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Administrator In the Measurements table, notice that the dihedral for H(3)-C(1)-C(2)-H(8) is now minus 0 degrees, as shown in the model. To compute steric energy: Tutorial 5: Mapping Conformations with the Dihedral Driver The dihedral driver allows you to map the conformational space of a model by varying one or two dihedral angles. At each dihedral angle value, the model is energy minimized using the MM2 force field and the steric energy of the model is computed and graphed. After the computation is complete you can view the data to locate the models with the lowest steric energy values and use these as starting points for further refinement in locating a stationery point. 1. From the Calculations menu, point to MM2, then choose Compute Properties. NOTE: The property tab defaults should remain as in the previous calculation. 2. Click Run. The final line in the Output box appears as follows: NOTE: The values of the energy terms can vary slightly based on the type of processor used to calculate them. The steric energy for the eclipsed conformation (~3.9 kcal/mole) is greater in energy than that of the staggered conformation (~1 kcal/mole), indicating that the staggered configuration is the conformation that is more likely to exist. To use the dihedral driver: 1. Select the bond in your model that defines the dihedral angle of interest. 2. Choose Dihedral Driver from the Calculations menu. The Dihedral Driver window opens. When the computation is completed, a graph is displayed showing the energy (kcal) vs. theta (angle of rotation). To view the conformation at any given point: 1. Point to a location (specific degree or energy setting) inside the Dihedral Driver Window. A dashed-line box appears. As you move the mouse, the box moves to define a specific point on the graph. NOTE: As a rule, steric energy values should only be used for comparing different conformations of the same model. 2. Click on the point of interest. 38 •Chem3D Tutorials CambridgeSoft Tutorial 5: Mapping Conformations with the Dihedral Driver
The model display rotates the dihedral to the selected conformation. NOTE: The dihedral is rotated in 5 degree increments through 360 degrees for a total of 72 conformations to produce the graph. You can view the minimized energy values for each point in the Output window. To rotate the other dihedral angle (other end of the bond): • Right-click in the Dihedral Driver window and choose Exchange. Rotating two dihedrals To rotate two dihedrals: 1. Use Shift+click to select two adjacent bonds. In this case, the middle atom’s position remains fixed 2. Choose Dihedral Driver from the Calculations menu. The Dihedral Driver window opens. When the computation is completed, a graph is displayed showing theta 1 vs. theta 2. NOTE: The graph is the result of rotating one angle through 360° in 15° increments while holding the other constant. The second angle is then advanced 15° and the operation is repeated. To view the conformation at any given point: • Click any block in the graph. The model display rotates both dihedrals to the selected conformation. Customizing the Graph You can use the right-click menu to set the rotation interval used for the computation. You can also select display colors for the graph, background, coordinates, and labels. You also use the right-click menu to copy the graph, or it’s data set, to other applications, or to save the data. Tutorial 6: Overlaying Models Overlays are used to compare structural similarities between models, or conformations of the same model. Chem3D provides two overlay techniques: • a “Fast Overlay” algorithm • the traditional “do it by hand” method based on minimization calculations This tutorial describes the Fast Overlay method. For the Minimization Method, see Comparing Models by Overlay on page 105. The Minimization Method is more accurate, but the Fast Overlay algorithm is more robust. In both tutorial examples, you will superimpose a molecule of Methamphetamine on a molecule of Epinephrine (Adrenalin) to demonstrate their structural similarities. 1. From the File menu, choose New Model. Open the Model Explorer if it is not already open. 2. Choose the Text tool from the Building Toolbar and click in the model window. A text box appears. 3. Type Epinephrine and press the Enter key. ChemOffice 2005/Chem3D Chem3D Tutorials • 39 Tutorial 6: Overlaying Models
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A Guide to CambridgeSoft Manuals An
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Chapter 31: Changes and Audit Trail
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Administrator Tutorial 7: Docking M
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Administrator Connection Table . .
Page 20 and 21: Administrator Specifying Properties
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Page 40 and 41: Administrator the activation each t
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Page 60 and 61: Administrator 2. Click the ChemDraw
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CS Software Problem Report For fast
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