ChemDraw User's Manual - CambridgeSoft

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AdministratorHiding the Crosshair . . . . . . . . . . . . . . . . . . . . . . 184Centering on a Page . . . . . . . . . . . . . . . . . . . . . . . 184Aligning Objects . . . . . . . . . . . . . . . . . . . . . . . . . . 185Distributing Objects. . . . . . . . . . . . . . . . . . . . . . . 185Front to Back Ordering . . . . . . . . . . . . . . . . . . . . 185Send to Back . . . . . . . . . . . . . . . . . . . . . . . . . . . 186Bring to Front . . . . . . . . . . . . . . . . . . . . . . . . . . 186Creating Tables. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 186Creating Tables with the Table Tool . . . . . . . . . 186Creating Tables with the Text Tool . . . . . . . . . . 188Creating the First Row (column headings) . 188Creating a New Row . . . . . . . . . . . . . . . . . . . . 189Adjusting Row or Column Spacing . . . . . . . 189Moving Around In Tables . . . . . . . . . . . . . . . 189Inserting a New Row . . . . . . . . . . . . . . . . . . . . 190Chapter 12: Sharing InformationUsing the Clipboard . . . . . . . . . . . . . . . . . . . . . . . . . . 191SMILES and SMIRKS Strings . . . . . . . . . . . . . . 191Creating SMILES Strings . . . . . . . . . . . . . . . . 191Pasting SMILES from Clipboard . . . . . . . . . 192Creating SLN Strings . . . . . . . . . . . . . . . . . . . 192Using Drag-and-Drop. . . . . . . . . . . . . . . . . . . . . . . . . 192Transferring Between ChemDraw Documents. . . 193Autoscaling. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193Bonds. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193Atom Labels. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193Captions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194Non-bond Objects and Color . . . . . . . . . . . . . . 194Pasting to an Empty Document Window . . . . 194Embedding Objects (Windows) . . . . . . . . . . . . . . . . 194Edit Graphic Object (Macintosh) . . . . . . . . . . . . . . 195Transferring PostScript (Macintosh) . . . . . . . . . . . . 195Importing and Exporting. . . . . . . . . . . . . . . . . . . . . . 196Graphics export border preference. . . . . . . . . . 197File Formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197Bitmap (.bmp) . . . . . . . . . . . . . . . . . . . . . . . . . . 198ChemDraw Template (*.ctp, *.ctr) . . . . . . . . 198ChemDraw (*.cdx) . . . . . . . . . . . . . . . . . . . . . . 198ChemDraw XML (*.xml) . . . . . . . . . . . . . . . . 198ChemDraw 3.5 (*.chm) . . . . . . . . . . . . . . . . . . 198ChemDraw 2.0 and ChemDraw 2.1 (*.chm) ImportOnly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199ChemDraw Stationery/Style Sheet (*.cds) . 199Connection Table (*.ct) . . . . . . . . . . . . . . . . . 199Chemical Markup Language (*.cml) . . . . . . 199Encapsulated PostScript (Macintosh)PostScript, *.eps (Windows) . . . . . . . . . . . . 199GIF Image (*.gif) . . . . . . . . . . . . . . . . . . . . . . . 200ISIS/SKC and ISIS/TGF . . . . . . . . . . . . . . . 200ISIS/Reactions (*.rxn) . . . . . . . . . . . . . . . . . . 200JDX (*.jdx, *.dx) Import Only . . . . . . . . . . . 201JPEG (*.jpg, *.jpeg) Import Only . . . . . . . . 201MDL MolFile (*.mol) . . . . . . . . . . . . . . . . . . 201Molecular Simulations MolFile (*.msm) . . 201PICT (Macintosh) . . . . . . . . . . . . . . . . . . . . . . 202PICT scaled 4X (Macintosh) . . . . . . . . . . . . . 202PNG file (*.png) . . . . . . . . . . . . . . . . . . . . . . . 202SMD (*.smd) . . . . . . . . . . . . . . . . . . . . . . . . . . 202SPC (.*spc) Import Only . . . . . . . . . . . . . . . 202Template Style Sheet (*.cts) . . . . . . . . . . . . . 202Windows Metafile (*.wmf) . . . . . . . . . . . . . . . 202TIFF file (*.tif) . . . . . . . . . . . . . . . . . . . . . . . . . 203Inserting Objects from Other Applications . . 204Transferring ChemDraw Documents AcrossPlatforms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 205Transferring from Macintosh to Windows. . . 205Transferring from Windows to Macintosh. . . 205Transferring Files to ChemDraw/Plus 3.1 forthe Macintosh . . . . . . . . . . . . . . . . . . . . . . . . . 205Chapter 13: ChemDraw/ExcelSetting Up ChemDraw/Excel . . . . . . . . . . . . . . . . . 207Importing Tables. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 208Converting and Upgrading . . . . . . . . . . . . . . . . . . . . 208Upgrading Workbooks . . . . . . . . . . . . . . . . . . . . 208Importing Hit Lists. . . . . . . . . . . . . . . . . . . . . . . . . . . 209Importing a Hitlist . . . . . . . . . . . . . . . . . . . . . . . . 209Error Messages. . . . . . . . . . . . . . . . . . . . . . . . . . . 209Exporting Tables. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 210Adding Structures . . . . . . . . . . . . . . . . . . . . . . . . . . . . 210Adding Structures with ChemDraw. . . . . . . . . 211Adding a Structure From a File . . . . . . . . . . . . 211Adding a Structure with a SMILES String . . . 211Adding Structures by Name . . . . . . . . . . . . . . . 212Saving Structures. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 212CambridgeSoft
Searching. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 212Filter Tables. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 212Similarity Searches . . . . . . . . . . . . . . . . . . . . . . . . 213Working with Structures . . . . . . . . . . . . . . . . . . . . . . 214Naming Structures. . . . . . . . . . . . . . . . . . . . . . . . 214Using the Clipboard . . . . . . . . . . . . . . . . . . . . . . 214Viewing Structures. . . . . . . . . . . . . . . . . . . . . . . . 214Showing and Hiding Structures . . . . . . . . . . 214Aligning Structures . . . . . . . . . . . . . . . . . . . . . 215Resizing Structures . . . . . . . . . . . . . . . . . . . . . 215Resizing Structures With a Macro . . . . . . . . 215Using ChemDraw/Excel Functions . . . . . . . . . . . . 215Using ChemProp Functions . . . . . . . . . . . . . . . 217ChemProp Properties . . . . . . . . . . . . . . . . . . . 217Inserting Functions . . . . . . . . . . . . . . . . . . . . . . . 218AppendicesAppendix A: Accessing the CambridgeSoftWeb SiteRegistering Online . . . . . . . . . . . . . . . . . . . . . . . . . . . 221Accessing the Online ChemDraw User’s Guide . 222Accessing CambridgeSoft Technical Support. . . . 222Finding Information on ChemFinder.com . . . . . . 222Finding Chemical Suppliers on ACX.com . . . . . . 223Finding ACX Structures and Numbers . . . . . . . . . 223ACX Structures . . . . . . . . . . . . . . . . . . . . . . . . . . 223ACX Numbers . . . . . . . . . . . . . . . . . . . . . . . . . . . 224Browsing SciStore.com . . . . . . . . . . . . . . . . . . . . . . . 224Browsing CambridgeSoft.com . . . . . . . . . . . . . . . . 225Using the ChemOffice SDK . . . . . . . . . . . . . . . . . . 225Appendix B: Technical SupportSerial Numbers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 227Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 228Performance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 228System Crashes. . . . . . . . . . . . . . . . . . . . . . . . . . . 228Appendix C: The Chemistry of ChemDrawDatabase Conventions . . . . . . . . . . . . . . . . . . . . . . . . 231Chemical Conventions . . . . . . . . . . . . . . . . . . . . . . . . 232Atom Labels. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 232Chemically Significant Text. . . . . . . . . . . . . . . . . 233Charges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 234Isotopes and Elements . . . . . . . . . . . . . . . . . . . . 235Radicals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 235H-Dot/H-Dash. . . . . . . . . . . . . . . . . . . . . . . . . . . 235Complexes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 235Multi-center Attachments . . . . . . . . . . . . . . . . . . 236Stereochemistry . . . . . . . . . . . . . . . . . . . . . . . . . . . 236Stereochemical Indicators . . . . . . . . . . . . . . . . 237Stereochemical Flags . . . . . . . . . . . . . . . . . . . . . . 237Polymer Representations. . . . . . . . . . . . . . . . . . . 238References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 238Query Properties. . . . . . . . . . . . . . . . . . . . . . . . . . 238Analysis Messages . . . . . . . . . . . . . . . . . . . . . . . . . 238Appendix D: How ChemNMR WorksChemNMR Limitations. . . . . . . . . . . . . . . . . . . . . . . 243Appendix E: How ChemProp WorksLogP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 245Henry’s Law . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 245Molar Refractivity . . . . . . . . . . . . . . . . . . . . . . . . . . . . 246ClogP and CMR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 246Topological Polar Surface Area . . . . . . . . . . . . . . . . 246Other Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 246Appendix F: Shortcuts and HotkeysChemDraw Hotkeys . . . . . . . . . . . . . . . . . . . . . . . . . . 252Appendix G: Document SettingsChemDraw Style Sheets or Stationery Pads. . . . . . 256Appendix H: Chemistry File FormatsConnection Table File Format. . . . . . . . . . . . . . . . . 267ChemDraw 9
Page 1 and 2: ChemOffice.Com®ChemDraw®Chemical
Page 3 and 4: License InformationChemOffice, Chem
Page 5 and 6: · Licensed users of ChemOffice Ent
Page 7 and 8: computer, except as provided below.
Page 9 and 10: Q: IS IT OK TO COPY MY COLLEAGUE’
Page 11 and 12: A Guide to CambridgeSoft ManualsAnd
Page 13 and 14: ContentsIntroductionWhat’s New in
Page 15 and 16: Method 2: Labeling an atom by point
Page 17: Chapter 10: Drawing Query Structure
Page 21 and 22: Administratorthey are presented. Ex
Page 23 and 24: Administrator12•IntroductionCambr
Page 25 and 26: The Mac GUI is shown below.Administ
Page 27 and 28: ToolUse to…AdministratorQueryTool
Page 29 and 30: AdministratorChemDraw window. Undoc
Page 31: AdministratorDouble-clicking on an
Page 36 and 37: 3. Click the checkbox next to Autos
Page 38 and 39: a file as a different format is use
Page 40 and 41: QuickDraw is the graphical format t
Page 42 and 43: Chapter 2: TutorialsOverviewThe tut
Page 44 and 45: .2. Double-click the atom.The hand
Page 46 and 47: 3. Click the third arrow from the l
Page 48 and 49: 2. Press the Enter or Return key to
Page 50 and 51: .Add second and third bonds:1. Poin
Page 52 and 53: Refine the shape of the arrow:1. Po
Page 54 and 55: 4. Click each of the atoms shown be
Page 56 and 57: 4. Select a folder in which to save
Page 58 and 59: Add labels to C1 and C6:3. Point to
Page 60 and 61: 3. Click Paste to paste the informa
Page 62 and 63: 2. Hold the mouse button and drag u
Page 64 and 65: Save and close the document:1. From
Page 66 and 67: The size of the orbital is constrai
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8. Click the Wedged Bond tool, poin
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Chapter 3: Drawing ChemicalStructur
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Adjustthis…If you want to …The
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You can use the tools on the Multip
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To draw a wedged bond:1. Click one
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If you click an atom in a ring, a s
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• Press the Ctrl or Command key w
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To convert ring types:1. With a bon
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Chapter 4:UltraStructNameStructName
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Converting Names toStructuresThere
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category ChemDraw 8 supports... Che
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Chapter 5: Drawing Captions andAtom
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• Subscript—Reduces the text by
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If you label C4, the second and thi
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5. To close the text box, click out
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4. The margin width is applied to a
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Hard-Coded HotKeysYou cannot edit h
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To edit atom number text:1. Click t
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Chapter 6: Drawing Orbitals,Symbols
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To draw a single lobe orbital:1. Ho
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To draw an H-dot or an H-dash:1. Ho
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The Arrow ToolsPaletteUse the Arrow
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Drawing LinesLines drawn with the l
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Some examples of shapes that you ca
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Deleting a SegmentTo delete a curve
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If you wantto...then...If you wantt
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Chapter 7: Manipulating DrawingsOve
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Selecting Entire StructuresTo selec
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The unselected bonds that are attac
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Reflecting ObjectsThrough PlanesYou
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3. The current median bond length f
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3. With the group selected, right-c
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Chapter 8: Advanced DrawingTechniqu
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Am Amyl AmericiumNp para-NeptuniumN
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ProExpanding LabelsMulti-Attached L
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3. Double-click on the cyclopentadi
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If you select only part of a struct
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Customizing the ColorPaletteYou can
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2. Click a color in the Color Wheel
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A new and untitled Template window
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Chapter 9: Working WithStructuresOv
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Propertym/zDescriptionMass/charge,
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3. Click the appropriate Position o
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To create a report and view results
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ProExpand GenericStructuresYou can
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The assigned atoms or bonds are hig
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Chapter 10:StructuresProDrawing Que
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• From the Structure menu, choose
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OptionSimple ringSearch ResultFinds
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Abnormal ValenceThe Abnormal Valenc
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The Bond Type options are described
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In the table below, points are may
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To Position …from the atom or bon
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. Not necessarily carbon (a generic
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A structure-based representation of
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Because of its prevalence the No Fl
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However, you are not interested in
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Always Display and PrintAtom Mappin
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ExportedQueryPropertiesISIS Mol Rxn
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ExportedQueryPropertiesISIS Mol Rxn
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Chapter 11: Working With PageLayout
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To create headers and footers:1. Fr
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Saving Page Setup SettingsYou can s
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A check mark appears next to the Sh
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Aligning ObjectsUse the Align comma
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The table appears in the document w
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7. Press Tab again to create a thir
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Chapter 12: Sharing InformationOver
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A clipping file or a scrap file is
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pasted in other types of documents.
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• SMDFormat Import ExportChemDraw
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.opened in versions 3.0, 3.0.1, 3.0
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For single step single or multi-lin
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different computers rather than usi
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Transferring ChemDrawDocuments Acro
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Chapter 13: ChemDraw/ExcelThe ChemD
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mats, but you may get error message
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Adding Structures withChemDrawThe C
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3. Select the search options:If you
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Aligning StructuresA structure may
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FunctionActionCHEM.COMPOSITION Retu
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AppendicesThis section contains the
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Appendix A: Accessing theCambridgeS
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Follow the links to do substructure
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You can search SciStore.Com for che
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Appendix B: Technical SupportOvervi
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4. If the problem still occurs, use
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Appendix C: The Chemistry ofChemDra
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+*/A series of anyCH 2 COOC(OPh) 3c
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Isotopes and ElementsBy default, Ch
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CIP rules are designed to order lig
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• Critical messages that may affe
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MessageThis label has anunrecognize
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Appendix D:WorksUltraHow ChemNMROve
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Appendix E:WorksProHow ChemPropChem
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Appendix F: Shortcuts andHotkeysSho
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Enter...to execute Command...Enter.
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Enter...to execute Command...Enter.
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HotkeyResultHotkeyResultTOTsxX1 n-B
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Appendix G: Document SettingsCreati
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Drawing, Atom Label, and Caption Te
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Page 272 and 273:
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Page 276 and 277:
Page 278 and 279:
Appendix H: Chemistry FileFormatsOv
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Double bonds are bit encoded using
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IndexNumerics13C, 1 H shifts, estim
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Bond Propertiesdefining 155descript
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Chemical Warnings (continued)suppre
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Deletingatom labels 87Backspace key
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File format (continued)CTR 198cts 2
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Inserting (continued)rows in tables
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Nicknames (continued)overview 121tr
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Printing (continued)ChemDraw Laser
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Saving customized settings 21Scalec
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System requirements 11TTable tool 1
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Use Defaults (continued)bond proper
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CAMBRIDGESOFTChemOffice Desktop toK
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CS ChemOfficeSoftware SuitesChemOff
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DESKTOPCS E-NotebookElectronic Jour
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DESKTOPCS ChemDrawChemical Structur
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DESKTOPCS Chem3DMolecular Modeling
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DESKTOPCS ChemFinderSearching and I
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DESKTOPCS ChemInfoReference and Che
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ENTERPRISEChemOffice WebServerEnter
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ENTERPRISEOracle CartridgeEnterpris
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KNOWLEDGEE-Notebook EnterpriseDeskt
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KNOWLEDGEDocument ManagerDesktop to
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KNOWLEDGE21CFR11 ComplianceElectron
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RESEARCH&Registration SystemChemica
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RESEARCH&Inventory ManagerChemical
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RESEARCH&CombiChem EnterpriseDeskto
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RESEARCH&BioAssay HTSBiological Ass
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RESEARCH&BioSAR BrowserBiological a
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CHEMICALChemACX DatabaseAvailable C
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CHEMICALThe Merck IndexChemistry’
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CHEMICALChemical DatabasesReference
Page 344 and 345:
CONSULTING &Consulting & ServicesDe
Page 347:
CS Software Problem ReportFor faste
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