Drawing stereochemistry: E/Z double bonds and R/S stereocentres
How to rank groups with the CIP rules, assign E/Z and R/S, and draw the configuration a name asks for with wedge and hash bonds.
Stereoisomers have the same atoms connected in the same order but arranged differently in space. A name shows this with a stereodescriptor: (E) or (Z) for a double bond, (R) or (S) for a stereocentre. To draw the right isomer you need one tool, the Cahn–Ingold–Prelog (CIP) priority rules, and two drawing conventions.
Ranking groups: the CIP rules in brief
- Higher atomic number wins at the first atom: Br > Cl > O > N > C > H.
- If the first atoms tie, look one bond further out. List the atoms attached to each of them, highest first, and compare the lists at the first difference. CH2CH3 (C,H,H) beats CH3 (H,H,H).
- Multiple bonds count as repeated atoms. A C=O carbon is treated as bonded to (O,O), so –CHO (O,O,H) outranks –CH2OH (O,H,H).
Double bonds: E and Z
On each carbon of the double bond, find the higher-priority group. If the two higher-priority groups are on the same side, the configuration is Z (German zusammen, together). If they are on opposite sides, it is E(entgegen, opposite).
In skeletal drawings the geometry is simply how you draw it: a zigzag through the double bond is E for but-2-ene; bending the chain back on the same side gives Z. The checker reads the geometry from your drawing.
Watch out: E/Z is not "cis/trans of the chain"
On C2, Br outranks CH3; on C3, CH3 outranks H. The Z isomer has Br and the C3 methyl on the same side, which leaves the two methyl groups, and so the carbon chain, on opposite sides. "Cis" and "trans" describe the chain; E and Z are defined only by priorities.
Stereocentres: R and S
A carbon bonded to four different groups is a stereocentre. To assign its configuration:
- Rank the four groups 1–4 with the CIP rules.
- Orient the molecule so that group 4 (often H) points away from you.
- Trace 1 → 2 → 3. Clockwise is R; anticlockwise is S.
If group 4 points towards you in your drawing (on a wedge), the direction you see is reversed: clockwise then means S.
Worked example: (R)-butan-2-ol
The groups on C2 rank OH (1) > CH2CH3 (2) > CH3 (3) > H (4). Draw the carbon chain as a zigzag in the plane of the paper and put one of the groups on C2 on a wedge or a hash bond (the figures use the methyl; the OH works just as well). Then check the direction 1 → 2 → 3 with H pointing away. If you got S, swap the wedge for a hash: that inverts the centre.
Drawing wedges and hashes in the editor
- Tap the middle of a bond at the stereocentre and choose Wedge (pointing towards you) or Hash (pointing away from you).
- The narrow end must be at the stereocentre. The editor puts it on the atom with more bonds; if it is on the wrong atom, tap the bond again and choose Flip.
- Use one wedge or hash per stereocentre; the other three bonds can stay in the plane.
- In the advanced editor (Ketcher), choose the wedge or hash bond in the bond tools and click a bond; clicking it again reverses it. A wavy bond there means "configuration unknown": it is valid, but it does not specify R or S, so it won't satisfy a name that does.
Mirror images and meso compounds
Swapping a wedge for a hash at a single stereocentre gives the enantiomer, the non-superimposable mirror image. With two stereocentres there can be up to four stereoisomers, but if the molecule has an internal mirror plane, one of them is a meso compound: it is superimposable on its mirror image and achiral. Butane-2,3-diol has three stereoisomers: (R,R), (S,S) and meso.
Common mistakes
- Forgetting the stereochemistry altogether. A plain drawing is correct in connectivity but does not specify the configuration.
- Reading R/S with H towards you without reversing the answer.
- Ranking by size instead of atomic number. A small –OH outranks a large alkyl group.
- Assuming Z means "cis chain". It does only when the chain carbons are the higher-priority groups.