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:


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)
The same subrules for isotopes and multiple bonds apply. Examine the above structures and you should see the top is (E)-2-chloro-2-butene and the bottom is (Z)-2-chloro-2-butene. 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.


Multiple sterogenic centers

It is of course possible to have more than one stereogenic center in the molecule. In these cases it is necessary to specify the location of each stereogenic center by using the numbering scheme for the molecule. The stereogenic centers are listed in numeric order, in brackets. For example:
 
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.



Tutorial Quiz: Stereochem

Return to Index