In organic chemistry, conformation (conformer) and configuration (chirality at a stereocenter) are related but different concepts. Conformers are different 3D shapes generated mainly by bond rotation, while configuration describes the fixed stereochemical arrangement at a chiral carbon (commonly represented in SMILES with @ / @@).

Our software can enumerate multiple conformers (when available), making it easier to compare those 3D conformers with the corresponding 2D structure. It can also visualize chiral carbon atoms directly, so users can check whether the 3D stereochemical interpretation is consistent with the SMILES notation.

We use 2-butanol as an example. The SMILES expression of 2-butanol is CC[C@@H](C)O. Here, [C@@H] is the chiral carbon center. In this tutorial, @@ indicates clockwise order, while @ indicates counterclockwise order.

The atom priority/order is generally read according to the sequence in the SMILES string (excluding hydrogen).

There are two ways to provide a molecular formula: draw in JSME, or directly type a SMILES string in Manual SMILES input. For example, enter the chiral 2-butanol expression:

manual_input_a Image

Enter CC[C@@H](C)O in the Manual SMILES input, then click the Analyze button on the right:

manual_input_b Image

First, the software queries the PubChem chemical database. If the compound is known, the compound name is shown (for example, 2-Butanol), followed by molecular weight (g/mol), then the 2D bond-line depiction, and then the 3D ball-and-stick model.

Note that this molecule is displayed with three common conformers (3D conformers). These are not necessarily the only possible conformers, but representative common ones. Click Next to view the next conformer.

manual_input_d Image

After reviewing conformers, you can use one of the most useful features of this software: displaying atom indices and, more importantly, stereocenters. The software automatically highlights stereocenters in orange.

Stereocenter Image

As shown above, the chiral carbon is atom 3 (only heavy atoms are labeled; hydrogens are not).

Stereocenter 3 Image

As shown, atom 3 is the stereocenter. Place the hydrogen attached to atom 3 at the back(pointing into the screen). The sequence starts from atom 2, then goes to atom 4, and then to atom 5 (oxygen). The rotation shown is clockwise, which is consistent with @@ (clockwise) in the SMILES expression.