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Tips for 3D editing
When using the 3D Edit Mode, you may notice that after dragging an atom to significantly change the molecule's conformation (e.g., flipping a cyclohexane from chair to boat) and then clicking "Optimize 3D," the structure snaps back to its original shape.
This happens because the force field optimization algorithm seeks the nearest low-energy minimum from its starting point, which is often the original, stable conformation.
To avoid this and successfully lock in your intended conformation, the key is to drag an atom that has fewer bonds and is located at a terminal position of the molecule.
Atoms that form the core skeleton of a molecule are highly constrained by numerous bonds. If you move one of these atoms slightly, the optimization process will exert strong forces to pull it back to its original, stable position.
In contrast, terminal atoms, such as hydrogens or carbons in a methyl group, are less constrained. By moving one of these atoms a significant distance, you can more effectively guide the entire molecule into a different energy well (a new conformation). This provides a better starting point for the optimizer, encouraging it to find a new stable structure instead of reverting to the old one.
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Good Practice: To flip a cyclohexane from a chair to a boat conformation:
- Instead of dragging a carbon atom in the ring, grab an axial hydrogen atom and pull it significantly across to the other side of the ring.
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Bad Practice:
- Slightly nudging a carbon atom within the ring.
- → In this case, the optimization will almost certainly force the structure back into its original, more stable chair conformation.
As a general rule, remember to "move the leaves of the tree, not the trunk." This principle will help you succeed with conformation changes in a wide variety of molecules.