Chem3D 8.0 Manual - CambridgeSoft

More documents

Recommendations

Info

AdministratorChapter 12: Gaussian Computations . . 177Gaussian 98. . . . . . . . . . . . . . . . . . . . . . . . . . . 177Minimize Energy . . . . . . . . . . . . . . . . . . . . . . 177The Job Type Tab . . . . . . . . . . . . . . . . . . . 177The Theory Tab. . . . . . . . . . . . . . . . . . . . . 178The Properties Tab . . . . . . . . . . . . . . . . . . 179The General Tab . . . . . . . . . . . . . . . . . . . . 179Job Description File Formats . . . . . . . . . . . . . 180.jdt Format . . . . . . . . . . . . . . . . . . . . . . 180.jdf Format. . . . . . . . . . . . . . . . . . . . . . 180Computing Properties . . . . . . . . . . . . . . . . . . . 180Creating a Gaussian Input File . . . . . . . . . . . . 181Running a Gaussian Input File . . . . . . . . . . . . 181Repeating a Gaussian Job . . . . . . . . . . . . . . . . 182Running a Gaussian Job . . . . . . . . . . . . . . . . . 182Chapter 13: GAMESS Computations . 183Installing GAMESS . . . . . . . . . . . . . . . . . . . . 183Minimize Energy . . . . . . . . . . . . . . . . . . . . . . 183The Theory Tab. . . . . . . . . . . . . . . . . . . . . 183The Job Type Tab . . . . . . . . . . . . . . . . . . . 184Specifying Properties to Compute . . . . . . 184Specifying the General Settings . . . . . . . . 185Saving Customized Job Descriptions . . . . . . . 185Running a GAMESS Job . . . . . . . . . . . . . . . . 185Repeating a GAMESS Job . . . . . . . . . . . . . . . 186Chapter 14: SAR Descriptors. . . . . . . . . . 187Chem3D Property Broker . . . . . . . . . . . . . . . . 187ChemProp Std Server . . . . . . . . . . . . . . . . . . 187ChemProp Pro Server . . . . . . . . . . . . . . . . . . . 189Limitations . . . . . . . . . . . . . . . . . . . . . . . . 190Error Messages . . . . . . . . . . . . . . . . . . . . . 190MM2 Server . . . . . . . . . . . . . . . . . . . . . . . . . . 190MOPAC Server. . . . . . . . . . . . . . . . . . . . . . . . 191GAMESS Server. . . . . . . . . . . . . . . . . . . . . . . 192Chapter 15: SAR DescriptorComputations . . . . . . . . . . . . . . . . . . . . 193Selecting Properties To Compute . . . . . . . . . . 193Sorting Properties . . . . . . . . . . . . . . . . . . . 193Removing Selected Properties . . . . . . . . . 193Property Filters . . . . . . . . . . . . . . . . . . . . . . . . 193Setting Parameters . . . . . . . . . . . . . . . . . . . . . 194Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194Chapter 16: ChemSAR/Excel. . . . . . . . . 195Configuring ChemSAR/Excel . . . . . . . . . . . . 195The ChemSAR/Excel Wizard . . . . . . . . . . . . 195Selecting ChemSAR/Excel Descriptors . . . . . 198Adding Calculations to an ExistingWorksheet . . . . . . . . . . . . . . . . . . . . . . . . . . 198Customizing Calculations. . . . . . . . . . . . . . . . 199Calculating Statistical Properties . . . . . . . . . . 199Descriptive Statistics . . . . . . . . . . . . . . . . 199Correlation Matrix . . . . . . . . . . . . . . . . . . 200Rune Plots. . . . . . . . . . . . . . . . . . . . . . . . . 200Chapter 17: Accessing theCambridgeSoft Web Site . . . . . . . . . . . 201Find Suppliers on ChemStore.com. . . . . . . . . 201Find Information on ChemFinder.com. . . . . . 201Browse ChemStore.com. . . . . . . . . . . . . . . . . 201Browse CambridgeSoft.com . . . . . . . . . . . . . 202Browse CS Chem3D Documentation. . . . . . . 202Browse CS Chem3D Technical Support . . . . 203Register Online. . . . . . . . . . . . . . . . . . . . . . . . 203Browse ChemOffice SDK . . . . . . . . . . . . . . . 204Appendix A: Substructures . . . . . . . . . . . . 1Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1Attachment point rules . . . . . . . . . . . . . . . . . 1Angles and measurements . . . . . . . . . . . . . . 1Defining Substructures. . . . . . . . . . . . . . . . . . . . 2Appendix B: Atom Types . . . . . . . . . . . . . . 5Assigning Atom Types. . . . . . . . . . . . . . . . . . . . 5Atom Type Characteristics . . . . . . . . . . . . . . 5Defining Atom Types. . . . . . . . . . . . . . . . . . . . . 6Appendix C: 2D to 3D Conversion . . . . . . 7Stereochemical Relationships. . . . . . . . . . . . . . . 7Example 1. . . . . . . . . . . . . . . . . . . . . . . . . . . 7Example 2. . . . . . . . . . . . . . . . . . . . . . . . . . . 7Example 3. . . . . . . . . . . . . . . . . . . . . . . . . . . 8Example 4. . . . . . . . . . . . . . . . . . . . . . . . . . . 8Labels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8vi • ContentsCambridgeSoft
Appendix D: MM2 . . . . . . . . . . . . . . . . . . . . . . 9MM2 Parameters . . . . . . . . . . . . . . . . . . . . . . . . 9Other Parameters . . . . . . . . . . . . . . . . . . . . . . . . 9Viewing Parameters . . . . . . . . . . . . . . . . . . . . . . 9Editing Parameters . . . . . . . . . . . . . . . . . . . . . . 10The MM2 Force Field in Chem3D. . . . . . . . . . 10Chem3D Changes to Allinger’s Force Field . . 10Charge-Dipole Interaction Term . . . . . . . . 11Quartic Stretching Term . . . . . . . . . . . . . . . 11Electrostatic and van der WaalsCutoff Terms . . . . . . . . . . . . . . . . . . . . . . 11Pi Orbital SCF Computation. . . . . . . . . . . . 11Appendix E: MOPAC . . . . . . . . . . . . . . . . 13MOPAC Background . . . . . . . . . . . . . . . . . . . . 13Potential Functions Parameters . . . . . . . . . . . . 13Adding Parameters to MOPAC . . . . . . . . . . . . 14Appendix F: Parameter Tables . . . . . . . . 15Parameter Table Use . . . . . . . . . . . . . . . . . . . . 15Parameter Table Fields. . . . . . . . . . . . . . . . . . . 16Atom Type Numbers . . . . . . . . . . . . . . . . . 16Quality . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16Reference . . . . . . . . . . . . . . . . . . . . . . . . . . 17Estimating Parameters . . . . . . . . . . . . . . . . . . . 17Creating Parameters . . . . . . . . . . . . . . . . . . . . . 17The Elements . . . . . . . . . . . . . . . . . . . . . . . . . . 18Symbol . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18Covalent Radius . . . . . . . . . . . . . . . . . . . . . 18Pattern. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18Color . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18Atom Types . . . . . . . . . . . . . . . . . . . . . . . . . . . 18Name. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18Symbol . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18van der Waals Radius . . . . . . . . . . . . . . . . . 19Atom Type Number . . . . . . . . . . . . . . . . . . 19Charge. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19Maximum Ring Size. . . . . . . . . . . . . . . . . . 19Rectification Type . . . . . . . . . . . . . . . . . . . 19Geometry . . . . . . . . . . . . . . . . . . . . . . . . . . 19Number of Double Bonds, Triple Bonds, andDelocalized Bonds . . . . . . . . . . . . . . . . . . 20Bound-to Order. . . . . . . . . . . . . . . . . . . . . . 20Bound-to Type . . . . . . . . . . . . . . . . . . . . . . 20Substructures . . . . . . . . . . . . . . . . . . . . . . . . . . 20References . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21Reference Number . . . . . . . . . . . . . . . . . . . 21Reference Description . . . . . . . . . . . . . . . . 21Bond Stretching Parameters. . . . . . . . . . . . . . . 21Bond Type . . . . . . . . . . . . . . . . . . . . . . . . . 21KS. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21Length. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21Bond Dipole . . . . . . . . . . . . . . . . . . . . . . . . 21Record Order . . . . . . . . . . . . . . . . . . . . . . . 22Angle Bending, 4-Membered Ring AngleBending, 3-Membered Ring Angle Bending 22Angle Type. . . . . . . . . . . . . . . . . . . . . . . . . 22KB . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23–XR2– . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23–XRH– . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23–XH2– . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23Record Order . . . . . . . . . . . . . . . . . . . . . . . 23Pi Atoms. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24Atom Type . . . . . . . . . . . . . . . . . . . . . . . . . 24Electron . . . . . . . . . . . . . . . . . . . . . . . . . . . 24Ionization . . . . . . . . . . . . . . . . . . . . . . . . . . 24Repulsion . . . . . . . . . . . . . . . . . . . . . . . . . . 24Pi Bonds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24Bond Type . . . . . . . . . . . . . . . . . . . . . . . . . 24dForce. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25dLength. . . . . . . . . . . . . . . . . . . . . . . . . . . . 25Record Order . . . . . . . . . . . . . . . . . . . . . . . 25Electronegativity Adjustments. . . . . . . . . . . . . 25MM2 Constants . . . . . . . . . . . . . . . . . . . . . . . . 25Cubic and Quartic Stretch Constants . . . . . 26Type 2 (-CHR-) Bending Force Parameters. .for C-C-C Angles . . . . . . . . . . . . . . . . . . 26Stretch-Bend Parameters . . . . . . . . . . . . . . 26Sextic Bending Constant . . . . . . . . . . . . . . 27Dielectric Constants . . . . . . . . . . . . . . . . . . 27Electrostatic and van der Waals CutoffParameters . . . . . . . . . . . . . . . . . . . . . . . . 27MM2 Atom Types . . . . . . . . . . . . . . . . . . . . . . 27Atom type number . . . . . . . . . . . . . . . . . . . 27R* . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27Eps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27Reduct. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28Atomic Weight . . . . . . . . . . . . . . . . . . . . . . 28Lone Pairs. . . . . . . . . . . . . . . . . . . . . . . . . . 28Chem3D 8 Contents • vii
Page 1 and 2: ChemOffice.Com®ChemOffice®Chem3D,
Page 3 and 4: CS Product RegistrationRegistering
Page 5 and 6: User’s GuideCS Chem3D 8.0for Wind
Page 7 and 8: CambridgeSoft Software License1. Gr
Page 9 and 10: No Waiver. The failure of either pa
Page 11 and 12: The failure of either party to asse
Page 13 and 14: ContentsIntroduction . . . . . . .
Page 15 and 16: Rotating Fragments. . . . . . . . .
Page 17: Choosing a Hamiltonian . . . . . .
Page 22 and 23: Administrator• Faster graphics-3D
Page 24 and 25: AdministratorInstallation and Syste
Page 26 and 27: AdministratorModel WindowThe Model
Page 28 and 29: Table ElementDescriptionObjectDescr
Page 30 and 31: To specify the rendering type, atom
Page 32 and 33: AdministratorYou can also build mod
Page 34 and 35: AdministratorElementBound-to orderS
Page 36 and 37: Customizing the UserInterfaceAdmini
Page 38 and 39: AdministratoroptionUse BackBuffer f
Page 40 and 41: AdministratorExamine the atoms and
Page 42 and 43: Administrator2. Release the mouse b
Page 44 and 45: AdministratorReplacing AtomsTo chan
Page 46 and 47: Change the model display type:Build
Page 48 and 49: You will also save the frames you c
Page 50 and 51: Tutorial 4: SearchingFor Conformati
Page 52 and 53: Administrator3. Click in the model
Page 54 and 55: Administrator5. In the Theory tab,
Page 56 and 57: AdministratorFor phenol, the greate
Page 58 and 59: Creating a Model UsingTemplatesChem
Page 60 and 61: The Cartesian Coordinates Options d
Page 62 and 63: Saving a Model with a Different Nam
Page 64 and 65: Administrator44 • Chapter 3: Crea
Page 66 and 67: AdministratorThe following table de
Page 68 and 69:
After you have the backbone, you ca
Page 70 and 71:
AdministratorThe interpretation of
Page 72 and 73:
AdministratorTo use a substructure
Page 74 and 75:
AdministratorThe standard measureme
Page 76 and 77:
AdministratorTo change the bond ord
Page 78 and 79:
Administratorvalues are the standar
Page 80 and 81:
AdministratorTo remove the formal c
Page 82 and 83:
AdministratorRefining a ModelAfter
Page 84 and 85:
AdministratorSelecting Atoms in a G
Page 86 and 87:
AdministratorWhen you choose Show A
Page 88 and 89:
AdministratorTo perform a rotation
Page 90 and 91:
To move three atoms to a plane and
Page 92 and 93:
Administratorit and other atoms. Al
Page 94 and 95:
AdministratorIf an atom is position
Page 96 and 97:
AdministratorModel TypesThe followi
Page 98 and 99:
AdministratorColoring DisplaysYou c
Page 100 and 101:
To change one of the colors in the
Page 102 and 103:
AdministratorAll atoms currently in
Page 104 and 105:
AdministratorDisplaying MolecularSu
Page 106 and 107:
AdministratorMolecular Surface Colo
Page 108 and 109:
AdministratorSolvent Accessible Sur
Page 110 and 111:
AdministratorTo display a Connolly
Page 112 and 113:
previously computed surface. If you
Page 114 and 115:
If you want todisplay …Then Selec
Page 116 and 117:
Administrator• From the Edit menu
Page 118 and 119:
AdministratorShowing Dihedral Angle
Page 120 and 121:
Administrator5. Select the C(2)-C(3
Page 122 and 123:
AdministratorThe color of the atoms
Page 124 and 125:
AdministratorTo begin the docking c
Page 126 and 127:
AdministratorTo perform an overlay,
Page 128 and 129:
To remove all frames after the fram
Page 130 and 131:
Administrator106 • Chapter 7: Ins
Page 132 and 133:
If you want to …Then select …Fi
Page 134 and 135:
AdministratorBMPThe Bitmap file for
Page 136 and 137:
When you save a file as a Connectio
Page 138 and 139:
AdministratorIf you want to …buil
Page 140 and 141:
Administratorexports .PDB. The .PDB
Page 142 and 143:
Administrator116 • Chapter 8: Pri
Page 144 and 145:
AdministratorComputational Chemistr
Page 146 and 147:
AdministratorThe following table su
Page 148 and 149:
Administrator• A single point cal
Page 150 and 151:
Administrator• Potential energy f
Page 152 and 153:
AdministratorE Stretch= 71.94 ∑ K
Page 154 and 155:
Administratorinclude interactions w
Page 156 and 157:
Administratorwhich are used to scal
Page 158 and 159:
AdministratorQuantum mechanical met
Page 160 and 161:
AdministratorLinear Combination of
Page 162 and 163:
AdministratorUHFThe UHF method trea
Page 164 and 165:
Administrator• Hypervalent compou
Page 166 and 167:
Administrator138 • Chapter 9: Com
Page 168 and 169:
AdministratorIf you want to …spec
Page 170 and 171:
AdministratorThe Total Steric Energ
Page 172 and 173:
AdministratorThe conformation you c
Page 174 and 175:
.AdministratorSticks < Ball and Sti
Page 176 and 177:
AdministratorThe simulation ends wh
Page 178 and 179:
AdministratorThe units are kcal/mol
Page 180 and 181:
AdministratorRepeating an MM2Comput
Page 182 and 183:
AdministratorChoose the appropriate
Page 184 and 185:
AdministratorTo determine the appro
Page 186 and 187:
AdministratorFirst excited quintet:
Page 188 and 189:
AdministratorMOPAC uses its default
Page 190 and 191:
AdministratorThe following contains
Page 192 and 193:
The heat of formation is composed o
Page 194 and 195:
AdministratorComparing Cation Stabi
Page 196 and 197:
Administratormeta>para>ortho, where
Page 198 and 199:
Administrator3. Click in the model
Page 200 and 201:
Form ofglycine∆H(kcal/mole)Solven
Page 202 and 203:
AdministratorThe following table co
Page 204 and 205:
AdministratorThe Message window dis
Page 206 and 207:
AdministratorDescriptionVibrational
Page 208 and 209:
You can create a structure from the
Page 210 and 211:
AdministratorIf you want to …reco
Page 212 and 213:
AdministratorSave a customized job
Page 214 and 215:
Administrator2. Type the full path
Page 216 and 217:
Administrator3. From the Basis Set
Page 218 and 219:
AdministratorA new model window is
Page 220 and 221:
PropertyDescriptionPropertyDescript
Page 222 and 223:
PropertyDescriptionError MessageCau
Page 224 and 225:
PropertyDescriptionThe GAMESS serve
Page 226 and 227:
The property filters are:Administra
Page 228 and 229:
AdministratorTo perform property ca
Page 230 and 231:
The Select Descriptors dialog box a
Page 232 and 233:
Administrator• Sum• Standard de
Page 234 and 235:
To access Browse ChemStore.com:The
Page 236 and 237:
AdministratorTo access the ChemOffi
Page 238 and 239:
AdministratorDefining Substructures
Page 240 and 241:
AdministratorA4 • CambridgeSoftDe
Page 242 and 243:
AdministratorIf an atom can be assi
Page 244 and 245:
AdministratorExample 3In Example 3,
Page 246 and 247:
AdministratorEditing ParametersYou
Page 248 and 249:
Administrator5. A matrix called the
Page 250 and 251:
AdministratorAdding Parameters toMO
Page 252 and 253:
AdministratorParameter Table UseEle
Page 254 and 255:
AdministratorThe ElementsThe Elemen
Page 256 and 257:
AdministratorTo view the menu of ge
Page 258 and 259:
AdministratorFinally, the 1-19 bond
Page 260 and 261:
AdministratorPi AtomsThe Pi Atoms t
Page 262 and 263:
AdministratorCubic and Quartic Stre
Page 264 and 265:
potential well increases, as does t
Page 266 and 267:
AdministratorThe counterintuitive f
Page 268 and 269:
Administratorcorrespondence between
Page 270 and 271:
AdministratorAlchemy FileThe follow
Page 272 and 273:
Administrator2. The first line of a
Page 274 and 275:
H 102 2.127594 1.865631 1.48999 21
Page 276 and 277:
Administrator6 1 1.40195 2 107.6989
Page 278 and 279:
41 3 1 0 0 0 0 0 0 0 0 0 0 1.222366
Page 280 and 281:
Administrator21 -1.2615 2.1277 0.01
Page 282 and 283:
Administrator24-42 Bond id, fromato
Page 284 and 285:
Administrator51 2 1 1 6 0 0.000 0 0
Page 286 and 287:
Administrator18. Line 49 contains a
Page 288 and 289:
AdministratorFORTRAN FormatsThe des
Page 290 and 291:
22 Chain Identifier No12-16 Serial
Page 292 and 293:
AdministratorLine 18 H 0 0 0Line 19
Page 294 and 295:
Administratorof hydrogens attached
Page 296 and 297:
AdministratorNumberof AtomsNumberof
Page 298 and 299:
AdministratorLine 30 @BONDLine 31 1
Page 300 and 301:
11-29 Atom type, name,coordinates a
Page 302 and 303:
AdministratorA66 • CambridgeSoftW
Page 304 and 305:
AdministratorTroubleshootingThis se
Page 306 and 307:
4. If the problem still occurs, Fax
Page 308 and 309:
AdministratorAtom typesassigning au
Page 310 and 311:
Administratorchem3d.h 17chem3d.tlb
Page 312 and 313:
AdministratorDisplay Stereo View 80
Page 314 and 315:
AdministratorFont 16Font size 16For
Page 316 and 317:
Administratorjdt file format 114, 1
Page 318 and 319:
AdministratorMolecular Surfacescalc
Page 320 and 321:
AdministratorParameters 12bond angl
Page 322 and 323:
AdministratorSelect Fragment comman
Page 324 and 325:
AdministratorTools palette 6, 44Too
Page 326 and 327:
Administratorxx • IndexCambridgeS
Page 328 and 329:
CAMBRIDGESOFTChemOffice Desktop toK
Page 330 and 331:
CS ChemOfficeSoftware SuitesChemOff
Page 332 and 333:
DESKTOPCS E-NotebookElectronic Jour
Page 334 and 335:
DESKTOPCS ChemDrawChemical Structur
Page 336 and 337:
DESKTOPCS Chem3DMolecular Modeling
Page 338 and 339:
DESKTOPCS ChemFinderSearching and I
Page 340 and 341:
DESKTOPCS ChemInfoReference and Che
Page 342 and 343:
ENTERPRISEChemOffice WebServerEnter
Page 344 and 345:
ENTERPRISEOracle CartridgeEnterpris
Page 346 and 347:
KNOWLEDGEE-Notebook EnterpriseDeskt
Page 348 and 349:
KNOWLEDGEDocument ManagerDesktop to
Page 350 and 351:
KNOWLEDGE21CFR11 ComplianceElectron
Page 352 and 353:
RESEARCH&Registration SystemChemica
Page 354 and 355:
RESEARCH&Inventory ManagerChemical
Page 356 and 357:
RESEARCH&CombiChem EnterpriseDeskto
Page 358 and 359:
RESEARCH&BioAssay HTSBiological Ass
Page 360 and 361:
RESEARCH&BioSAR BrowserBiological a
Page 362 and 363:
CHEMICALChemACX DatabaseAvailable C
Page 364 and 365:
CHEMICALThe Merck IndexChemistry’
Page 366 and 367:
CHEMICALChemical DatabasesReference
Page 368 and 369:
CONSULTING &Consulting & ServicesDe
Page 370 and 371:
Administrator
Page 372 and 373:
MENUSCreate a new model window.Open
Page 374 and 375:
WORKING WITH SELECTIONSIf you want
Page 376:
CS ChemOffice®Desktop to Enterpris
show all

Chem3D 8.0 Manual - CambridgeSoft

Create successful ePaper yourself

Delete template?

Save as template?