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Administrator 5. Press the Enter key. TIP: The Text building tool will also accept structures in SMILES notation, either typed in or cut and pasted from other documents. Another, simpler, way of building this model is to type Pentane in the Name=Struct text box and then modify the appropriate hydrogens. Refine the model as follows. 1. Click the Select tool 2. Select the model by dragging diagonally across it. 3. From the Structure menu, choose Clean Up. If you want a more accurate representation of a low energy conformation, optimize the geometry of the model by clicking the MM2 tool on the Calculation toolbar. To specify text equivalent to the structure of 1,2-dimethyl cyclopentane shown below: H 2 C CH H 2 C CH CH 2 H 3 C CH 3 1. From the File menu, choose New. 2. Click the Text Building tool . 3. Click in the empty space in the model window. 4. Type CH(CH3)CH(CH3)CH2CH2CH2. 5. Press the Enter key. The trans-isomer appears. 6. Select the model and choose Clean Up from the Structure menu. TIP: You don’t have to click the Select tool every time you want to select something. Just hold down the letter S on your keyboard while working with any building tool, and you temporarily activate the Select tool. You cannot specify stereochemistry when you build models with labels. The structure of 1,2-dimethyl cyclopentane appears in the trans conformation. To obtain the cis-isomer: 1. Click the Select tool . 2. Select C(1). 3. From the Structure menu, choose Invert. The cis-isomer appears. You can rotate the molecule to see the differences between the isomers after you invert the molecule. Using Substructures Labels are useful to build simple structures. However, if you make larger, more complex structures, you will find it easier to use a combination of labels and pre-defined substructures. Over 200 substructures are pre-defined in Chem3D. These substructures include the most commonly used organic structures. TIP: Pre-defined substructures are listed in the substructures.xml file. You can view the list by pointing to Parameter Tables on the View menu and selecting Substructures. Text typed in the text box is case sensitive. You must type it exactly as it appears in the Substructures table. Build a model of nitrobenzene: 1. From the File menu, choose New. 2. Click the Text Building tool . 3. Click the empty space in the model window. 34 •Chem3D Tutorials <strong>CambridgeSoft</strong> Tutorial 3: Building Models with the Text Building Tool
4. Type Ph(NO2) in the text box. 5. Press the Enter key. A model of nitrobenzene appears. The substructure in this example is the phenyl group. Substructures are defined with specific attachment points for other substituents. For phenyl, the attachment point is C(1). 3. Select the Trackball tool , and rotate the model so you are viewing it down the center of the helix as shown below: Build a peptide model: 1. From the File menu, choose New. 2. Click the Text Building tool . 3. Click an empty space in the Model window. A text box appears. 4. Type H(Ala)12OH. 5. Press the Enter key. 6. Rotate this structure to see the alpha helix that forms. Change the model display type: 1. Click the arrow on the right side of the Model Display Mode tool on the Model Display toolbar. 2. Select Wire Frame as the Model Type. TIP: You can also click on the icon. Successive clicks cycle through the Display Mode options. 4. Use the Model Display Mode tool to choose Ribbons as the Model Type to see an alternative display commonly used for proteins. Tutorial 4: Examining Conformations This tutorial uses steric energy values to compare two conformations of ethane. The conformation with the lower steric energy value represents the more likely conformation. Build ethane: 1. Draw a single bond in the ChemDraw panel. A model of ethane appears. 2. View the Measurements table: a. From the Structure menu, point to Measurements, and then choose Bond Lengths. <strong>ChemOffice</strong> 2005/Chem3D Chem3D Tutorials • 35 Tutorial 4: Examining Conformations
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A Guide to CambridgeSoft Manuals An
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Chapter 31: Changes and Audit Trail
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Page 18 and 19: Administrator Connection Table . .
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Page 24 and 25: Administrator Chapter 28: Introduci
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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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The Open dialog box appears. To cho
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A data source tree appears, contain
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ChemFinder saves the form with a .c
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Administrator In addition, this gui
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Administrator You can organize coll
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Administrator Desired Result Change
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Administrator To export to MS Word:
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Administrator 410• E-Notebook Use
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Administrator NO 2 NO 2 Me Me HC(OE
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Administrator • Top of Arrow as R
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Administrator Ethanol was selected,
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Administrator you enter an invalid
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3. Click the Search In... checkbox
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2. Select Session Manager.... The S
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• Removing a Transition Listener
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Parameter Table Use Parameter Table
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Administrator xxxviii• CambridgeS
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CAMBRIDGESOFT ChemOffice Desktop to
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DESKTOP CS E-Notebook Electronic Jo
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DESKTOP CS ChemDraw Chemical Struct
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DESKTOP CS ChemFinder Searching and
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ENTERPRISE ChemOffice WebServer Ent
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KNOWLEDGE E-Notebook Enterprise Des
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KNOWLEDGE Document Manager Desktop
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KNOWLEDGE 21CFR11 Compliance Electr
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RESEARCH & Registration System Chem
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RESEARCH & Inventory Manager Chemic
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RESEARCH & CombiChem Enterprise Des
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CHEMICAL Chemical Databases Referen
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