Right/Left Hand Stereo Centers?

In chemstry study, a stereo center a labeled as R (Rectus, Right in Latin) Hand or S (Sinister, Left in Latin) according to the following rules.

1. Assign precedence ranks to its 4 neighboring branches, as #1, #2, #3, and #4. Neighboring branch with #1 has the highest rank.

• If two immediate neighboring atoms have different atomic masses, the one with higher mass has a higher precedence rank.
• If two immediate neighboring atoms have the same atomic mass, masses of next level neighbors are used to determine their precedence rank.
• If two neighboring branches have a precedence rank, then this is not a stereo center!

2. Determine R/S-hand.

• Arrange neighbors 3 highest ranks #1, #2, #3 on a flat plane.
• View the molecule from the side of the plane opposite to neighbor #4.
• View the molecule from the side of the plane opposite to neighbor #4.
• Circling 3 neighbors on the plane from #1 to #2, then to #3.
• If the circle turns in clockwise direction, then this is a R-Hand stereo center.
• If the circle turns in counterclockwise direction, then this is a S-Hand stereo center.

With the R/S-Hand Stereo Centers definitions describbe above, we can figure out the algorithm used by Open Babel to determine the wedge/hash bonds.

Case 1: Without Implicit Hydrogen Neighbors

• Use normal bonds for 3 highest ranks #1, #2, #3.
• For a R-Hand stereo center, use hash bond for the lowest rank #4.
• For a S-Hand stereo center, use wedge bond for the lowest rank #4.

For example, the following pictures shows a pair of R-Hand (on the right) and S-Hand (on the left) stereo centers without implicit Hydrogen neighbors. Note that it is the lowest rank atom getting changed into a Hash or Wedge bond to present the stereo center.

If you specify the S-Hand stereo center with downward bond on atom F in the SDF file shown below, Open Babel will correct with upward bond on atom C.

Without Implicit Hydrogen Neighbors
FYIcenter.com

  5  4  0  0  0  0  0  0  0  0999 V2000
    1.1887    1.0905    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1887    2.4905    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
    2.5229    0.6663    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3108    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.8301    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  6  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  1  5  1  0  0  0  0
M  END

Case 2: With an Implicit Hydrogen Neighber

• Use normal bonds for 2 middle ranks #2, #3. Remember that the implicit Hydrogen neighbor has the lowest rank #4.
• For a R-Hand stereo center, use wedge bond to for highest rank #1.
• For a S-Hand stereo center, use hash bond to the lowest rank #1.

For example, the following pictures shows a pair of R-Hand (on the right) and S-Hand (on the left) stereo centers with an implicit Hydrogen neighbor.

⇒ Custom Wedge/Hash with SVG output

⇐ Wedge/Hash Bond Changed by Open Babel

⇑ Stereochemistry with Open Babel

⇑⇑ Open Babel Tutorials