Stereochemistry and R/S configurations – You spin me right round baby right round. Like a record baby.
Performing 3-D visualizations of atomic stereochemistry is one of the hardest aspects of organic chemistry for new students to learn and understand. One of the great aides in this area is a molecular modeling set, which will allow you to hold a representation of a tetrahedral carbon in your hands and rotate it yourself. Another great way to do it is to use an online viewer (like the one here)
Along those lines, assigning R/S configuration to a chiral carbon can be made more difficult if the lowest priority group is not in the rear. For example:
It not completely obvious that this is the R stereoisomer from this view. There are a couple of things that we can do to this molecule to make the configuration more apparent. First, we could think of this as a Newman projection instead of the standard tetrahedral carbon.
The other (easier) way to do this is to just rotate the tetrahedral carbon. The way to do this is to freeze one of the groups and rotate the other three. As long as they are rotated and not switched, (they can be rotated in either direction, clockwise or counterclockwise) it will be the same molecule.
Any of the four groups can be held in place while the other three are rotated. Once rotated to a point where the lowest priority group is in the back, it becomes much easier to assign R/S configuration. Further, this method is not just confined to small molecules, as shown below.
In the example above, CH3 is the lowest priority group. By keeping the alkyl chain stationary, we can rotate the other groups clockwise in order to place the methyl group in back. Now it is more apparent that it is in the R configuration.
Take Home Message: Don’t get angry. Determining stereochemistry is easy. Just rotate your molecule to place the lowest priority group in back.