Chem3D Users Manual - CambridgeSoft

More documents

Recommendations

Info

Administrator Geometry The geometry for an atom type describes both the number of bonds that extend from this type of atom and the angles formed by those bonds. Possible geometries are: • 0 Ligand • 1 Ligand • 5 Ligands • Bent • Linear • Octahedral • Square planar • Tetrahedral • Trigonal bipyramidal • Trigonal planar • Trigonal pyramidal NOTE: Standard bond angle parameters are used only when the central atom has a tetrahedral, trigonal or bent geometry. Number of Double Bonds, Triple Bonds, and Delocalized Bonds The number of double bonds, number of triple bonds, and number of delocalized bonds are integers ranging from zero to the number of ligands as specified by the geometry. Chem3D uses this information both to assign atom types based on the bond orders and to assign bond orders based on atom types. Bound-to Order Specifies the order of the bond acceptable between this atom type and the atom type specified in the bound-to type. For example, for C Carbonyl, only double bonds can be formed to bound-to type O Carboxylate. If there is no bound-to type specified, this field is not used. Possible bond orders are: • Single • Double • Triple • Delocalized NOTE: The bound-to order should be consistent with the number of double, triple, and delocalized bonds for this atom type. If the bound-to type of an atom type is not specified, its bound-to order is ignored. Bound-to Type Specifies the atom type that this atom must be bound to. If there is no restriction, this field is empty. Used conjunction with the Bound-to Order field. Non-blank Bound-to-Type values: • C Alkene • C Carbocation • C Carbonyl • C Carboxylate • C Cyclopentadienyl • C Cyclopropene • C Epoxy • C Isonitrile • C Metal CO • C Thiocarbonyl • H Alcohol • H Thiol • N Ammonium • N Azide Center • N Azide End 276• Parameter Tables CambridgeSoft Atom Types
• N Isonitrile • N Nitro • O Carbonyl • O Carboxylate • O Epoxy • O Metal CO • O Nitro • O Oxo • O Phosphate • P Phosphate • S Thiocarbonyl Substructures The Substructure table (Substructures.xml) contains substructures to use in your model. To use a substructure simply type its name in the Replacement text box (or paste it, after copying the name cell to the Clipboard) and press the Enter key when an atom(s) is selected, or double-click an atom. You can also copy the substructures picture to the Clipboard and paste it into a model window. The substructure is attached to selected atom(s) in the model window. If no atom is selected, a fragment is added. You can also define your own substructures and add them to the table. The table below shows the substructure table window with the substructure records open (triangles facing down). Clicking a triangle closes the record. The picture of the substructure is minimized. References The References table (References.xml) contains information concerning the source for other parameters. Use of the References table does not affect the other tables in any way. Two fields are used for each reference record: the reference number and the reference description. Reference Number The reference number is an index by which the references are organized. Each measurement also contains a reference field that should contain a reference number, indicating the source for that measurement. Reference Description The reference description contains whatever text you need to describe the reference. Journal references or bibliographic data are common examples of how you can describe your references. Bond Stretching Parameters The Bond Stretching Parameters table (Bond Stretching Parameters.xml) contains information about standard bond lengths between atoms of various atom types. In addition to standard bond lengths are information used in MM2 calculations in Chem3D. The Bond Stretching table contains parameters needed to compute the bond stretching and electrostatic portions of the force field for the bonds in your model. The Bond Stretching Parameters record consists of six fields: Bond Type, KS, Length, Bond Dpl, Quality, and Reference. Bond Type The Bond Type field contains the atom type numbers of the two bonded atoms. For example, Bond Type 1-2 is a bond between an alkane carbon and an alkene carbon. Appendices ChemOffice 2005/Appendix Parameter Tables • 277 Substructures
Page 1:
ChemOffice.Com ® ChemOffice ® Che
Page 4 and 5:
License Information ChemOffice, Che
Page 6 and 7:
· Licensed users of ChemOffice Ent
Page 8 and 9:
computer, except as provided below.
Page 10 and 11:
Q: IS IT OK TO COPY MY COLLEAGUE’
Page 12 and 13:
A Guide to CambridgeSoft Manuals An
Page 14 and 15:
Administrator Setting Molecular Sur
Page 16 and 17:
Administrator Methods Available in
Page 18 and 19:
Administrator Defining Atom Types.
Page 20 and 21:
Administrator • CambridgeSoft
Page 22 and 23:
Administrator provides a balance be
Page 24 and 25:
Administrator the activation each t
Page 26 and 27:
Administrator The following table d
Page 28 and 29:
Administrator • Stereo Pairs—A
Page 30 and 31:
Administrator • Bond Angles—Dis
Page 32 and 33:
Administrator The Building Toolbar
Page 34 and 35:
Administrator The Calculation Toolb
Page 36 and 37:
Administrator 1. Right-click in the
Page 38 and 39:
Administrator • In the Model Sett
Page 40 and 41:
Administrator modes and color setti
Page 42 and 43:
Administrator 30 •Chem3D Basics C
Page 44 and 45:
Administrator 2. Click the ChemDraw
Page 46 and 47:
3. Move the pointer over the C-C bo
Page 48 and 49:
Administrator Add serial numbers an
Page 50 and 51:
Administrator 5. Press the Enter ke
Page 52 and 53:
. Administrator b. From the Structu
Page 54 and 55:
Administrator In the Measurements t
Page 56 and 57:
A molecule of Epinephrine appears.
Page 58 and 59:
Administrator Tutorial 7: Docking M
Page 60 and 61:
Administrator To save the iteration
Page 62 and 63:
The allyl radical, CH 2 =CHCH 2·,
Page 64 and 65:
Administrator Determine the raw spi
Page 66 and 67:
Administrator atoms are relatively
Page 68 and 69:
To change the structural display ty
Page 70 and 71:
Administrator When sizing by partia
Page 72 and 73:
Administrator Depth Fading3D enhanc
Page 74 and 75:
• Select Parallel to rotate the r
Page 76 and 77:
Administrator • From the Computat
Page 78 and 79:
Administrator Surface Type Solid De
Page 80 and 81:
Administrator 2. Adjust the slider
Page 82 and 83:
Administrator Density surface is ca
Page 84 and 85:
Administrator 72 •Displaying Mode
Page 86 and 87:
Administrator The following table d
Page 88 and 89:
Administrator When Correct Atom Typ
Page 90 and 91:
Administrator To use the same text
Page 92 and 93:
Administrator Example 2. Building a
Page 94 and 95:
Administrator copied into blank tab
Page 96 and 97:
Administrator 3. Type the atom type
Page 98 and 99:
Administrator Clean Up Structure or
Page 100 and 101:
Setting Serial Numbers this step, y
Page 102 and 103:
Administrator Refining a Model Afte
Page 104 and 105:
Administrator Selecting Multiple At
Page 106 and 107:
Administrator New in Chem3D version
Page 108 and 109:
Administrator Dragging moves atoms
Page 110 and 111:
Administrator 3. Hold down the Shif
Page 112 and 113:
To position a plane in your model p
Page 114 and 115:
Administrator • Second Positioned
Page 116 and 117:
Administrator For example, consider
Page 118 and 119:
Administrator If you want to displa
Page 120 and 121:
Administrator Example: To examine t
Page 122 and 123:
Administrator Chem3D provides two o
Page 124 and 125:
Administrator change a property. By
Page 126 and 127:
Administrator To add to a group: 1.
Page 128 and 129:
To stop spinning: • On the Movie
Page 130 and 131:
Administrator If you want to … Th
Page 132 and 133:
Administrator EPS The PostScript fi
Page 134 and 135:
If you want the file to … Then cl
Page 136 and 137:
Molecular Design Limited MolFile (.
Page 138 and 139:
Administrator 7. Leave the last lin
Page 140 and 141:
Administrator 128•Printing and Ex
Page 142 and 143:
Administrator • Semiempirical Ext
Page 144 and 145:
Method Type Advantages Disadvantage
Page 146 and 147:
Administrator • A single point ca
Page 148 and 149:
Administrator • Molecular mechani
Page 150 and 151:
Administrator constant), while θ 0
Page 152 and 153:
Administrator The van der Waals int
Page 154 and 155:
Administrator 6. The modified value
Page 156 and 157:
the same wave function and a consta
Page 158 and 159:
Administrator A variety of other ba
Page 160 and 161:
Administrator Molecular wave functi
Page 162 and 163:
Administrator activation barriers.
Page 164 and 165:
3. From the Calculations menu, poin
Page 166 and 167:
minimizing a second model, the mini
Page 168 and 169:
Administrator move to lower the ene
Page 170 and 171:
. Administrator Molecular Dynamics
Page 172 and 173:
Administrator If you want to … Th
Page 174 and 175:
Administrator The Compute Propertie
Page 176 and 177:
Administrator To run a previously c
Page 178 and 179:
Administrator The procedures assume
Page 180 and 181:
Administrator improvements in each
Page 182 and 183:
Administrator • Overall errors in
Page 184 and 185:
Administrator The following table c
Page 186 and 187:
Administrator TRIPLET QUARTET QUINT
Page 188 and 189:
Administrator Chemical symbol ++ ba
Page 190 and 191:
Administrator 4. Click Run. A new m
Page 192 and 193:
Administrator Minimizing Energy Min
Page 194 and 195:
Administrator criteria, to optimize
Page 196 and 197:
Administrator 6. Hold down the S ke
Page 198 and 199:
Administrator Dipole Moment The dip
Page 200 and 201:
Administrator Molecular Surfaces Mo
Page 202 and 203:
The following table contains the ke
Page 204 and 205:
Administrator 3. Click in the model
Page 206 and 207:
Keyword Description 7. On the Prope
Page 208 and 209:
Administrator Hyperfine Coupling Co
Page 210 and 211:
Administrator 198•MOPAC Computati
Page 212 and 213:
Administrator If you want to … re
Page 214 and 215:
Administrator In the Results In tex
Page 216 and 217:
Administrator Repeating a Gaussian
Page 218 and 219:
Property Description Property Descr
Page 220 and 221:
Property Description Error Message
Page 222 and 223:
Administrator Property Electronic E
Page 224 and 225:
Administrator To specify the calcul
Page 226 and 227:
Administrator 3. Click Open. The ap
Page 228 and 229:
Administrator • Server—limits t
Page 230 and 231:
Administrator To perform property c
Page 232 and 233:
The Step 4 of 4 dialog box appears.
Page 234 and 235:
Administrator • From the ChemOffi
Page 236 and 237:
Administrator Accessing the Online
Page 238 and 239: Administrator To find a structure t
Page 240 and 241: Administrator 228• Accessing the
Page 242 and 243: Administrator Performance Below are
Page 244 and 245: Administrator Defining Substructure
Page 246 and 247: Administrator If an atom can be ass
Page 248 and 249: Key Drag Shift+Drag Administrator Q
Page 250 and 251: Administrator 238• Keyboard Modif
Page 252 and 253: Administrator Example 3 In Example
Page 254 and 255: Administrator 14 13 H 2.197 -0.8229
Page 256 and 257: Administrator Connection tables by
Page 258 and 259: Administrator FORTRAN Formats The F
Page 260 and 261: 5 6 1.11606 3 109.41 5 109.41 -1 21
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
Page 276 and 277: Administrator Line 56 -2794 21139 6
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 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
Page 306 and 307: Administrator Adding Parameters to
Page 308 and 309: Administrator fragments 84 paramete
Page 310 and 311: Administrator CC1 see Cartesian coo
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
Page 330 and 331: SOLUTIONS Enterprise Solutions APPL
Page 332 and 333: Desktop to Enterprise Solutions Che
Page 334 and 335: SOFTWARE E-Notebook Ultra Ultimate
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
Page 358 and 359:
DISCOVERY • Reagent lists can be
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
Page 375:
CS ChemOffice ® Desktop to Enterpr
show all

Chem3D Users Manual - CambridgeSoft

You also want an ePaper? Increase the reach of your titles

Delete template?

Save as template?