Chem3D Users Manual - CambridgeSoft

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move to lower the energy. However, for saddle
points (transition states), the region is fairly flat and
the minimizer is satisfied that a minimum is
reached. If you suspect your starting point is not a
minimum, try setting the dihedral angle off by
about 2 degrees and minimize again.
Comparing Two Stable
Conformations of
Cyclohexane
In the following example you compare the
cyclohexane twist-boat conformation and the chair
global minimum.
To build a model of cyclohexane:
1. From the File menu, choose New.
An empty model window appears.
2. Select the Text Building tool.
3. Click in the model window.
A text box appears.
4. Type CH2(CH2)5 and press the Enter key.
CAUTION
While there are other, perhaps easier, methods of creating
a cyclohexane model, you should use the method described
to follow this example.
• From the MM2 submenu of the Calculations
menu, choose Minimize Energy, and click
Run.
When the minimization is complete, reorient
the model so it appears as follows.
The conformation you converged to is not the
well-known chair conformation, which is the global
minimum. Instead, the model has converged on a
local minimum, the twisted-boat conformation.
This is the closest low-energy conformation to your
starting conformation.
Had you built this structure using substructures that
are already energy minimized, or the ChemDraw
panel, you would be close to the chair
conformation. The minimizer does not surmount
the saddle point to locate the global minimum, and
the closest minimum is sought.
The energy values in the Output window should be
approximately as follows:
Before minimizing, it is wise to use the Clean Up
Structure command to refine the model. This
generally improves the ability of the Minimize
Energy command to reach a minimum point.
1. From the Edit menu, choose Select All.
2. From the Structure menu, choose Clean Up.
NOTE: The Clean Up command is very similar to the
minimize energy command in that it is a preset, short
minimization of the structure.
To perform the minimization:
The major contributions are from the 1,4 VDW and
Torsional aspects of the model.
For cyclohexane, there are six equivalent local
minima (twisted-boat), two equivalent global
minima (chair), and many transition states (one of
which is the boat conformation).
156•MM2 and MM3 Computations
CambridgeSoft
Minimize Energy