The examples of structures considered here are structure of ammonia and its inversion, D / L configurations of molecules, C60 with an included atom, a micelle and a protein.
The structure of ammonia
Ammonia has a pyramidal structure with nitrogen at its apex and the three hydrogens at the base. The HNH angle is 107.3º close to the tetrahedral angle of 109º 28'. The lone pair of electrons is situated above the N atom and away from the H–atoms. An interesting feature of this structure is that the N atom can go back and forth through the triangle formed by the three hydrogens to the other side of the triangle. This is referred to as umbrella inversion or “tunneling”. The action of the ammonia maser is based on this phenomenon.
Figure 1.1 Ammonia
D and L Glyceraldehydes
A carbon atom bonded to four distinct groups is referred to as an asymmetric or a chiral carbon atom. One simple example of a molecule containing an asymmetric carbon atom is d glyceraldehyde, shown in Fig 1.2. The mirror image of D glyceraldehyde, L glyceraldehyde is also shown. In the figure, H and OH groups are above the plane of paper and the CHO and CH2OH groups are below the plane of the paper. By rotating D glyceraldehyde with respect to any axis, it cannot be converted to L glyceraldehyde. (Try this using molecular models). This is similar to a person having a mole on his left cheek. In the mirror, the mole appears on his right cheek. If one rotates the person by 180º, the mole still remains on the left cheek and the rotated person differs from the mirror image.
If you look at the carbon center, with the hydrogen atom further away form it, the groups CHO, CH2OH and OH which are nearer to the eye than the H atom, are arranged clockwise. In the L configuration, they are arranged counterclockwise. These asymmetric molecules rotates the plane of polarization of a plane polarized light. The configuration of molecules are critical, e.g. a molecule can act as a drug only in one of the two configurations (not the always). Naturally occurring amino acids have L configurations.
Figure 1.2 D and L Glyceraldehydes. The left part of the figure has a mirror plane separating D and L glyceraldehydes. The right part shows the rotation of the molecule with respect to the C-H bond when the bond is directed away from the eye.
