Chem3D Users Manual - CambridgeSoft

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Administrator Rectification, when deselecting 92 Rectifying atoms 90 Red-blue anaglyphs 59 Reduct field 284 Reference description field 277 Reference field 273 Reference number field 277 References table 272, 277 References, MM2 289 References, MOPAC 293 Refining a model 90 Reflecting a model through a plane 89 Refractivity, ChemProp Pro 207 Registration, online 223 Removing bonds and atoms 76 measurements from a table 108 selected properties 215 Rendering types 55 Repeating a GAMESS Job 214 Repeating a Gaussian Job 204 Repeating an MM2 Computation 163 Repeating MOPAC Jobs 178 Replacing atoms 37 atoms with substructures 81 Replaying molecular dynamics 160 Repulsion field 280 Requirements Windows 11 Reserializing a model 88 Resetting defaults 115 Resizing models 100 Resizing models 235 Resolve density matrix 172 Restrict movement of select atoms, MM2 159 Restrictions on the wave function 145 RGB indexed color 120 RHF 145, 147, 166 RHF spin density 189 RHF spin density, example 197 Ribbons display 57 RMAX keyword 171 RMIN keyword 171 Roothaan-Hall matrix equation 146 ROSDAL 262 ROSDAL file format 126 Rotating around a bond 98 around a specific axis 98 dihedral angles 97, 98 fragments 97 models 96 two dihedrals 43 using trackball 97 with mouse buttons 235 X/Y-axis rotation 97 Z-axis rotation 97 Rotating fragments 45 Rotation bars 14 Run GAMESS Input File command 213 Run Gaussian Input File command 203 Run Gaussian Job command 204 Rune plots 222 Running GAMESS jobs 213 Gaussian input files 203 Gaussian jobs 204 minimizations 153 MOPAC input files 177 MOPAC jobs 178 S Saddle point 133 Sample code, SDK web site 227 xvi• CambridgeSoft
SAR descriptors, definition 205 Save All Frames checkbox 124 Save As command 119 Saving customized job descriptions 213 Scaling a model 101 SciStore.com 226 SDK Online, accessing 227 Searching for chemical information online 224 for conformations 43 Select Fragment command 93 Select tool 91 Select tool, hotkey 38 Selecting 91 adding atoms to a selection 92 all children 95 atoms 91 atoms and bonds 91 bonds 91 by clicking 91 by distance 94 by double click 93 by dragging 92 by radius 94 ChemSAR/Excel Descriptors 220 defining a group 93 fragments 93 moving 95 multiple atoms or bonds 92 properties to compute 215 selection rectangle 92 Selection rectangle 92 Self consistent field 146 Semi-empirical methods 146, 166 limitations 130 speed 131 uses 131 Semi-empirical methods, brief theory 143 Separating fragments 44 Serial numbers see also Atom labels see also Serial numbers, displaying 61 Serial numbers, tutorial example 36 Set Z-Matrix commands 103 Setting bond angles 86 bond lengths 86 bond order 83 changing structural display 55, 56 charges 87 constraints 87 default atom label display options 61 dihedral angles 86 measurements 85 measurements, atom movement 86 model building controls 73 molecular surface colors 67 molecular surface isovalues 66 molecular surface types 65 non-bonded distances 86 origin atoms 104 parameters 216 serial numbers 88 solid sphere size 57 solvent radius 67 surface mapping 68 surface resolution 67 Sextic bending constant 283 Shift+selecting 92 Show Internal Coordinates command 101 Show Surface button 65 Show Used Parameters command 161, 163, 273 Showing Chem3D Chem3D 9.0.1 xvii •
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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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Page 282 and 283: Administrator 12. Line 30, “@BOND
Page 284 and 285: Parameter Table Use Parameter Table
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Page 320 and 321: Administrator repeating jobs 178 RH
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Page 328 and 329: Desktop Software Enterprise Solutio
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Page 336 and 337: SOFTWARE ChemDraw Ultra Ultimate Dr
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
Page 344 and 345: SOLUTIONS •Development and deploy
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
Page 352 and 353: MANAGEMENT • E-Notebook Enterpris
Page 354 and 355: DISCOVERY • Accessed through your
Page 356 and 357: DISCOVERY • Integrated with Regis
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Page 360 and 361: DISCOVERY •Effectively manages da
Page 362 and 363: DISCOVERY • Catalog driven data m
Page 364 and 365: DATABASES • Fully structure-searc
Page 366 and 367: DATABASES • Encyclopedic referenc
Page 368 and 369: DATABASES • Extensive collection
Page 370: SERVICES · Business Case Developme
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