Chem3D Users Manual - CambridgeSoft

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Administrator CC1 see Cartesian coordinate file format CC2 see Cartesian coordinate file format CCD see Cambridge Crystal Data Bank file format CCITT Group 3 and 4 120 Centering a selection 100 Changing atom to another atom type 83 atom to another element 82 bond order 83 elements 77 orientation 99 stereochemistry 88 Z-matrix 101 Charge field 275 Charge property 186 Charge, adding formal 77 Charge-Charge contribution 140 Charge-Charge energy, MM2 209 Charge-Dipole energy, MM2 209 Charge-Dipole interaction term 291 Charges 186 Charges, adding 80 Charges, from an electrostatic potential 186 Charges, pop-up information 105 Chem3D changes to Allinger’s force field 290 property broker 205 synchronizing with ChemDraw 74 ChemBioNews.Com 226 ChemClub.com 223 ChemDraw panel 22 synchronizing with Chem3D 74 transferring models to 127 ChemDraw panel 74 ChemFinder.com 225 Chemicals, purchasing online 226 ChemOffice SDK, accessing 227 ChemProp Pro critical pressure 207 critical temperature 207 critical volume 207 free energy 207 full report 207 Gibbs free energy 207 heat of formation 207 Henry’s law constant 207 Ideal gas thermal capacity 207 LogP 207 melting point 207 molar refractivity 207 refractivity 207 server 207 solubility 208 standard Gibbs free energy 207 thermal capacity 207 vapor pressure 208 Water solubility 208 ChemProp Std server 205 ChemProp Std server properties 205 ChemProp, error messages 208 ChemProp, limitations 208 ChemSAR/Excel descriptors 220 statistics 221 wizard 217 ChemSAR/Excel wizard 217 ChemStore.com see SciStore.com Choosing a Hamiltonian 148, 167 Choosing the best method see Computational methods Chromatek stereo viewers 59 CI, microstates used 171 CIS 172 Cleaning up a model 90 iv• CambridgeSoft
Clipboard copying to 127 exporting with 127 Clipboard, importing with 75 Close Contacts command 275 Closed shell system 174 CMYK Contiguous 120 Color applying to individual atoms 60 background 60 by depth 59 by depth for Chromatek stereo viewers 59 by element 58 by group 59 by partial charge 59 displays 58 field 274 settings 58 Coloring groups 114 Coloring the background window 60 Commands close contacts 275 compute properties 161, 184 import file 14 Comments panel 23 Comparing cation stabilities in a homologous series of molecules 191 models by overlay 43 the stability of glycine zwitterion in water and gas phase 194 two stable conformations of cyclohexane 156 Compression 120 Computational chemistry, definition 129 Computational methods choosing the best method 130 defined 129 limitations 130 model size 130 overview 129 parameter availability 130 potential energy surfaces 130 RAM 130 uses of 130 Compute Properties dialog box 215 Gaussian 202 MM2 161 MOPAC 184 removing properties 215 selecting properties 215 Compute Properties command 161, 184 Computing partial charges 52 Computing properties 202 Computing steric energy, tutorial example 41 Configuration interaction 147, 167 Configuring ChemSAR/Excel 217 Conformations, examining 39 Conformations, searching 43 Conjugated pi-system bonds table 272 Connection table file format 122 Connection tables 122 Connolly accessible surface area, description 205 Connolly molecular surface 69 ChemProp Std 206 displaying 69 overview 69 Connolly solvent-excluded volume, ChemProp Std 206 Constraining movement 95 Constraints, setting 87 Chem3D Chem3D 9.0.1 • v
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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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Page 262 and 263: Administrator 41 4 1 0 0 0 0 0 0 0
Page 264 and 265: Administrator 32 3 12 1 0 0 0 33 3
Page 266 and 267: Administrator 13 * 3D displacement
Page 268 and 269: Administrator The field value for C
Page 270 and 271: Administrator Line 4e: C 1.53597 1
Page 272 and 273: Administrator CONECT 4 2 9 10 11 CO
Page 274 and 275: Administrator COMPND ATOM HETATM CO
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Page 278 and 279: Administrator 7 2 10 1 8 3 6 1 9 3
Page 280 and 281: Administrator Line 16 6 C -0.559 1.
Page 282 and 283: Administrator 12. Line 30, “@BOND
Page 284 and 285: Parameter Table Use Parameter Table
Page 286 and 287: Administrator 3. Type the informati
Page 288 and 289: Administrator Geometry The geometry
Page 290 and 291: Administrator KS The KS, or bond st
Page 292 and 293: Administrator one attached hydrogen
Page 294 and 295: Administrator bond length between t
Page 296 and 297: Administrator R* The R* field is th
Page 298 and 299: Administrator The V1 torsional cons
Page 300 and 301: Administrator VDW Interactions The
Page 302 and 303: Administrator Editing Parameters Yo
Page 304 and 305: Administrator 6. The pi molecular o
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Page 308 and 309: Administrator fragments 84 paramete
Page 312 and 313: Administrator Copy As Bitmap comman
Page 314 and 315: Administrator Examining angles, tut
Page 316 and 317: Administrator density 67 editing 67
Page 318 and 319: Administrator editing 107 non-bonde
Page 320 and 321: Administrator repeating jobs 178 RH
Page 322 and 323: Administrator Rectification, when d
Page 324 and 325: Administrator all atoms 95 atoms or
Page 326 and 327: Administrator Translucent surface t
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
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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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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