes, and the spatial orientations of their hydroxyl groups. To analyze the differences between two monosaccharides, begin with structural drawings of the molecules, oriented so the ether linkages are in comparable positions. Then examine the stmctures to locate differences in constituents and bond orientations. 

Geometrical isomers differ only in the spatial orientation of groups about a plane or direction, i.e., they differ in orientation either (i) around a double bond (see 2-butene) or (ii) across the ring in a cyclic compound (see 1,2-dichlorocyclobutane). Both cis and trans isomers exist. 

Stereoisomers, on the other hand, are compounds with the same molecular formula, and the same sequence of covalently bonded atoms, but with a different spatial orientation. Two major classes of stereoisomers are recognized, conformational isomers and configurational isomers. 

In the catalytic system shown in Scheme 9, a hydrogen bond between one hydroxy function of the diol catalyst and the carbonyl group of the substrate is regarded as the driving force of catalysis. Here, the spatial orientation of the bulky a-1-naphthyl substituents of the TADDOL (a,a,a, a -tetraaryl-l,3-dioxolan-4,5-dimethanol) scaffold generates the chiral environment controlling the enantioselectivity of the reaction. 

Of central importance for the formation of a specific protein-DNA complex are hydrogen bonds. The H-bonds are clearly identifiable in high resolution structures. H-bonds occur where a H-bond donor and acceptor he with 0.27-0.31 nm of each other. Energetically most favorable is the hnear arrangement of the H-bond, with deviations from hnearity leading to a reduction in energy. This characteristic is responsible for the stereospecific orientation of H-bond acceptors and donors. The H-bond thus contributes significantly to the spatial orientation between protein and nucleic acid. 

The spatial orientations of the atomic orbitals of the hydrogen atom are very important in the consideration of the interaction of orbitals of different atoms in the production of chemical bonds. 

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