ChemDraw
Chemical Structure Drawing Standard
®
CS ChemDraw 7.0
for Windows and Macintosh
CS ChemDraw is a stand alone application within
CS ChemOffice, an integrated suite including
CS Chem3D for molecular modeling and analysis,
CS ChemFinder for searching and information integration, and
CS ChemInfo for chemical and reference databases.
User’s Guide
ChemDraw Contents
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Contents
Introduction
About ChemDraw ..................................................... 1
What’s New in ChemDraw 7 .................................... 1
For Users of ChemDraw 5 ..................................1
For Users of ChemDraw 5 and 6 ........................1
About This User’s Guide........................................... 2
Conventions............................................................... 2
Additional Information.............................................. 3
Quick Reference Card .........................................3
Online Help .........................................................3
Online Help.................................................... 3
ToolTips......................................................... 3
Context-sensitive Help (Windows)................ 3
CambridgeSoft Web Pages .................................3
Installation and System Requirements...................... 4
Windows Requirements ......................................4
Macintosh Requirements ....................................4
Chapter 1: ChemDraw Basics
Overview................................................................... 5
Starting ChemDraw................................................... 5
ChemDraw’s Graphical User Interface (GUI) .......... 5
The Tools Palette ................................................7
Showing and Hiding Palettes......................... 8
Docking and Undocking Palettes................... 8
Tearing Off Palettes ....................................... 8
Setting the Default Tool................................. 8
Toolbars ..............................................................9
Docking and Undocking Toolbars................. 9
The Status Bar or Message Area
(Windows) ..........................................................9
Customizing ChemDraw........................................... 9
Setting Preferences .............................................9
Document and Object Settings .........................10
Default Style Sheet or Stationery Pad.......... 10
Saving Customized Settings as
Style Sheets or Stationery Pads.................... 10
Applying Document Settings From
Other Documents ......................................... 11
Applying Object Settings from
Other Documents ......................................... 11
Using Documents.................................................... 12
Setting the Default Document Location ...........12
Creating a Document ........................................12
Creating a New Document........................... 12
Creating a Document Using a
Style Sheet or Stationery Pad....................... 12
Opening a Document ........................................13
Setting the Default Open File Format.......... 13
Saving Changes Automatically .........................13
Reversing and Repeating Actions .....................14
Undoing Actions .......................................... 14
Redoing Actions........................................... 14
Repeating Actions........................................ 14
Discarding Recent Changes to a Document ......15
Saving Documents ............................................15
Setting the Default Save File Format........... 15
Saving a Document with a
Different Name or Location......................... 16
Saving a Document in a
Different File Format ................................... 16
Closing a Document ..........................................16
Accessing Documents Quickly ............................... 17
The ChemDraw Items Folder ............................17
The Open Special Submenu ..............................17
The Window Menu ...........................................17
Printing.................................................................... 18
Printing Background Color ...............................18
Macintosh Print Preferences .............................18
Optimize Pictures for High-Resolution
Non-PostScript Printing (Macintosh)........... 18
Include PostScript (Macintosh).................... 19
Include ChemDraw Laser Prep
(Macintosh) .................................................. 19
Scripts (Macintosh) ................................................. 19
Closing ChemDraw................................................. 19
Chapter 2: Tutorials
Overview ................................................................. 21
Tutorial 1: Reaction Schemes ................................. 21
Tutorial 2: Drawing an Intermediate....................... 28
Tutorial 3: Using Rings........................................... 32
Tutorial 4: Fischer Projections................................ 35
Tutorial 5: Perspective Drawings............................ 40
Tutorial 6: Newman Projections ............................. 44
Tutorial 7: Showing Stereochemistry...................... 47
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Chapter 3:
Drawing Chemical Structures
Overview................................................................. 49
Drawing Settings..................................................... 49
Displaying the Info Window................................... 52
Drawing Bonds ....................................................... 52
Setting the Default Tool ...................................53
Drawing Constrained Bonds .............................53
Drawing with Fixed Lengths ....................... 53
Drawing with Fixed Angles......................... 53
Toggling Fixed Lengths and Fixed Angles.. 53
Dative Bonds and Wedged Bonds ....................53
Adding a Bond by Clicking ..............................54
Adding Bonds by Dragging ..............................54
Changing the Highlight Box Size .....................54
Multiple Bonds ................................................55
Double Bonds .............................................. 55
Double Either Bonds.................................... 55
Triple Bonds ................................................ 55
Quadruple Bonds ......................................... 55
Drawing Rings ........................................................ 56
Drawing a Ring .................................................56
Drawing a Ring by Clicking .............................56
Drawing Cyclohexane Chair Rings ..................57
Drawing Resonance Delocalized Rings ...........57
Drawing Cyclopentadiene and
Benzene Rings ..................................................57
Drawing Acyclic Chains......................................... 58
Drawing Chains ................................................58
Adding Chains ..................................................58
Changing Chain Direction ................................59
Editing Bonds.......................................................... 59
Changing Bond Types ......................................59
Changing Double Bonds ...................................59
Changing Orientation of Wedged and
Dative Bonds ....................................................60
Changing Alignment of Double Bonds ............60
Moving Atoms ..................................................60
Changing Bond Crossings ................................61
Changing the Bond Order .................................61
Automatic Warnings ............................................... 62
Automatic Drawing—Structures from
Chemical Names ..................................................... 63
Converting Names to Structures .......................63
Inserting Names........................................... 63
Paste Special ................................................ 64
Converting Captions to Structures ....................64
Chapter 4:
Drawing Captions and Atom Labels
Creating Text........................................................... 65
Formatting Text....................................................... 65
Setting the Baseline Style .................................66
Specifying Line Spacing ...................................66
Aligning Text ....................................................66
Captions ....................................................... 66
Atom Labels................................................. 67
Automatic Alignment................................... 67
Changing the Default Caption or
Atom Label Text Format ..................................68
Specifying Document Settings for
New Text...................................................... 68
Setting an Individual Text Format
Before Typing .............................................. 69
Changing the Spacing of
Individual Text Objects................................ 69
Fractional Character Widths (Macintosh).... 69
Coloring Text ....................................................69
Creating Captions.................................................... 70
Changing the Caption Width ............................70
Editing a Caption ..............................................70
Adding Chemical Names ........................................ 71
Labeling Atoms with the Text Tool........................ 72
Specifying the Margin Width ...........................72
Editing Atom Labels .........................................72
Deleting an Atom Label ....................................73
Labeling Atoms with HotKeys................................ 73
Method 1: Labeling the last atom drawn ..........73
Method 2: Labeling an atom by pointing .........73
Method 3: Labeling an atom with
a selection tool ..................................................73
Method 4: Labeling multiple atoms ..................73
Hard-Coded HotKeys .......................................74
Creating HotKeys .............................................74
Labeling Atoms With a Bond or Ring Tool............ 75
Repeating an Atom Label........................................ 75
Numbering Atoms................................................... 75
Showing and Hiding Atom Numbers ...............76
Editing Atom Numbers .....................................77
Positioning Atom Number Indicators ...............77
Typing Non-Roman Text........................................ 78
Creating a New Line and Closing Text Boxes........ 78
Using the Text Tool with the Lasso Tool................ 79
Using Bitmap Fonts When Available
(Macintosh) ............................................................. 79
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Chapter 5: Drawing Orbitals,
Symbols, Arrows, Arcs, and Other
Shapes
Overview................................................................. 81
The Orbital Tool Palette.......................................... 81
s-orbitals ............................................................82
Sigma Orbitals ..................................................82
Single Lobe Orbitals .........................................82
p-orbitals ...........................................................83
Hybrid Orbitals .................................................83
d-orbitals ...........................................................83
dz2-orbitals .......................................................83
The Chemical Symbols Tool................................... 84
H-dot and H-dash ..............................................84
Lone Pair ...........................................................84
Radical ..............................................................85
Radical Cation and Radical Anion ....................85
Charge Symbols ................................................85
Rotating a Symbol ............................................86
Selecting Tools From a Palette................................ 86
The Arrow Tool....................................................... 86
Selecting an Arrow ...........................................86
Drawing an Arrow ............................................86
Editing an Arrow ..............................................87
The Drawing Elements Tool ................................... 87
Selecting a Drawing Element ...........................87
Drawing Boxes .................................................87
Drawing Circles and Ovals ...............................88
Resizing or Rotating Drawing Elements ..........88
Distorting Circle and Ovals ..............................88
Drawing Lines ...................................................88
The Brackets Tool................................................... 89
Drawing Single Brackets ..................................89
Drawing Paired Brackets ..................................89
Drawing Daggers ..............................................89
Framing Objects...................................................... 89
The Arc Tool........................................................... 90
Drawing Arcs ....................................................90
Editing Arcs ......................................................90
The Pen Tool........................................................... 90
Drawing Bézier Curves by Dragging ................91
Drawing Segments by Clicking ........................91
Editing a Curve .................................................92
Changing the Shape of a Curve.................... 92
Adding a Segment........................................ 92
Deleting a Segment...................................... 93
Applying a Style to a Shape ..............................93
Filled and Closed Styles............................... 93
Shaded Style................................................. 93
Plain Style .................................................... 93
Chapter 6: Manipulating Drawings
Overview ................................................................. 95
Using a Selection Tool ............................................ 95
Selecting Objects with the Lasso Tool ..............95
Selecting Objects with the Marquee Tool .........95
Toggling Between Selection Tools ...................96
Toggling Between Other Tools .........................96
Selecting Objects by Clicking ...........................96
Setting the Highlight Box Tolerance ................96
Selecting Entire Structures ................................97
Making Multiple Selections ..............................97
Removing Objects from the Selection ..............97
Selecting All Objects ........................................97
Deselecting All Objects ....................................97
Deleting Objects ................................................97
Moving Objects .................................................98
Using the Clipboard ..........................................98
Cutting.......................................................... 98
Pasting.......................................................... 98
Moving Atoms ..................................................99
Duplicating Objects ..........................................99
Rotating Objects.................................................... 100
Reflecting Objects Through Planes....................... 101
Flipping Objects......................................... 101
Creating Mirror Images.............................. 101
Resizing Objects.................................................... 101
The Resize Handle ..........................................101
Scaling Objects ...............................................102
Distorting a Selection ......................................102
Joining Objects...................................................... 103
Setting the Maximum Distance Tolerance ......103
Grouping Objects .................................................. 104
Ungrouping Objects ........................................104
Creating Integral Groups .................................104
Chapter 7:
Advanced Drawing Techniques
Overview ............................................................... 105
Using Nicknames .................................................. 105
Applying Nicknames ......................................105
Defining Nicknames .......................................106
Troubleshooting Nicknames ...........................107
Viewing Nicknames ........................................108
Deleting Nicknames .............................................. 108
Contracting Labels ................................................ 108
Expanding Labels.................................................. 109
Using Multi-Center Bonds .................................... 109
Creating a Multi-Center Bond ........................109
Viewing Attachment Points ............................110
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Multi-Attached Labels .......................................... 111
Adding Bonds to an Atom Label ....................111
Using Clean Up Structure ..................................... 111
Using Variable Attachment Positions................... 112
Working with Color .............................................. 113
Coloring Objects .............................................114
Displaying the Color Palette ...........................114
Customizing the Color Palette .......................115
Windows Color Settings .................................115
Adding or Customizing
Windows Colors ........................................ 116
Macintosh Color Settings ...............................116
Adding or Customizing
Macintosh Colors....................................... 117
Removing Colors ............................................117
Templates and Color .......................................117
Saving Color Palette Settings .........................117
Drawing With Templates...................................... 117
The Templates Tool ........................................118
Choosing a Template ......................................118
Using Templates .............................................118
Drawing a Template................................... 118
Fusing a Template With an
Existing Structure ...................................... 118
Drawing with the Same Template ............. 119
Creating Templates and Template Documents..... 119
Creating Templates .........................................119
Orientation of Templates ................................120
Resizing Template Panes ................................120
Template Panels ..............................................120
Saving Template Documents ..........................121
Chapter 8: Working With Structures
Overview............................................................... 123
Checking Chemistry.............................................. 123
Check Structure ..............................................123
Check Structure when Copying to
Clipboard or Exporting ...................................124
Viewing Analysis Information.............................. 124
Viewing Chemical Properties ............................... 125
Showing Stereochemistry ..................................... 126
Stereochemistry Indicators .............................127
Hiding Indicators ....................................... 127
Removing Indicators.................................. 127
Positioning Indicators ................................ 127
Converting Structures to 3D ................................. 128
Spectrum-Structure Assignments.......................... 128
Assigning Structures to Spectra ......................128
Viewing Spectral Assignments .......................129
Removing Spectral Assignments ....................129
NMR Shift Information—ChemNMR Pro .......... 129
Chapter 9:
Drawing Query Structures
What Are Query Structures?................................. 131
Atom Properties .................................................... 131
Viewing Atom Property Values ......................132
Removing Atom Properties ............................132
Atom Property Options ...................................133
Substituents................................................ 133
Implicit Hydrogens .................................... 134
Ring Bond Count ............................................134
Unsaturation ....................................................134
Reaction Change .............................................135
Reaction Stereo ...............................................135
Translation ......................................................135
Abnormal Valence ..........................................136
Bond Properties..................................................... 136
Viewing Bond Property Values ......................137
Removing Bond Properties .............................137
Bond Property Options ...................................137
Bond Types................................................ 137
Topology.................................................... 138
Reaction Center.......................................... 139
Query Tools Palette............................................... 139
Query Indicators.................................................... 139
Viewing Query Indicators.......................... 139
Hiding Query Indicators ............................ 139
Removing Query Indicators....................... 140
Positioning Query Indicators ..................... 140
Drawing Stereochemical Symbols........................ 140
Drawing Free Sites................................................ 140
Generic Nicknames............................................... 141
Element Lists......................................................... 142
Element Not-Lists ................................................. 142
Link Nodes............................................................ 143
Representing Polymers and
Other Repeating Units........................................... 143
Setting Bracket Properties ..............................143
Bracket Usage .................................................144
Structure-based Polymer Representations . 144
Source-based Polymer Representations..... 145
Repeat Pattern .................................................146
Flip Type .........................................................146
Exporting Bracket Properties ..........................146
Alternative Groups................................................ 147
Defining an Alternative Group .......................147
Defining Attachment Points ...........................148
Multiple Attachment Points ............................148
Showing Attachment Rank Indicators ............149
Attachment Point Numbering .........................149
Anonymous Alternative Groups ........................... 150
