Chem3D Users Manual - CambridgeSoft

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Administrator 30 •Chem3D Basics CambridgeSoft Model Building Basics
Chapter 2: Chem3D Tutorials Overview The following section gives detailed examples of some general tasks you can perform with Chem3D. For examples of MOPAC calculations, see Chapter 10, “MOPAC Computations” on page 165. In this section: • Tutorial 1: Working with ChemDraw on page 31. • Tutorial 2: Building Models with the Bond Tools on page 32. • Tutorial 3: Building Models with the Text Building Tool on page 36. • Tutorial 4: Examining Conformations on page 39. • Tutorial 5: Mapping Conformations with the Dihedral Driver on page 42. • Tutorial 6: Overlaying Models on page 43. • Tutorial 7: Docking Models on page 46. • Tutorial 8: Viewing Molecular Surfaces on page 48. • Tutorial 9: Mapping Properties onto Surfaces on page 49. • Tutorial 10: Computing Partial Charges on page 52. Tutorial 1: Working with ChemDraw The following tutorial introduces model building with Chem3D. It assumes that no defaults have been changed since installation. If what you see is not like the description, you may need to reset the defaults. To reset defaults: • From the File menu, open the Model Settings dialog box. Click the Reset button. Open a new model window if one is not already opened. To view models as shown in this tutorial, select Cylindrical Bonds from the drop-down menu of the Model Display mode tool on the Model Display toolbar. The installation default for the ChemDraw panel is activated, hidden. You should see a tab labeled ChemDraw on the upper right side of the GUI. ChemDraw tab If you do not see the tab: 1. From the View menu, select ChemDraw Panel. The ChemDraw Panel opens in its default position, attached to the right edge of the model window. If the tab is visible: ChemOffice 2005/Chem3D Chem3D Tutorials • 31 Tutorial 1: Working with ChemDraw
Page 1: ChemOffice.Com ® ChemOffice ® Che
Page 4 and 5: License Information ChemOffice, Che
Page 6 and 7: · Licensed users of ChemOffice Ent
Page 8 and 9: computer, except as provided below.
Page 10 and 11: Q: IS IT OK TO COPY MY COLLEAGUE’
Page 12 and 13: A Guide to CambridgeSoft Manuals An
Page 14 and 15: Administrator Setting Molecular Sur
Page 16 and 17: Administrator Methods Available in
Page 18 and 19: Administrator Defining Atom Types.
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Page 32 and 33: Administrator The Building Toolbar
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Administrator Example 2. Building a
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Administrator copied into blank tab
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Administrator 3. Type the atom type
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Administrator Clean Up Structure or
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Setting Serial Numbers this step, y
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Administrator Refining a Model Afte
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Administrator Selecting Multiple At
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Administrator New in Chem3D version
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Administrator Dragging moves atoms
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Administrator 3. Hold down the Shif
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To position a plane in your model p
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Administrator • Second Positioned
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Administrator For example, consider
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Administrator If you want to displa
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Administrator Example: To examine t
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Administrator Chem3D provides two o
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Administrator change a property. By
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Administrator To add to a group: 1.
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To stop spinning: • On the Movie
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Administrator If you want to … Th
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Administrator EPS The PostScript fi
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If you want the file to … Then cl
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Molecular Design Limited MolFile (.
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Administrator 7. Leave the last lin
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Administrator 128•Printing and Ex
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Administrator • Semiempirical Ext
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Method Type Advantages Disadvantage
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Administrator • A single point ca
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Administrator • Molecular mechani
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Administrator constant), while θ 0
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Administrator The van der Waals int
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Administrator 6. The modified value
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the same wave function and a consta
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Administrator A variety of other ba
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Administrator Molecular wave functi
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Administrator activation barriers.
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3. From the Calculations menu, poin
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minimizing a second model, the mini
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Administrator move to lower the ene
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. Administrator Molecular Dynamics
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Administrator If you want to … Th
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Administrator The Compute Propertie
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Administrator To run a previously c
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Administrator The procedures assume
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Administrator improvements in each
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Administrator • Overall errors in
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Administrator The following table c
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Administrator TRIPLET QUARTET QUINT
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Administrator Chemical symbol ++ ba
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Administrator 4. Click Run. A new m
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Administrator Minimizing Energy Min
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Administrator criteria, to optimize
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Administrator 6. Hold down the S ke
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Administrator Dipole Moment The dip
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Administrator Molecular Surfaces Mo
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The following table contains the ke
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Administrator 3. Click in the model
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Keyword Description 7. On the Prope
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Administrator Hyperfine Coupling Co
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Administrator 198•MOPAC Computati
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Administrator If you want to … re
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Administrator In the Results In tex
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Administrator Repeating a Gaussian
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Property Description Property Descr
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Property Description Error Message
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Administrator Property Electronic E
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Administrator To specify the calcul
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Administrator 3. Click Open. The ap
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Administrator • Server—limits t
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Administrator To perform property c
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The Step 4 of 4 dialog box appears.
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Administrator • From the ChemOffi
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Administrator Accessing the Online
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Administrator To find a structure t
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Administrator 228• Accessing the
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Administrator Performance Below are
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Administrator Defining Substructure
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Administrator If an atom can be ass
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Key Drag Shift+Drag Administrator Q
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Administrator 238• Keyboard Modif
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Administrator Example 3 In Example
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Administrator 14 13 H 2.197 -0.8229
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Administrator Connection tables by
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Administrator FORTRAN Formats The F
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5 6 1.11606 3 109.41 5 109.41 -1 21
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Administrator 41 4 1 0 0 0 0 0 0 0
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Administrator 32 3 12 1 0 0 0 33 3
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Administrator 13 * 3D displacement
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Administrator The field value for C
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Administrator Line 4e: C 1.53597 1
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Administrator CONECT 4 2 9 10 11 CO
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Administrator COMPND ATOM HETATM CO
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Administrator Line 56 -2794 21139 6
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Administrator Line 16 6 C -0.559 1.
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Administrator 12. Line 30, “@BOND
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Parameter Table Use Parameter Table
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Administrator 3. Type the informati
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Administrator Geometry The geometry
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Administrator KS The KS, or bond st
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Administrator one attached hydrogen
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Administrator bond length between t
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Administrator R* The R* field is th
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Administrator The V1 torsional cons
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Administrator VDW Interactions The
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Administrator Editing Parameters Yo
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Administrator 6. The pi molecular o
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Administrator Adding Parameters to
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Administrator fragments 84 paramete
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Administrator CC1 see Cartesian coo
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Administrator Copy As Bitmap comman
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Administrator Examining angles, tut
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Administrator density 67 editing 67
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Administrator editing 107 non-bonde
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Administrator repeating jobs 178 RH
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Administrator Rectification, when d
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Administrator all atoms 95 atoms or
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Administrator Translucent surface t
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Desktop Software Enterprise Solutio
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SOLUTIONS Enterprise Solutions APPL
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Desktop to Enterprise Solutions Che
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SOFTWARE E-Notebook Ultra Ultimate
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SOFTWARE ChemDraw Ultra Ultimate Dr
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SOFTWARE Chem3D Ultra Ultimate Mode
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SOFTWARE ChemFinder/Word • Search
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SOFTWARE The Merck Index • Encycl
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SOLUTIONS •Development and deploy
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SOLUTIONS •Adds chemical data typ
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MANAGEMENT •Custom organization o
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MANAGEMENT • Indexes chemical str
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MANAGEMENT • E-Notebook Enterpris
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DISCOVERY • Accessed through your
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DISCOVERY • Integrated with Regis
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DISCOVERY • Reagent lists can be
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DISCOVERY •Effectively manages da
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DISCOVERY • Catalog driven data m
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DATABASES • Fully structure-searc
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DATABASES • Encyclopedic referenc
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DATABASES • Extensive collection
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SERVICES · Business Case Developme
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CS ChemOffice ® Desktop to Enterpr
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Chem3D Users Manual - CambridgeSoft

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