What does R configuration mean?

It is a stereochemical label to indicate the relative spatial orientation of each atom in a molecule with a non-superimposable mirror image.

R indicates that a clockwise circular arrow that goes from higher priority to lower priority crosses over the lowest priority substituent and that lowest-priority substituent is in the back.

The R and S stereoisomers are non-superimposable mirror images, which means if you reflect them on a mirror plane, they do not become the exact same molecule when you overlay them.

When you label a molecule as R or S, you consider the priorities of each substituent on the chiral carbon (connected to four different functional groups).

Let's take this chiral amino acid for example:

Some general ways you could determine the priorities are:

1. HIgher atomic number of the directly-attached atom gives higher priority
2. Atomic number of the atom attached to the one is considered in step 1 if two substituents have the same first atom
3. Higher number of same-atom branches determines greater priority if the overall substituents are too similar (e.g. isopropyl has higher priority than ethyl)

With (R)-alanine:

• `"NH"_2` has priority 1 due to highest atomic number for `"N"`.
• `"COOH"` has priority 2 due to the higher atomic number of `"O"` vs. `"H"` in `"CH"_3`
• `"CH"_3` has priority 3 as a result.
• `"H"` has priority 4.

Now, if you draw a circular arrow starting at `"NH"_2`, going to `"COOH"`, crossing over `"H"` since it is in the back, and to `"CH"_3`, then you would have gone clockwise.

Since the lowest priority atom is in the back, the clockwise arrow corresponds to the R configuration.

If you had started from the same R configuration but oriented `"H"` in the front and `"CH"_3` in the back, it would have been S configuration. Let's call this S configuration A, where you just nudge two substituents to flip them from front/back to back/front.

If you reflect the same R configuration over a mirror plane, keeping the orientations of `"H"` in the back and `"CH"_3` in the front after the flip, the configuration is also S. Let's call this S configuration B, where you've actually done a reflection.

If you start from S configuration B, and flipped it over a vertical axis (literally rotating `180^o` in space), you would get S configuration A.