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Polymers
Polymer structures cannot be expressed by SMILES. However, Struct>Name supports many homopolymers, copol-
ymers and alternating polymers. For example:
Figure 8.4: polyaziridine compound with sulfamic acid (1:1)
Other compounds
Phosphorous and Arsenic compounds
Si, Ge, Sn, and Pb compounds
Boron compounds
Organometallic compounds
Struct>Name generates names with proper CIP stereochemistry descriptors.
Struct>Name provides direct support for stoichoimetry specified as bracket properties, including fractional stoi-
chiometry. Also, the manner in which the stoichiometry of 0.5 ("hemi") and 1.5 ("sesqui") is handled has also been
improved. For example:
Figure 8.5: 2-(aminooxy)acetic acid hemihydrochloride
Struct>Namefollows IUPAC rules as closely as possible when generating chemical names.. However, while han-
dling indicated hydrogens, it conforms to CAS nomenclature recommendations. For example, the carbon atom
between two oxygen atoms in 1,3-dioxole can never form double bonds as its two neighbors (oxygen atoms) have no
free valences. While preferred IUPAC (PIN) name for that structure is 2H-1,3-dioxole, Struct>Name generates the
name 1,3-dioxole. The name produced by Struct>Name conforms to CAS nomenclature recommendations in this
regard.
Unsupported structures
This feature has a few limitations for interpreting some structures such as:
ChemBioDraw 13.0
Chapter 8: Struct=Name 123 of 401
- ChemBioDraw 13.0 User Guide 1
- Table of Contents 2
- Table of Contents ii 3
- Table of Contents iii 4
- Table of Contents iv 5
- Table of Contents v 6
- What’s new 7
- What’s new vii 8
- What’s new viii 9
- Introduction 10
- Troubleshooting 11
- Performance 11
- Applications and drivers 12
- Getting started 13
- Toolbars 14
- Documents 15
- Deleting a keyword 16
- Discarding changes 16
- Undo, redo, and repeat 16
- Saving documents 16
- Autosave 17
- Default file format 17
- Dropbox interface 17
- Signing into Dropbox 17
- Upload files 18
- Download files 19
- Basic drawings 21
- Quadruple bonds 22
- Dative bonds 22
- Wedged bonds 22
- Changing bonds 22
- Changing bond types 23
- Changing double bonds 23
- Aligning double bonds 23
- Moving atoms 23
- Reducing ring size 24
- Bond crossing 24
- Fixed bonds 24
- Drawing fixed length bond 24
- Drawing fixed angle bonds 24
- Changing fixed values 25
- Periodic table 25
- Captions 26
- Formatting 27
- Coloring text 28
- Caption width 29
- About fonts 29
- Character map 29
- Using hotkeys 30
- Nicknames 31
- Using nicknames 31
- Applying nicknames 31
- Expanding nicknames 32
- Annotations 33
- Drawing rings 35
- Spiro and sprout rings 36
- Cyclohexane chair rings 36
- Aromatic structures 37
- Delocalized rings 37
- Resonance structures 37
- Changing chain direction 38
- Fixed length 38
- Fixed angle 38
- Adding chains to structures 38
- Specifying chain length 38
- Arrow heads 39
- Arrow types 39
- Hollow arrows 40
- Connecting arrows 41
- Curved arrows 42
- Colored arrows 42
- Coloring block arrows 42
- Drawing elements 43
- Circles and ovals 43
- Brackets 44
- Freehand shapes 46
- Selecting objects 47
- The lasso tool 47
- The marquee tool 47
- Selecting entire structures 48
- Selecting objects by clicking 48
- Selecting multiple objects 48
- Deselecting all objects 48
- Deselecting one object 48
- Resizing objects 49
- Rotating objects 50
- Moving the center of rotation 50
- Moving objects 51
- Copying objects 51
- The info window 52
- Mirror images 52
- Deleting objects 53
- Joining structures 53
- Grouping objects 53
- Ungrouping objects 54
- Scaling objects 54
- Centering objects 55
- Aligning objects 55
- Distributing objects 55
- Clean Up Structure 56
- Check structure 57
- Chemical warnings 57
- Warning preferences 58
- Warning Description 59
- Linear Atom 59
- BioDraw templates 60
- Advanced BioDraw 61
- Anatomy templates 61
- Bio Instruments 62
- Microorganisms 62
- Organelles 62
- Customizable objects 63
- Membrane line 64
- Membrane arc 64
- Helix proteins 64
- DNA molecules 65
- Coloring residues 65
- Ribosomes 66
- Plasmid maps 66
- Creating a plasmid map 66
- Adding regions 67
- Adding markers 67
- Moving markers 67
- Resizing regions 67
- Enhancing the drawing 68
- Drawing biopolymers 69
- Biopolymer editor 70
- Protecting groups 71
- Pasting sequences 72
- Paste text strings 73
- Expanding sequences 74
- Contracting labels 74
- Modifying sequence residues 74
- Removing residues 76
- Replacing residues 77
- Adding residues 77
- Hybrid biopolymers 78
- IUPAC codes 79
- Branched peptides 82
- Disulfide bridges 83
- Lactam bridges 84
- Tutorials 86
- Tutorial 2: Drawing rings 87
- The structure is complete 89
- Drawing the Newman projection 98
- Tutorial 6: Stereochemistry 99
- Adding atom labels 100
- Tutorial 7: Templates 102
- Advanced drawing techniques 104
- Creating labels 105
- Expanding labels 106
- Multiple atoms 106
- Attachment points 108
- Atom numbering 110
- Structure perspective 111
- Mass fragmentation 112
- Drawing reactions 113
- Drawing an arrow 114
- Drawing the product 114
- Clean Up Reaction 116
- The reaction interpreter 117
- Electron and radical pushing 118
- Stoichiometry grid 119
- Templates 122
- Customizing templates 123
- Modifying a template 123
- Adding a template 123
- Annotating a template 123
- Defining nicknames 124
- Nicknames and atom labels 126
- Deleting nicknames 126
- Troubleshooting nicknames 126
- ChemScript 127
- Struct=Name 129
- Non-ringed structures 130
- Ringed structures 130
- Fused ring systems 131
- Bridged fused ring systems 131
- Polymers 132
- Other compounds 132
- Unsupported structures 132
- Name>Struct 133
- Converting clipboard names 134
- Converting captions 134
- Supported structures 134
- ChemBioDraw 13.0 135
- Chemistry features 136
- ChemBioFinder hotlink 137
- Stereochemistry 138
- Hiding indicators 139
- Formatting indicators 139
- Removing indicators 139
- Positioning indicators 139
- Relative stereochemistry 140
- Chemical annotations 141
- S-orbitals 142
- Sigma orbitals 142
- Single lobe orbitals 142
- Hybrid orbitals 142
- Chemical symbols 143
- H–dot and H–dash 143
- Lone pair/diradical 143
- Charge symbols 144
- Chemical properties 145
- Boiling point 146
- Critical pressure 147
- Critical temperature 147
- Critical volume 147
- CLogP/CMR 147
- Gibbs free energy 147
- Heat of formation 148
- Henry’s law constant 148
- Melting point 148
- ChemBioFinder properties 151
- Viewing chemical properties 151
- 3D viewing 152
- In the document window 153
- In ChemBio3D preview 153
- Resizing spots 156
- Custom spots 156
- Gel electrophoresis tool 156
- Parameters in ChemNMR 159
- Spectrometer frequency 159
- NMR shifts 160
- Modifying NMR frequency 160
- Viewing spectral assignments 161
- Removing spectral assignments 161
- Custom shift correction data 161
- NMR data format 161
- Updating the ChemNMR database 162
- Restoring default NMR data 162
- Example supplementary data 162
- ChemNMR limitations 164
- NMR references 165
- ChemDraw/Excel 166
- Importing hit lists 167
- Exporting tables 167
- Synchronizing tables 168
- Adding structures 169
- Searching 170
- Opening a database 171
- Normal searches 171
- Similarity searches 171
- R-Group analysis 172
- Working with structures 172
- Using the clipboard 173
- ChemDraw/Excel functions 174
- Chemical name 175
- Chemical composition 175
- Chemical formula 175
- Molecular weight 176
- Exact mass 176
- Number of atoms 176
- SMILES string 177
- Formal charge 177
- Melting/freezing point 178
- Vapor pressure 179
- Ideal gas thermal capacity 180
- Molar refractivity 181
- Water solubility 181
- Balaban index 183
- Cluster count 183
- Topological index 183
- Number of rotatable bonds 184
- Polar surface area 184
- Shape attribute 184
- Shape coefficient 184
- Sum of degrees 185
- Sum of valence degrees 185
- Topological diameter 185
- Total connectivity 185
- Total valence connectivity 185
- Wiener index 186
- Lipinski rule of five 187
- Ghose modifications 187
- Henry’s Law constant 192
- Total Valence Connectivity 196
- CombiChem 197
- Entering a generic reaction 198
- Creating reactant worksheets 199
- Searching for reactants 199
- Creating an experiment 200
- Experiment worksheets 201
- Configuring plates 202
- Assigning plates 202
- Browsing plates 203
- Viewing related structures 203
- ChemBioFinder/Office 204
- Editing the hitlist 205
- ChemDraw for Excel 205
- Query structures 206
- Generic nickname hotkeys 207
- Defining generic nicknames 207
- Atom properties 209
- Query indicators 210
- Positioning query indicators 211
- Hiding a query indicators 211
- Removing atom properties 211
- Atom property options 211
- Substituents 211
- Implicit hydrogens 213
- Ring bond count 213
- Unsaturation 214
- Reaction change 214
- Reaction stereo 214
- Free sites 215
- Translation 216
- Bond properties 217
- Viewing bond properties 218
- Removing bond properties 218
- Bond property options 219
- Bond types 219
- Topology 219
- Element lists 220
- Setting bracket properties 222
- Bracket usage 222
- Structure-based polymers 222
- Source-based polymers 223
- Multiple groups 224
- Link nodes 225
- Alternative groups 226
- Defining alternative groups 227
- Multiple attachment points 229
- Attachment point numbering 230
- Hiding rank indicators 230
- R-group reaction queries 231
- Anonymous alternative groups 232
- Expand generic structures 233
- R-Logic queries 234
- Atom-to-Atom mapping 235
- Displaying and printing 236
- Automatic mapping 236
- Manual mapping 236
- Stereochemical symbols 238
- 3D properties 239
- Export compatibility 240
- Sharing information 244
- Pasting SMILES 245
- Creating SLN strings 245
- Creating InChI™ strings 245
- Creating InChIKey strings 245
- Transferring objects 246
- Embedding objects 247
- Exporting 247
- Importing 248
- ISIS™ compatibility 249
- Attached data 249
- Modifying attached data 249
- File formats 250
- Transferring across platforms 252
- Preferences and settings 253
- Default document location 254
- Default open file format 254
- Setting the default tool 254
- Highlight box tolerance 254
- The ChemDraw items folder 255
- Default styles 255
- Saving customized styles 255
- Setting preferences 256
- Windows XP 258
- Windows Vista 258
- Customizing toolbars 268
- Document and object settings 268
- Drawing settings 269
- Configuring documents 270
- Configuring objects 271
- Analysis and properties 271
- Formatting captions 272
- Style indicators 273
- Specifying line spacing 273
- Aligning text 273
- Automatic alignment 274
- Changing the default format 275
- Biopolymer settings 276
- Customizing hotkeys 277
- {description}”/> 278
- Working with color 279
- Color by element 280
- The color palette 281
- Customizing colors 281
- Document settings 282
- Adv. Synth Catal 283
- J.Chin. Chem. Soc 283
- J. Mol. Mod. (1 column) 284
- New Document 284
- New Slide 284
- Phytomedicine 285
- Science of Synthesis 286
- Synthesis, Synlett 286
- Verlag Helvetica Chimica Acta 287
- Wiley Document 287
- Page layout 288
- Headers and footers 289
- Printing 290
- Saving page setup settings 291
- 35mm slide boundary guides 291
- Viewing drawings 292
- The crosshairs 293
- Moving the crosshair 293
- Positioning objects 293
- Creating a table 293
- Resizing tables 294
- Customizing borders 294
- Using the text tool 295
- Creating a new row 296
- Inserting a new row 296
- Chemical interpretation 297
- Bond conventions 298
- Atom labels 299
- Chemically significant text 301
- Isotopes and elements 302
- Radicals 303
- H-Dot/H-Dash 303
- Complexes 303
- Multi-center attachments 304
- Cahn-Ingold-Prelog 305
- Stereochemical indicators 305
- Stereochemical flags 305
- Polymer representations 307
- References 307
- Analysis messages 307
- Property calculations 310
- The ChemBio3D MOPAC interface 312
- Other properties 312
- Miscellaneous properties 312
- Shortcuts and hotkeys 313
- Bond hotkeys 314
- Function hotkeys 315
- Shortcuts 316
- Structure 318
- Registering online 321
- User’s guide 321
- Technical support 321
- ACX structures and numbers 322
- ACX structures 322
- ACX numbers 322
- ChemBio3D ActiveX Control 322
- SciStore.com 322
- PerkinElmer Informatics 323
- Using the ChemOffice SDK 323
- Index 315 of 401 324
- Index 316 of 401 325
- Index 317 of 401 326
- Index 318 of 401 327
- Index 319 of 401 328
- Index 320 of 401 329
- Index 321 of 401 330
- Index 322 of 401 331
- Index 323 of 401 332
- Index 324 of 401 333
- Index 325 of 401 334
- Index 326 of 401 335
- Index 327 of 401 336
- Index 328 of 401 337
- Index 329 of 401 338
- Index 330 of 401 339
- Index 331 of 401 340
- Index 332 of 401 341
- Index 333 of 401 342
- Index 334 of 401 343
- Index 335 of 401 344
- Index 336 of 401 345
- Index 337 of 401 346
- Index 338 of 401 347
- Index 339 of 401 348
- Index 340 of 401 349
- Index 341 of 401 350
- Index 342 of 401 351
- Index 343 of 401 352
- Index 344 of 401 353
- Index 345 of 401 354
- Index 346 of 401 355
- Index 347 of 401 356
- Index 348 of 401 357
- Index 349 of 401 358
- Index 350 of 401 359
- Index 351 of 401 360
- Index 352 of 401 361
- Index 353 of 401 362
- Index 354 of 401 363
- Index 355 of 401 364
- Index 356 of 401 365
- Index 357 of 401 366
- Index 358 of 401 367
- Index 359 of 401 368
- Index 360 of 401 369
- Index 361 of 401 370
- Index 362 of 401 371
- Index 363 of 401 372
- Index 364 of 401 373
- Index 365 of 401 374
- Index 366 of 401 375
- Index 367 of 401 376
- Index 368 of 401 377
- Index 369 of 401 378
- Index 370 of 401 379
- Index 371 of 401 380
- Index 372 of 401 381
- Index 373 of 401 382
- Index 374 of 401 383
- Index 375 of 401 384
- Index 376 of 401 385
- Index 377 of 401 386
- Index 378 of 401 387
- Index 379 of 401 388
- Index 380 of 401 389
- Index 381 of 401 390
- Index 382 of 401 391
- Index 383 of 401 392
- Index 384 of 401 393
- Index 385 of 401 394
- Index 386 of 401 395
- Index 387 of 401 396
- Index 388 of 401 397
- Index 389 of 401 398
- Index 390 of 401 399
- Index 391 of 401 400
- Index 392 of 401 401
- Index 393 of 401 402
- Index 394 of 401 403
- Index 395 of 401 404
- Index 396 of 401 405
- Index 397 of 401 406
- Index 398 of 401 407
- Index 399 of 401 408
- Index 400 of 401 409
- Index 401 of 401 410
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