Although we will sometimes find that observing the conventions for perspective drawings and accurately representing real structures are mutually incompatible, one can have no excuse for ignorance of the real structures of basic organic molecules. All good graduate-level organic texts now include a chapter on conformational analysis; every organic chemist therefore should develop a core of knowledge about molecular shapes. Violations of the rules or of the realities of structure, when they are necessary, should be knowing, not ignorant.
The two families of cyclopentane conformers, envelope and twist, differ little in energy. Both offer pseudoequatorial positions for single ligands, as in (a) and (b):
The envelope conformation has only the 'flap' atom out of the plane of the other four carbons, whereas the twist structure has one atom above and one below the plane defined by the other three.
The chair conformers of cyclohexane should be familiar in appearance (c):
However, it is important to maintain substituent relationships by deriving the inverted chair from the original, as shown here. Remember that ring inversion interconverts axial and equatorial bonds, but does not change the overall orientation of a bond relative to the ring. That is, equatorial 'up' becomes axial 'up' upon ring flipping. When the chair is flipped to the boat, the substituent remains attached by its original bond type; subsequent pseudorotation is required to alter this (d).
Cyclohexenes often are drawn as if they too existed in the chair conformation. However, the requirements of p-bonding mean that the two sp2 carbons and the four atoms directly attached to them must lie in a common plane (e):
The displacement of the remaining two ring atoms from this plane is typically somewhat exaggerated, and the substituent is placed on a pseudoequatorial position. When cyclohexene rings are part of a larger structure such as a steroid (part j), one usually has no choice but to use the chair-like representation, but one should remain aware of its inaccuracy.
For adjacent bonds on a cyclohexane to be trans-, they must be both equatorial or both axial; hence trans-decalin exists in only a single chair-chair conformer; adjacent cis- bonds are equatorial and axial, so two chair-chair conformers are possible for the cis-stereoisomer (f, g):
Notice that generating the ring-inverted conformer does not lead to a 'pretty' perspective drawing; one must redraw from a different viewpoint. The redrawing should always be explicitly labeled as such; otherwise, one can accidently interconvert configurational stereoisomers while interconverting conformational ones.
The 'prettiness' problem shows up again when one makes perspective drawing of structures containing even more rings:
Ultimately the only solution to this problem is drawing the structure on a computer screen with a program that allows real-time rotational and translational motions.
Fortunately for steroid chemists, the perhydrophenanthrene foundation of steroids has the trans-, anti-, trans- stereochemistry that is the easiest one to draw (j):
Note that although the OH group of cholestanol looks axial in the drawing, that is a trick of perspective; inspection of a model will reveal that it remains equatorial.