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Administrator staggered form. The majority of the energy contribution is from the torsional energy and the 1,4 VDW interactions. NOTE: The values of the energy terms shown here are approximate and can vary slightly based on the type of processor used to calculate them. 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. The dihedral angle in the Actual column becomes 0, corresponding to the imposed constraint. The difference in energy between the global minimum (Total, previous calculation) and the transition state (Total, this calculation) is 2.73 kcal/mole, which is in agreement with literature values. To further illustrate points about minimization: • Delete the value from the Optimal column for the dihedral angle and click the MM2 icon on the Calculation toolbar. After the minimization is complete, you are still at 0 degrees. This is an important consideration for working with the MM2 minimizer. It uses first derivatives of energy to determine the next logical 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. CAUTION While there are other, perhaps easier, methods of creating a cyclohexane model, you should use the method described to follow this example. 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: • From the MM2 submenu of the Calculations menu, choose Minimize Energy, and click Run. 152•MM2 and MM3 Computations CambridgeSoft Minimize Energy
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: 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). Locating the Global Minimum Finding the global minimum is extremely challenging for all but the most simple molecules. It requires a starting conformation which is already in the valley of the global minimum, not in a local minimum valley. The case of cyclohexane is straightforward because you already know that the global minimum is either of the two possible chair conformations. To obtain the new starting conformation, change the dihedrals of the twisted conformation so that they represent the potential energy valley of the chair conformation. The most precise way to alter a dihedral angle is to change its Actual value in the Measurements table when dihedral angles are displayed. An easier way to alter an angle, especially when dealing with a ring, is to move the atoms by dragging and then cleaning up the resulting conformation. To change a dihedral angle: • Drag C1 below the plane of the ring, then drag C4 above the plane of the ring. The major contributions are from the 1,4 VDW and Torsional aspects of the model. ChemOffice 2005/Chem3D MM2 and MM3 Computations • 153 Minimize Energy
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A Guide to CambridgeSoft Manuals An
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