Chem3D Users Manual - CambridgeSoft

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Administrator Examining angles, tutorial example 34 bond length and bond order, tutorial example 33 conformations 39 dihedral angles, tutorial example 34 Excited state, RHF 174, 175 Excited state, UHF 175 Exporting models using different file formats 118 with the clipboard 127 Extended Hückel method 63, 146, 166 Extended Hückel surfaces, tutorial example 49 Extended Hückel, molecular surface types available 65 External tables 24 External tables, overview 271 Extrema 133 F FAQ, online, accessing 224 Fast overlay, tutorial 43 File format Alchemy 241 Cambridge Crystal Data Bank 246 Cartesian coordinates file 243 editing atom types 241 examples 241 internal coordinates file 246 MacroModel 249 MDL MolFile 251 MOPAC 257 MSI MolFile 253 Protein Data Bank file 259 ROSDAL 262 SYBYL MOL2 267 SYBYL MOLFile 265 File formats 262 .3dm 121 .alc (Alchemy) 118, 121 .avi (Movie) 121 .bmp (Bitmap) 119 .cc1 (Cartesian coordinates) 118, 121 .cc2 (Cartesian coordinates) 118, 121 .cdx 118 .con (connection table) 122 .ct (connection table) 118, 122 .cub (Gaussian Cube) 122 .dat (MacroModel) 123 .emf (Enhanced Metafile) 119 .eps (Encapsulated postscript) 120 .fch (Gaussian Checkpoint) 122 .gif (Graphics Interchange Format) 121 .gjc (Gaussian Input) 118, 122 .gjf (Gaussian Input) 122 .gpt (MOPAC graph) 126 .int (Internal coordinates) 118, 123 .jdf (Job description file) 126 .jdt (Job Description Stationery) 126 .mcm (MacroModel) 118, 123 .ml2 (SYBYL) 126 .mol (MDL) 118, 124 .mop 118 .mop (MOPAC) 124 .mpc (MOPAC) 124 .msm (MSI ChemNote) 118, 124 .pdb (Protein Data Bank) 118, 126 .png 121 .rdl (ROSDAL) 118, 126 .sm2 (SYBYL) 118, 126 .smd (Standard Molecular Data, STN Express) 118, 126 .sml (SYBYL) 118, 126 .xyz (Tinker) 126 .zmt (MOPAC) 124 Alchemy 121 viii• CambridgeSoft
Bitmap 119 Gaussian Input 122 Postscript 120 QuickTime 121 TIFF 120 File menu 14 Filters, property 215 Fock matrix 145 Force constant field 287 Force constants 200 Formal Charge, ChemProp Std 206 Formal charge, definition 52 Formats for chemistry modeling applications 121 FORTRAN Formats 242, 246, 249, 250, 253, 257, 259, 260, 267 Fragments creating 84 rotating 97 selecting 93 Fragments, rotating 45 Fragments, separating 44 Frame interval control 158 Free Energy, ChemProp Pro 207 Freehand rotation 97 Fujitsu, Ltd. 293 G GAMESS Installing 211 installing 211 minimize energy command 211 overview 211 property server 210 server 210 specifying methods 211 Gaussian 03 199 about 9 checkpoint file format 122 compute properties command 202 copy measurements to messages control 200 create input file command 202 cube file format 122 display every iteration control 200 file formats 122 general tab 201 input file format 203 job type tab 199 minimize energy command 199 molecular surface types available 65 overview 199 properties tab 202 specifying basis sets 200 specifying keywords 201 specifying methods 200 specifying path to store results 202 specifying population analyses 201 specifying solvation models 201 specifying spin multiplicities 201 specifying wave functions 200 theory tab 200 tutorial example 49 Unix, visualizing surfaces 71 General tab, GAMESS 213 tab, Gaussian 201 General tab 181, 201 Geometry field 276 Geometry optimization 134 Geometry optimization, definition 130 Gibbs free energy, ChemProp Pro 207 GIF file format 121 Global minimum 133 Gradient norm 185 Grid Chem3D Chem3D 9.0.1 • ix
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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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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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