chapter 3

CHAPTER 3: GRAPHICAL REPRESENTATION OF NONPLANAR MOLECULES

The ability to represent the 3D-structures of molecules as their 2D-projections, and to view such projections with the 3D-perception is critical for any discussion of interactions between 3D objects (e.g. receptor-antagonist interactions). Several conventions have been employed to facilitate this task.

In order to be able to represent a tetrahedral carbon with its four substituents as a 2D-projection one can employ either Fisher projection, or the "wedge" projection.

Fisher projection:

The tetrahedral atom is viewed perpendicularly to an edge formed by connecting two of its ligands. The convention is that the two vertical bonds in the projection are pointing behind the plane of projection (plane of paper sheet), and the two horizontal bonds are pointing towards the viewer.

Note: the rotation of the Fisher projection by 90^o and 270^o results in projection of the mirror image (enantiomer, see Figure above). In contrast, the rotation by 180^o results in the projection of the identical molecule (not shown).

Wedge projection:

It is obtained by viewing the tetrahedral center perpendicularly to the plane formed by three atoms. One of the remaining atoms is oriented behind the plane of projection (dashed bond), one towards the viewer (boldface bond). Note that, in contrast to Fisher projection, the rotation of the wedge projection about axes perpendicular or coplanar with the plane of projection does not change anything. This projection is therefore by far less ambiguous than Fisher projection. In the case of large linear molecule the molecule backbone has to be drawn in the fully extended conformation.

Newman projection:

The molecule with two tetrahedral centers is viewed along the C-C axis. The atom in front is represented as a three-way branch, the atom in the back as a circle with three outgoing bonds. This projection is most useful inconsideration of steric relation between ligands linked to adjacent tetrahedral centers and is most popular.

Sawhorse projection:

The C-C bond is viewed at an angle. The atom shown on the left of the projection is also the one in the front. This projection is difficult to use with acyclic molecules but is most popular for representation of cyclic molecules e.g. saturated six-membered rings.

Haworth projection:

Stereodiagrams:

In complex molecules the best 3D-perception is obtained by showing the same object as a dual image, each half of which is a projection of the 3D-molecule viewed at a slightly different angle. The 3D-image is obtained using the corresponding 3D-viewing glasses, or the viewer can be trained to get the 3D-perception with naked eyes only.