Chem3D Users Manual - CambridgeSoft

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Administrator Translucent surface type 66 Triple bonds field 276 Troubleshooting atoms shift on MOPAC input 177 background color 60 MOPAC quits 176 online 224 Type 2 (-CHR-) bending force parameters for C-C-C angles 282 U UHF 145, 147, 166 UHF spin density 189 UHF spin density, example 196 Uncoordinated bonds, creating 76 Unix, Gaussian files 71 Use Current Z-Matrix button 123 Use tight convergence criteria 200, 212 User guide, online 224 User interface 13 User-imposed constraints 142 Using .jdf Files 163 bond tools, tutorial example 31 ChemDraw to create models 39 display mode 114 double bond tool, tutorial example 34 hardware stereo graphic enhancement 62 labels 77 labels for substructures 38 labels to create models 37 measurements table, tutorial example 39 MM2, tutorial example 41 MOPAC keywords 170 Name=Struct 75 rotation dial 99 selection rectangle 92 stereo pairs 61 substructures 78 table editor to enter text 78 text building tool 77 text building tool, tutorial example 36 trackball tool, tutorial example 31 Using the zoom control 101 UV energies 172 V V1 field 285 V2 field 285 V3 field 286 van der Waals cutoff distance 283 cutoff term 291 cutoffs 139 energy 139, 209 energy, MM2 209 radius field 275 surface, definition 69 Van der Waals radii atom size control 57 dot surfaces display 58 Vapor pressure, ChemProp Pro 208 VDW interactions 288 VDW interactions table 272 VECTORS keyword 171 Vibrational energies 171 View focus 85 View menu 15 Viewing Highest Occupied Molecular Orbitals 49 Lowest Unoccupied Molecular Orbitals 49 molecular surfaces 48 parameters 289 Visualizing surfaces from other sources 71 xx• CambridgeSoft
W Wang-Ford charges 187 Water solubility, ChemProp Pro 208 Wave equations 144 Web site, CambridgeSoft, accessing 227 What’s new in Chem3D 9.0.1 10 What’s new in Chem3D 9.0 10 Wire frame display 56 Wire mesh surface type 66 WMF and EMF 119 X X- Y- or Z-axis rotations 97 –XH2– field 280 –XR2– field 279 –XRH– field 279 Z Zero point energy 171 Z-matrix 28 changing 101 overview 108 pop-up information 105 Zwitterion, creating a 80 Chem3D Chem3D 9.0.1 • xxi
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ChemOffice.Com ® ChemOffice ® Che
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License Information ChemOffice, Che
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· Licensed users of ChemOffice Ent
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computer, except as provided below.
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Q: IS IT OK TO COPY MY COLLEAGUE’
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A Guide to CambridgeSoft Manuals An
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Administrator Setting Molecular Sur
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Administrator Methods Available in
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Administrator Defining Atom Types.
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Administrator • CambridgeSoft
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Administrator provides a balance be
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Administrator the activation each t
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Administrator The following table d
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Administrator • Stereo Pairs—A
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Administrator • Bond Angles—Dis
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Administrator The Building Toolbar
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Administrator The Calculation Toolb
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Administrator 1. Right-click in the
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Administrator • In the Model Sett
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Administrator modes and color setti
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Administrator 30 •Chem3D Basics C
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Administrator 2. Click the ChemDraw
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3. Move the pointer over the C-C bo
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Administrator Add serial numbers an
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Administrator 5. Press the Enter ke
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. Administrator b. From the Structu
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Administrator In the Measurements t
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A molecule of Epinephrine appears.
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Administrator Tutorial 7: Docking M
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Administrator To save the iteration
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The allyl radical, CH 2 =CHCH 2·,
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Administrator Determine the raw spi
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Administrator atoms are relatively
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To change the structural display ty
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Administrator When sizing by partia
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Administrator Depth Fading3D enhanc
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• Select Parallel to rotate the r
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Administrator • From the Computat
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Administrator Surface Type Solid De
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Administrator 2. Adjust the slider
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Administrator Density surface is ca
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Administrator 72 •Displaying Mode
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Administrator The following table d
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Administrator When Correct Atom Typ
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Administrator To use the same text
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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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Page 328 and 329: Desktop Software Enterprise Solutio
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Page 338 and 339: SOFTWARE Chem3D Ultra Ultimate Mode
Page 340 and 341: SOFTWARE ChemFinder/Word • Search
Page 342 and 343: SOFTWARE The Merck Index • Encycl
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Page 346 and 347: SOLUTIONS •Adds chemical data typ
Page 348 and 349: MANAGEMENT •Custom organization o
Page 350 and 351: MANAGEMENT • Indexes chemical str
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Page 354 and 355: DISCOVERY • Accessed through your
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Page 362 and 363: DISCOVERY • Catalog driven data m
Page 364 and 365: DATABASES • Fully structure-searc
Page 366 and 367: DATABASES • Encyclopedic referenc
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