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Administrator When Correct Atom Types and Rectify settings are selected in the Building control panel, the atom type is set according to the bond tool used (C Alkane in this example) and the appropriate number of hydrogens are added. To add bonds to the model: 4. Point to an atom and drag in the direction you want to create another atom. bond allows you to specify a connection between two atoms without a strict definition of the type of bond. This bond is often used in coordination complexes for inorganic compounds, where another element might be substituted. Dummy atoms are also useful for positioning atoms in a Z-matrix, perhaps for export to another application for further analysis. This is a common use when models become large and connectivities are difficult to specify. 1. Click and hold the mouse button on an atom 2. Drag in any direction and release the mouse button When the Rectify option is set in the Building control panel, the hydrogen is replaced by a carbon. To add an uncoordinated bond and dummy atom: 1. Select the Uncoordinated Bond tool . 2. Point to an atom and drag from the atom. An uncoordinated bond and a dummy atom are added to the model. The atom created is labeled “Du”, the Chem3D element symbol for Dummy atoms. Dummy atom 5. Repeat adding bonds until you have the model you want. After you have the backbone, you can change the carbons to different heteroatoms. Creating Uncoordinated Bonds Use the Uncoordinated Bond tool to create an uncoordinated bond with a dummy atom (labeled Du). Uncoordinated Bonds and dummy atoms are ignored in all computations. An uncoordinated Removing Bonds and Atoms When you remove bonds and atoms: • Click a bond to remove only that bond. • Click an atom to remove the atom and all attached bonds. To remove an atom or bond, do one of the following: • Click the Eraser tool and click the atom or bond. 54 •Building and Editing Models <strong>CambridgeSoft</strong> Building With the Bond Tools
• Select the atom or bond, and from the Edit menu, choose Clear. • Select the atom or bond and press Delete. NOTE: If automatic rectification is on, you will not be able to delete hydrogen atoms. Turn rectification off when editing a model. Building With The Text Tool The Text tool allows you to enter text that represents elements, atom types (elements with specific hybridization), substructures, formal charges, and serial numbers. The text you enter must be found in either the Elements, Atom Types, or Substructures tables. The match must be exact, including correct capitalization. These tables can be found in the Parameter Tables list on the View menu. NOTE: For all discussions below, all the Building control panel options in the Chem 3D Setting dialog box are assumed to be turned on. Some general rules about using the Text Tool are as follows: • Text is case sensitive. For example, the correct way to specify a chlorine atom is Cl. The correct way to specify the phenyl group substructure is to type Ph. PH or ph will not be recognized. • Pressing the Enter key applies the text to the model. • Typing a formal charge directly after an element symbol will set the formal charge for that atom. For example PhO- will create a model of a phenoxide ion instead of phenol. • If you double click an atom, the contents of the previous text box are applied to that atom. If the atom is one of several selected atoms, then the contents of the previous text box are applied to all of the selected atoms. • If a tool other than the Text tool is selected, double-clicking in the model window is equivalent to clicking with the Text tool selected. Triple-clicking in the model window is equivalent to double-clicking with the Text tool selected. The interpretation of the text in a text box depends on whether atoms are selected as follows: • If the model window is empty, a model is built using the text. • If you have one or more atoms selected, the text is added to the model at that selection if possible. If the specifications for a selected atom are violated, the connection cannot be made. • If you have a model in the window, but do not have anything selected, a second fragment is added, but is not connected to the model. • When a text box is visible, you can modify the selection by Shift+clicking or Shift-dragging across atoms. Using Labels To use an element symbol in a text box: 1. Select the Text tool. 2. Click in the model window. A text box appears. 3. Type C. 4. Press the Enter key. A model of methane appears. The atom type is automatically assigned as a C Alkane, and the appropriate number of hydrogens are automatically added. <strong>ChemOffice</strong> 2005/Chem3D Building and Editing Models • 55 Building With The Text Tool
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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 . .
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Administrator Specifying Properties
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Administrator Undoing Changes . . .
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Administrator Chapter 28: Introduci
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Administrator Atom Properties . . .
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Administrator Deleting a Field Type
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Administrator Example 2. . . . . .
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Administrator Reaction Center . . .
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Administrator In addition to browsi
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Page 40 and 41: Administrator the activation each t
Page 42 and 43: Administrator The following table d
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Administrator Chem3D provides two o
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Administrator A variety of other ba
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Administrator activation barriers.
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3. From the Calculations menu, poin
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Compute Properties The Compute Prop
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Administrator C(2)-C(3)-C(4) bond a
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Administrator criteria, to optimize
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Administrator Dipole Moment The dip
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Administrator Molecular Surfaces Mo
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Administrator • From the View men
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to see some of the information avai
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Administrator The Table view appear
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Administrator To search over a list
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Administrator 250•ChemFinder Tuto
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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 To save a metafile fr
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Administrator Adding a Data Box Men
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Administrator 282•Relational Data
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Administrator ChemFinder creates a
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Administrator • If you are editin
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Administrator The record is permane
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Administrator Using Log Files Durin
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Administrator Export to SDFile When
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Administrator benz OR *bromo* Benze
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Administrator 360•ChemFinder/Orac
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Administrator Reactant List Format
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Administrator • You can configure
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Administrator For more information
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Administrator 3. From the Molecules
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Administrator • Enhanced table of
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Administrator In addition, this gui
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Administrator 388• Introducing E-
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Administrator You can organize coll
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Administrator Your system configura
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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 Type in the AutoText
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Administrator Type of Measurement m
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Administrator Advanced Text Searchi
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Administrator • Username - An opt
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Administrator The Field Properties
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Administrator reactants and product
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Administrator To access the Add-In
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Administrator In the query table fi
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Administrator contained collection
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Administrator Chemical Structure Se
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Administrator To add states to a co
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• Removing a Transition Listener
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Administrator • Unlocked Contents
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Administrator If the user wants to
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Administrator To view the export te
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Administrator To edit this data, 1.
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Administrator Setting the Region fo
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Administrator 2. If Inherits Securi
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To change the Transition Security P
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Administrator The Security tab appe
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Administrator Desired Result Remove
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Administrator Section Listeners E-N
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Administrator 604 • CambridgeSoft
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Administrator Accessing the Online
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Administrator The CS ChemOffice SDK
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Administrator Troubleshooting This
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Administrator 14 13 H 2.197 -0.8229
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Parameter Table Use Parameter Table
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Administrator Subforms (continued)
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Administrator User interface 9 User
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Administrator xxxviii• CambridgeS
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CAMBRIDGESOFT ChemOffice Desktop to
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CS ChemOffice Software Suites ChemO
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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 Chem3D Molecular Modelin
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DESKTOP CS ChemFinder Searching and
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DESKTOP CS ChemInfo Reference and C
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ENTERPRISE ChemOffice WebServer Ent
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ENTERPRISE Oracle Cartridge Enterpr
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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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RESEARCH & BioAssay HTS Biological
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RESEARCH & BioSAR Browser Biologica
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CHEMICAL ChemACX Database Available
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CHEMICAL The Merck Index Chemistry
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CHEMICAL Chemical Databases Referen
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CONSULTING & Consulting & Services
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CS Software Problem Report For fast
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