Stereogenic carbon (and other tetrahedral stereogenic atoms!) are assigned a configuration designator based on a priority assignment among the four groups, and a standard method for describing the topologic arrangement of those priority groups.  The methodology is straightforward; in practice there are a couple important things to stay aware of.

  1. Look at the four atoms connected to the stereocenter.  Assign priority (1-4, high-to-low) based on:
    • First, the atomic number of the atom;
    • If no difference, the atomic mass of the atom;
    • If no difference, then look at the priorities of the next-attached atoms for otherwise identical groups.  Assign priority based on the first difference identified.  Keep moving outward until a difference is found--if the two groups are identical the original carbon atom is not a stereocenter!
  2. The hard part:  orient the molecule (either a model, a drawing, or a mental image) so that you view from the stereocenter to the 4th (low) priority group.
  3. Identify the order of rotation from Priority 1 to 2 to 3.
    • Clockwise:  the stereocenter is R.
    • Counterclockwise:  the stereocenter is S.
Some examples (the stereogenic atom is higlighted with a magenta halo):
Molecule
 Priority assignment


R_BrClFMe.pdb		 BrClFMe

S_MeBnAmine.pdb		 MeBnAmine.png

IP_CHexene.pdb		 Isopropylcyclohexene

IP_CHexenol.pdb
(Yes, this does have a second stereocenter. Try identifying its configuration.)		 Isopropyl Cyclohexenol

Double bonds are treated as two single bonds to the same element.  This can get complicated, but always trace out connectivity to find the first point of difference.
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