Basic Organic Nomenclature

Stereochemistry

There is one final level of complexity to add in naming organic compounds, stereo or configurational isomers. Stereo isomers refer to compounds which have the same molecular formula with the atoms of the molecule bonded in the same pattern, but in different locations in space. Look at the two structures for bromochlorofluoromethane below. Convince yourself they have the atoms located differently in space around the carbon atom.

Note: 3D images in line drawings make use of solid wedges to indicate an atom above the plane of the page and dashed wedges for atoms behind the plane of the page, normal lines are assumed to lay in the plane of the page.
 

Compound Name	Line Drawing	3D Model
bromochlorofluoromethane
bromochlorofluoromethane

The two molecules are stereo isomers, distinguished by the placement of the atoms. The Cahn-Ingold-Prelog rules are used for naming both geometric isomers (e.g. E- or Z- alkenes, see below) and configurational isomers (e.g. R- or S- for enantiomers). Each atom at the stereogenic center (formerly called a chiral center or atom) is assigned a priority based on its' atomic number. The configuration of the atom is then determined by the order of priority of the atoms. The following rules will aid in assigning R or S configurations to a stereogenic atom.

1.  Identify the stereogenic centers (most commonly an sp³ C with 4 different groups attached)
2. Assign the priority to each group (high = 1, low = 4) based on atomic number of the atom attached to the stereogenic center
3. Position the lowest priority group away from you, as if you were looking along the C-(4) sigma bond. If you are using a model, grasp the lowest priority group in your fist, pointing the remainder of the molecule towards you.
4. For the other 3 groups, determine the direction of high to low priority (1 to 3)
5. If this is clockwise, then the center is R (Latin: rectus = right)
6. If this is counter clockwise, then it is S (Latin: sinister = left)

Examine the two isomers above and determine their configuration. The top is (R)-bromochlorofluoromethane and the bottom is (S)-bromochlorofluoromethane. Note: with only a single stereogenic center in the molecule it is not necessary to indicate its location by a number, and the configuration is in brackets.

Subrules:

• Isotopes: H vs D? Use atomic mass number so D > H
• Same atom attached? By moving out one unit at a time, locate the first point of difference and apply rules there. i.e. a -CH₃ vs a -CH₂CH₃ both the carbons have the same atomic numbers so move out one atom in the chain, this will give a H atom for the methyl group, and a C atom for the ethyl group. The C has a higher atomic number hence the ethyl group has a higher priority than a methyl group.
• Multiple bonds? Open up the multiple bond so that the carbon atom is bonded to the same number of atoms by single bonds, i.e.

The geometrical isomers of alkenes has been discussed with respect to simple linear chains using a cis- / trans- nomenclature (see alkenes). Unfortunately this fails if there are two groups attached at either end of the double bond. The Cahn-Ingold-Prelog rules discussed above for stereo isomers can also be applied to complex geometrical isomers. Compare the two geometrical isomers of 2-chloro-2-butene below.
 

Compound Name	Line Drawing	3D Model
2-chloro-2-butene
2-chloro-2-butene

With two groups attached to one end of the double bond the cis- / trans- nomenclature is no longer appropriate, but an new term E or Z is applied based on the Chan-Ingold-Prelog rules. The following rules will aid in assigning E or Z configurations to an alkene.

1. Imagine the alkene as 2 pieces, each containing one of the sp² C
2. Assign the priority (high = 1, low = 2) to each group on each sp² C based on atomic number
3. Determine the relative position of the 2 high priority groups
4. If they are on the same side then it is a Z-alkene (German; zusammen = together)
5. If they are on opposite sides then it is an E-alkene (German; entgegen = opposite)

Multiple sterogenic centers

Compound Name	Line Drawing
(2R,4S)-4-chloro-2-pentanol
(1Z,4E)-1,5-dichloro-2-methyl-1,4-pentadiene
(2Z,4R)-2-amino-4-chloro-2-pentene

Note: it is the first atom in the double bond that is used as the locant for the E or Z designation.

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