ChemSketch: How to view the chair or boat conformations in 3D

Description

Cyclohexane and related ring systems can adopt various conformations such as chair and boat. ChemSketch together with 3D Viewer can generate these 3D conformers starting from a SMILES string or a flat 2D drawing, allowing you to visualize more realistic structures.

Solution

The chair conformer of cyclohexane can be reliably generated in 3D by following these steps:

1. From the Tools menu, choose Generate Structure from SMILES and enter the following SMILES string: C1CCCCC1.
2. From the ACD/Labs menu, choose 3D Viewer to open it.
3. Return to ChemSketch and select the flat 2D drawing of cyclohexane generated in step 1.
4. Select 3-Copy to 3D from the bottom bar.
5. In 3D Viewer, from the Tools menu, choose 3D Optimization. The chair conformer for cyclohexane should now be shown in 3D.

To generate the boat conformer for cyclohexane, follow these steps:

1. Repeat steps 1-3 above to generate a flat cyclohexane molecule.
2. Click 3D Rotation and rotate the molecule such that there is one vertex on the left and right, and it is sitting almost perpendicular to the plane of the screen.

From left to right, the generation of the boat conformer for cyclohexane, starting from a flat molecule.

3. Enable Select/Move to grab the left and right vertices and position them upwards to form the boat.
4. Add explicit hydrogens to the structure (from the Tools menu, choose Add Explicit Hydrogens).
5. From the bottom toolbar, click 2-Copy to 3D and the boat conformer for cyclohexane should now be displayed in 3D.

Note: Performing 3D optimization using the 2D templates of cyclohexane as a starting point will result in a twisted boat conformation in most cases. To access the 2D templates, from the Templates menu, choose Template Window (or press F5). Select Rings from the drop-down menu. Click a drawing and click a second time to paste it into the drawing area.