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ChemDraw 8.0 User's Manual - CambridgeSoft

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CS ChemDraw 8.0

for Windows and Macintosh

User’s Guide

ChemDraw is a stand alone application within

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Databases Desktop Applications Software

Tips Enterprise Solutions

Includes

A Guide to CambridgeSoft Manuals

ChemDraw

Chem3D

ChemFinder

E-Notebook Desktop

ChemDraw/Excel

ChemFinder/Office

CombiChem/Excel

ChemSAR/Excel

MOPAC, MM2

CS Gaussian, GAMESS Interface

Purchase/Excel

ChemOffice WebServer

Oracle Cartridge

E-Notebook Enterprise

Document Manager

Registration System

Formulations & Mixtures

Inventory Manager

Discovery LIMS

BioAssay HTS

BioSAR Browser

ChemDraw/Excel

The Merck Index

ChemACX

ChemSCX

ChemMSDX

ChemINDEX

ChemRXN

NCI & AIDS

Structure Drawing Tips

Searching Tips

Importing SD Files

Manuals

Chemical Structure

Drawing Standard

ChemDraw

ChemOffice

Chem3D, ChemFinder

& E-Notebook

ChemOffice

Enterprise Solutions

And Databases

Contents

Section I: ChemDraw . . . . . . . . . . . . . . . . . . . . . . . 1

What’s New in ChemDraw 8 . . . . . . . . . . . . . . . 1

For Users of ChemDraw 7 . . . . . . . . . . . . . . . . . 2

For Users of ChemDraw 5 or 6. . . . . . . . . . . . . . 2

About This User’s Guide . . . . . . . . . . . . . . . . . . 3

Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

Additional Information . . . . . . . . . . . . . . . . . . . . 3

Quick Reference Card . . . . . . . . . . . . . . . . . . . . . 3

Help System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

CambridgeSoft Web Pages . . . . . . . . . . . . . . . . . 4

Installation and System Requirements . . . . . 4

Microsoft ® Windows ® Requirements. . . . . . . . . 4

Macintosh ® Requirements. . . . . . . . . . . . . . . . . . 4

Site License Network Installation Instructions . 4

Chapter 1: ChemDraw Basics . . . . . . . . . . . . . . 5

The ChemDraw Graphical User Interface . . . 5

The Main Tools Palette . . . . . . . . . . . . . . . . . . . . 6

Setting the Default Tool. . . . . . . . . . . . . . . . . . . . 8

Tearing Off Palettes . . . . . . . . . . . . . . . . . . . . . . . 8

Optional Toolbars. . . . . . . . . . . . . . . . . . . . . . . . . 8

Showing and Hiding Toolbars . . . . . . . . . . . . . . 9

Docking and Undocking Toolbars . . . . . . . . . . . 9

The Status Bar or Message Area (Windows). . . 9

The Analysis Window . . . . . . . . . . . . . . . . . . . . . 9

The Chemical Properties Window . . . . . . . . . . 10

The Info Window . . . . . . . . . . . . . . . . . . . . . . . . 10

Periodic Table. . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Character Map . . . . . . . . . . . . . . . . . . . . . . . . . . 11

Customizing ChemDraw. . . . . . . . . . . . . . . . . . 12

Setting Preferences. . . . . . . . . . . . . . . . . . . . . . . 12

Document and Object Settings . . . . . . . . . . . . . 12

Default Style Sheet or Stationery Pad . . . . 12

Saving Customized Settings as Style

Sheets or Stationery Pads . . . . . . . . . . . . . 13

Applying Document Settings From

Other Documents . . . . . . . . . . . . . . . . . . . . 13

Applying Object Settings from

Other Documents . . . . . . . . . . . . . . . . . . . . 14

Using Documents. . . . . . . . . . . . . . . . . . . . . . . . 14

Setting the Default Document Location. . . . . . 14

Creating a Document . . . . . . . . . . . . . . . . . . . . .14

Creating a New Document . . . . . . . . . . . . . .14

Creating a Document Using a Style Sheet

or Stationery Pad . . . . . . . . . . . . . . . . . . . . .14

Opening a Document . . . . . . . . . . . . . . . . . . . . .15

Setting the Default Open File Format . . . . .15

Saving Changes Automatically . . . . . . . . . . . . .15

Reversing and Repeating Actions . . . . . . . . . . .15

Undoing Actions . . . . . . . . . . . . . . . . . . . . . . .15

Redoing Actions . . . . . . . . . . . . . . . . . . . . . . .16

Repeating Actions . . . . . . . . . . . . . . . . . . . . .16

Discarding Recent Changes to a Document . . .16

Saving Documents . . . . . . . . . . . . . . . . . . . . . . .16

Setting the Default Save File Format . . . . .17

Saving a Document with a Different Name

or Location . . . . . . . . . . . . . . . . . . . . . . . . . .17

Saving a Document in a Different

File Format . . . . . . . . . . . . . . . . . . . . . . . . . .17

Closing a Document . . . . . . . . . . . . . . . . . . . . . .18

Accessing Documents Quickly . . . . . . . . . . . .18

The ChemDraw Items Folder. . . . . . . . . . . . . . .18

The Open Special Submenu. . . . . . . . . . . . . . . .18

The Window Menu . . . . . . . . . . . . . . . . . . . . . . .18

Printing. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .19

Printing Background Color . . . . . . . . . . . . . . . .19

Macintosh Print Preferences . . . . . . . . . . . . . . .19

Optimize Pictures for High-Resolution

Non-PostScript Printing . . . . . . . . . . . . . . . .19

Include PostScript . . . . . . . . . . . . . . . . . . . . .20

Include ChemDraw Laser Prep . . . . . . . . . .20

Scripts (Macintosh). . . . . . . . . . . . . . . . . . . . . . .20

Closing ChemDraw . . . . . . . . . . . . . . . . . . . . . . .20

Chapter 2: Tutorials . . . . . . . . . . . . . . . . . . . . . . . 21

Tutorial 1: Reaction Schemes . . . . . . . . . . . . .21

Tutorial 2: Drawing an Intermediate . . . . . . . .28

Tutorial 3: Using Rings . . . . . . . . . . . . . . . . . . .31

Tutorial 4: Fischer Projections . . . . . . . . . . . .35

Tutorial 5: Perspective Drawings . . . . . . . . . .39

Tutorial 6: Newman Projections . . . . . . . . . . .44

Tutorial 7: Showing Stereochemistry. . . . . . .46

ChemDraw 8 Contents • i

Administrator

Chapter 3: Drawing Chemical Structures 49

Drawing Settings . . . . . . . . . . . . . . . . . . . . . . . . .49

Configuring Settings for Documents. . . . . . . . .51

Configuring Settings for Objects . . . . . . . . . . . .51

Drawing Bonds . . . . . . . . . . . . . . . . . . . . . . . . . .52

Multiple Bonds . . . . . . . . . . . . . . . . . . . . . . . . . .52

Double Bonds . . . . . . . . . . . . . . . . . . . . . . . . .52

Double Either Bonds . . . . . . . . . . . . . . . . . . .53

Triple Bonds . . . . . . . . . . . . . . . . . . . . . . . . . .53

Quadruple Bonds . . . . . . . . . . . . . . . . . . . . . .53

Drawing Constrained Bonds . . . . . . . . . . . . . . .53

Drawing with Fixed Lengths . . . . . . . . . . . . .53

Drawing with Fixed Angles . . . . . . . . . . . . . .54

Toggling Fixed Lengths and Fixed Angles 54

Dative Bonds and Wedged Bonds . . . . . . . . . . .54

Adding a Bond by Clicking . . . . . . . . . . . . . . . .54

Adding Bonds by Dragging . . . . . . . . . . . . . . . .55

Changing the Highlight Box Size . . . . . . . . . . .55

Drawing Rings . . . . . . . . . . . . . . . . . . . . . . . . . . .55

Drawing a Ring . . . . . . . . . . . . . . . . . . . . . . . . . .55

Drawing a Ring by Clicking . . . . . . . . . . . . . . .56

Drawing Cyclohexane Chair Rings . . . . . . . . . .56

Drawing Resonance Delocalized Rings . . . . . .56

Drawing Cyclopentadiene and Benzene Rings 57

Drawing Acyclic Chains . . . . . . . . . . . . . . . . . .57

Drawing Chains. . . . . . . . . . . . . . . . . . . . . . . . . .57

Adding Chains. . . . . . . . . . . . . . . . . . . . . . . . . . .58

Changing Chain Direction . . . . . . . . . . . . . . . . .58

Editing Bonds. . . . . . . . . . . . . . . . . . . . . . . . . . . .58

Changing Bond Types. . . . . . . . . . . . . . . . . . . . .58

Changing Double Bonds. . . . . . . . . . . . . . . . . . .59

Changing Orientation of Wedged and

Dative Bonds . . . . . . . . . . . . . . . . . . . . . . . . . . .59

Changing Alignment of Double Bonds. . . . . . .59

Moving Atoms. . . . . . . . . . . . . . . . . . . . . . . . . . .60

Changing Bond Crossings . . . . . . . . . . . . . . . . .60

Changing the Bond Order. . . . . . . . . . . . . . . . . .61

Automatic Warnings . . . . . . . . . . . . . . . . . . . . . .61

Automatic Drawing—Structures from

Chemical Names . . . . . . . . . . . . . . . . . . . . . . . .62

Converting Names to Structures . . . . . . . . . . . .62

Insert Structure . . . . . . . . . . . . . . . . . . . . . . . .62

Paste Special . . . . . . . . . . . . . . . . . . . . . . . . .63

Converting Captions to Structures. . . . . . . . . . .63

Chapter 4: Drawing Captions and Atom

Labels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65

Creating a New Line and Closing Text Boxes. 65

Formatting Text. . . . . . . . . . . . . . . . . . . . . . . . . . 66

Setting Font parameters . . . . . . . . . . . . . . . . . . . 66

Setting the Baseline Style . . . . . . . . . . . . . . . . . 66

Specifying Line Spacing . . . . . . . . . . . . . . . . . . 67

Aligning Text . . . . . . . . . . . . . . . . . . . . . . . . . . . 67

Captions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67

Atom Labels . . . . . . . . . . . . . . . . . . . . . . . . . . 68

Automatic Alignment . . . . . . . . . . . . . . . . . . 68

Changing the Default Caption or Atom

Label Text Format . . . . . . . . . . . . . . . . . . . . . . 69

Specifying Document Settings for

New Text . . . . . . . . . . . . . . . . . . . . . . . . . . . 69

Setting an Individual Text Format

Before Typing . . . . . . . . . . . . . . . . . . . . . . . 69

Changing the Spacing of Individual

Text Objects . . . . . . . . . . . . . . . . . . . . . . . . . 69

Fractional Character Widths (Macintosh) . 70

Coloring Text . . . . . . . . . . . . . . . . . . . . . . . . . . . 70

Creating Captions . . . . . . . . . . . . . . . . . . . . . . . 70

Changing the Caption Width. . . . . . . . . . . . . . . 71

Editing a Caption . . . . . . . . . . . . . . . . . . . . . . . . 71

Adding Chemical Names . . . . . . . . . . . . . . . . . 72

Labeling Atoms with the Text Tool . . . . . . . . 72

Specifying the Margin Width . . . . . . . . . . . . . . 73

Editing Atom Labels . . . . . . . . . . . . . . . . . . . . . 73

Deleting an Atom Label . . . . . . . . . . . . . . . . . . 73

Labeling Atoms with HotKeys . . . . . . . . . . . . 74

Method 1: Labeling the last atom drawn . . . . . 74

Method 2: Labeling an atom by pointing. . . . . 74

Method 3: Labeling an Atom with a

Selection Tool . . . . . . . . . . . . . . . . . . . . . . . . . . 74

Method 4: Labeling multiple atoms . . . . . . . . . 75

Hard-Coded HotKeys . . . . . . . . . . . . . . . . . . . . 75

Creating HotKeys. . . . . . . . . . . . . . . . . . . . . . . . 75

Labeling Atoms With a Bond or Ring Tool . 76

Repeating an Atom Label. . . . . . . . . . . . . . . . . 76

Atom Numbering . . . . . . . . . . . . . . . . . . . . . . . . 76

Showing and Hiding Atom Numbers . . . . . . . . 77

Editing Atom Numbers . . . . . . . . . . . . . . . . . . . 77

Positioning Atom Number Indicators. . . . . . . . 78

Using the Text Tool with the Lasso Tool . . . 78

Using Bitmap Fonts When

Available (Macintosh) . . . . . . . . . . . . . . . . . . . 79

ii • Contents CambridgeSoft

Chapter 5: Drawing Orbitals, Symbols,

Arrows, Arcs, and Other Shapes. . . . . . . . . . 81

Selecting Tools From a Palette . . . . . . . . . . . . . 81

The Orbital Tools 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 Tools Palette . . . . . . 84

H-dot and H-dash . . . . . . . . . . . . . . . . . . . . . . . . 84

Lone Pair. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84

Radical . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85

Radical Cation and Radical Anion . . . . . . . . . . 85

Charge Symbols . . . . . . . . . . . . . . . . . . . . . . . . . 85

Attachment Points . . . . . . . . . . . . . . . . . . . . . . . 86

Rotating a Symbol . . . . . . . . . . . . . . . . . . . . . . . 86

The Arrow Tools Palette . . . . . . . . . . . . . . . . . . 86

Drawing an Arrow . . . . . . . . . . . . . . . . . . . . . . . 86

Editing an Arrow . . . . . . . . . . . . . . . . . . . . . . . . 87

The Drawing Elements Tools Palette . . . . . . 87

Drawing Boxes. . . . . . . . . . . . . . . . . . . . . . . . . . 87

Drawing Circles and Ovals . . . . . . . . . . . . . . . . 87

Resizing or Rotating Drawing Elements . . . . . 88

Distorting Circle and Ovals. . . . . . . . . . . . . . . . 88

Drawing Lines . . . . . . . . . . . . . . . . . . . . . . . . . . 88

The Brackets Tools Palette . . . . . . . . . . . . . . . 88

Drawing Single Brackets. . . . . . . . . . . . . . . . . . 88

Drawing Paired Brackets. . . . . . . . . . . . . . . . . . 89

Drawing Daggers . . . . . . . . . . . . . . . . . . . . . . . . 89

Framing Objects . . . . . . . . . . . . . . . . . . . . . . . . . 89

The Arc Tools Palette . . . . . . . . . . . . . . . . . . . . 89

Drawing Arcs . . . . . . . . . . . . . . . . . . . . . . . . . . . 89

Editing Arcs . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89

The Pen Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90

Drawing Bézier Curves by Dragging. . . . . . . . 90

Drawing Segments by Clicking . . . . . . . . . . . . 91

Editing a Curve. . . . . . . . . . . . . . . . . . . . . . . . . . 91

Changing the Shape of a Curve . . . . . . . . . 92

Adding a Segment . . . . . . . . . . . . . . . . . . . . 92

Deleting a Segment . . . . . . . . . . . . . . . . . . . 92

Applying a Style to a Shape . . . . . . . . . . . . . . . 92

Filled and Closed Styles . . . . . . . . . . . . . . . 92

Shaded Style . . . . . . . . . . . . . . . . . . . . . . . . .93

Plain Style . . . . . . . . . . . . . . . . . . . . . . . . . . . .93

The TLC Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . .93

Rf Display . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .94

Resizing Spots . . . . . . . . . . . . . . . . . . . . . . . . . . .95

Chapter 6: Manipulating Drawings . . . . . . . 97

Using a Selection Tool . . . . . . . . . . . . . . . . . . . .97

Selecting Objects with the Lasso Tool . . . . . . .97

Selecting Objects with the Marquee Tool. . . . .97

Toggling Between Selection Tools . . . . . . . . . .98

Toggling Between Other Tools . . . . . . . . . . . . .98

Selecting Objects by Clicking . . . . . . . . . . . . . .98

Setting the Highlight Box Tolerance . . . . . . . . .98

Selecting Entire Structures . . . . . . . . . . . . . . . . .98

Making Multiple Selections . . . . . . . . . . . . . . . .99

Removing Objects from the Selection . . . . . . .99

Selecting All Objects . . . . . . . . . . . . . . . . . . . . .99

Deselecting All Objects . . . . . . . . . . . . . . . . . . .99

Deleting Objects . . . . . . . . . . . . . . . . . . . . . . . . .99

Moving Objects. . . . . . . . . . . . . . . . . . . . . . . . . .99

Using the Clipboard . . . . . . . . . . . . . . . . . . . . .100

Cutting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .100

Pasting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .100

Moving Atoms. . . . . . . . . . . . . . . . . . . . . . . . . .100

Duplicating Objects . . . . . . . . . . . . . . . . . . . . .101

Rotating Objects . . . . . . . . . . . . . . . . . . . . . . . .101

Structure Perspective . . . . . . . . . . . . . . . . . . .102

Flatten Command . . . . . . . . . . . . . . . . . . . . . . .102

Reflecting Objects Through Planes . . . . . . .103

Flipping Objects . . . . . . . . . . . . . . . . . . . . . .103

Creating Mirror Images . . . . . . . . . . . . . . . .103

Resizing Objects . . . . . . . . . . . . . . . . . . . . . . . .103

The Resize Handle . . . . . . . . . . . . . . . . . . . . . .103

Scaling Objects . . . . . . . . . . . . . . . . . . . . . . . . .104

Distorting a Selection . . . . . . . . . . . . . . . . . . . .105

Joining Objects . . . . . . . . . . . . . . . . . . . . . . . . .105

Grouping Objects . . . . . . . . . . . . . . . . . . . . . . .106

Ungrouping Objects . . . . . . . . . . . . . . . . . . . . .106

Creating Integral Groups . . . . . . . . . . . . . . . . .106

Chapter 7: Advanced Drawing

Techniques. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109

Using Nicknames . . . . . . . . . . . . . . . . . . . . . . .109

Applying Nicknames . . . . . . . . . . . . . . . . . . . .109

Defining Nicknames . . . . . . . . . . . . . . . . . . . . .110

Troubleshooting Nicknames . . . . . . . . . . . . . .111

ChemDraw 8 Contents • iii

Administrator

Viewing Nicknames . . . . . . . . . . . . . . . . . . . . .112

Deleting Nicknames . . . . . . . . . . . . . . . . . . . . .112

Contracting Labels . . . . . . . . . . . . . . . . . . . . . .112

Expanding Labels . . . . . . . . . . . . . . . . . . . . . . .113

Multi-Attached Labels . . . . . . . . . . . . . . . . . . .113

Adding Bonds to an Atom Label . . . . . . . . . . .114

Using Multi-Center Bonds. . . . . . . . . . . . . . . .114

Creating a Multi-Center Bond . . . . . . . . . . . . .114

Viewing Attachment Points . . . . . . . . . . . . . . .115

Using Variable Attachment Positions . . . . .115

Using Structure CleanUp. . . . . . . . . . . . . . . . .116

Working with Color . . . . . . . . . . . . . . . . . . . . . .117

Coloring Objects . . . . . . . . . . . . . . . . . . . . . . . .118

Displaying the Color Palette . . . . . . . . . . . . . .118

Customizing the Color Palette . . . . . . . . . . . .119

Windows Color Settings. . . . . . . . . . . . . . . . . .119

Adding or Customizing Windows Colors .120

Macintosh Color Settings . . . . . . . . . . . . . . . . .120

Adding or Customizing Macintosh Colors 121

Removing Colors . . . . . . . . . . . . . . . . . . . . . . .121

Templates and Color . . . . . . . . . . . . . . . . . . . . .121

Saving Color Palette Settings. . . . . . . . . . . . . .121

Drawing With Templates . . . . . . . . . . . . . . . . .121

The Templates Tool. . . . . . . . . . . . . . . . . . . . . .122

Choosing a Template. . . . . . . . . . . . . . . . . . . . .122

Using Templates . . . . . . . . . . . . . . . . . . . . . . . .122

Drawing a Template . . . . . . . . . . . . . . . . . .123

Fusing a Template With an Existing

Structure . . . . . . . . . . . . . . . . . . . . . . . . . . .123

Drawing with the Same Template . . . . . . .123

Creating Templates and Template Documents123

Creating Templates . . . . . . . . . . . . . . . . . . .124

Orientation of Templates . . . . . . . . . . . . . .124

Resizing Template Panes . . . . . . . . . . . . .124

Template Panels . . . . . . . . . . . . . . . . . . . . .124

Saving Template Documents . . . . . . . . . . .125

Chapter 8: Working With Structures . . . . 127

Checking Chemistry . . . . . . . . . . . . . . . . . . . . .127

Check Structure . . . . . . . . . . . . . . . . . . . . . . . . .127

Check Structure when Copying to

Clipboard or Exporting . . . . . . . . . . . . . . . . . .128

Viewing Analysis Information . . . . . . . . . . . .128

Showing Stereochemistry. . . . . . . . . . . . . . . .129

Stereochemistry Indicators. . . . . . . . . . . . . . . .130

Hiding Indicators . . . . . . . . . . . . . . . . . . . . .130

Removing Indicators . . . . . . . . . . . . . . . . . .130

Positioning Indicators . . . . . . . . . . . . . . . . . 130

Converting Structures to 3D . . . . . . . . . . . . . . 131

Viewing Chemical Properties . . . . . . . . . . . . 131

Viewing the Chemical Properties Window . . 131

Mass Fragmentation Tool. . . . . . . . . . . . . . . . 133

Spectrum-Structure Assignments . . . . . . . 134

Assigning Structures to Spectra . . . . . . . . . . . 134

Viewing Spectral Assignments . . . . . . . . . . . . 134

Removing Spectral Assignments . . . . . . . . . . 134

NMR Shift Information—ChemNMR . . . . . 135

Chapter 9:

Drawing Query Structures . . . . . . . . . . . . . . . 137

Atom Properties . . . . . . . . . . . . . . . . . . . . . . . . 137

Viewing Atom Property Values . . . . . . . . . . . 138

Removing Atom Properties. . . . . . . . . . . . . . . 138

Atom Property Options. . . . . . . . . . . . . . . . . . 138

Substituents. . . . . . . . . . . . . . . . . . . . . . . . . . . . 139

Implicit Hydrogens . . . . . . . . . . . . . . . . . . . . . 139

Ring Bond Count . . . . . . . . . . . . . . . . . . . . . . . 140

Unsaturation . . . . . . . . . . . . . . . . . . . . . . . . . . . 140

Reaction Change . . . . . . . . . . . . . . . . . . . . . . . 141

Reaction Stereo. . . . . . . . . . . . . . . . . . . . . . . . . 141

Translation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141

Isotopic Abundance . . . . . . . . . . . . . . . . . . . . . 141

Abnormal Valence . . . . . . . . . . . . . . . . . . . . . . 142

Bond Properties . . . . . . . . . . . . . . . . . . . . . . . . 143

Viewing Bond Property Values. . . . . . . . . . . . 143

Removing Bond Properties . . . . . . . . . . . . . . . 143

Bond Property Options . . . . . . . . . . . . . . . . . . 144

Bond Types . . . . . . . . . . . . . . . . . . . . . . . . . 144

Topology . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145

Reaction Center . . . . . . . . . . . . . . . . . . . . . 145

3D Properties. . . . . . . . . . . . . . . . . . . . . . . . . . . 145

Query Tools Palette . . . . . . . . . . . . . . . . . . . . . 147

Query Indicators . . . . . . . . . . . . . . . . . . . . . . . . 147

Viewing Query Indicators . . . . . . . . . . . . . . 147

Hiding Query Indicators . . . . . . . . . . . . . . . 147

Removing Query Indicators . . . . . . . . . . . . 147

Positioning Query Indicators . . . . . . . . . . . 147

Drawing Stereochemical Symbols. . . . . . . . 148

Drawing Free Sites. . . . . . . . . . . . . . . . . . . . . . 148

Generic Nicknames . . . . . . . . . . . . . . . . . . . . . 148

Element Lists. . . . . . . . . . . . . . . . . . . . . . . . . . . 149

Element Not-Lists. . . . . . . . . . . . . . . . . . . . . . . 150

Link Nodes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150

iv • Contents CambridgeSoft

Representing Polymers and Other

Repeating Units. . . . . . . . . . . . . . . . . . . . . . . . 151

Setting Bracket Properties. . . . . . . . . . . . . . . . 151

Bracket Usage. . . . . . . . . . . . . . . . . . . . . . . . . . 152

Structure-based Polymer

Representations . . . . . . . . . . . . . . . . . . . . 152

Source-based Polymer Representations 152

Repeat Pattern. . . . . . . . . . . . . . . . . . . . . . . . . . 153

Flip Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154

Alternative Groups. . . . . . . . . . . . . . . . . . . . . . 154

Defining an Alternative Group . . . . . . . . . . . . 154

Defining Attachment Points . . . . . . . . . . . . . . 155

Multiple Attachment Points . . . . . . . . . . . . . . 156

Showing Attachment Rank Indicators . . . . . . 156

Attachment Point Numbering . . . . . . . . . . . . . 157

Anonymous Alternative Groups. . . . . . . . . . 157

Atom-to-Atom Mapping . . . . . . . . . . . . . . . . . 157

Always Display and Print Atom Mapping. . . 158

Automatic Mapping . . . . . . . . . . . . . . . . . . . . . 158

Manual Mapping . . . . . . . . . . . . . . . . . . . . . . . 158

Clearing Reaction Mapping . . . . . . . . . . . . . . 159

Exporting Reaction Mapping . . . . . . . . . . . . . 159

Export Compatibility . . . . . . . . . . . . . . . . . . . . 159

Chapter 10: Working with Page Layout. . 163

Controlling the Drawing Area . . . . . . . . . . . . 163

Setting up Pages . . . . . . . . . . . . . . . . . . . . . . . 163

Paged Document Setup . . . . . . . . . . . . . . . . . . 163

Poster Documents Setup . . . . . . . . . . . . . . . . . 164

Creating Headers and Footers. . . . . . . . . . . . . 164

Page Setup. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165

Page Orientation. . . . . . . . . . . . . . . . . . . . . . . . 166

Reduce or Enlarge . . . . . . . . . . . . . . . . . . . . . . 166

Saving Page Setup Settings. . . . . . . . . . . . . . . 166

35mm Slide Boundary Guides . . . . . . . . . . . 166

Changing Perspectives . . . . . . . . . . . . . . . . . 167

Magnifying with the View Menu . . . . . . . . . . 167

Magnify . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167

Actual Size . . . . . . . . . . . . . . . . . . . . . . . . . . 167

Reduce . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167

Fit to Window . . . . . . . . . . . . . . . . . . . . . . . . 167

Using the Magnification Control . . . . . . . . . . 168

Arranging Objects . . . . . . . . . . . . . . . . . . . . . . 168

Using Rulers . . . . . . . . . . . . . . . . . . . . . . . . . . . 168

Showing Rulers . . . . . . . . . . . . . . . . . . . . . . . . 168

Hiding Rulers . . . . . . . . . . . . . . . . . . . . . . . . . . 169

Using the Crosshair . . . . . . . . . . . . . . . . . . . . . 169

Displaying the Crosshair . . . . . . . . . . . . . . . . .169

Moving the Crosshair . . . . . . . . . . . . . . . . . . . .169

Aligning Objects using the Crosshair . . . . . . .169

Hiding the Crosshair . . . . . . . . . . . . . . . . . . . . .170

Centering on a Page . . . . . . . . . . . . . . . . . . . . .170

Aligning Objects . . . . . . . . . . . . . . . . . . . . . . . .170

Distributing Objects . . . . . . . . . . . . . . . . . . . . .171

Front to Back Ordering. . . . . . . . . . . . . . . . . . .171

Send to Back . . . . . . . . . . . . . . . . . . . . . . . .171

Bring to Front . . . . . . . . . . . . . . . . . . . . . . . .171

Creating Tables . . . . . . . . . . . . . . . . . . . . . . . . .172

Creating Tables with the Table Tool . . . . . . . .172

Creating Tables with the Text Tool . . . . . . . . .174

Creating the First Row

(column headings) . . . . . . . . . . . . . . . . . . .174

Creating a New Row . . . . . . . . . . . . . . . . . .174

Adjusting Row or Column Spacing . . . . . .175

Moving Around In Tables . . . . . . . . . . . . . .175

Inserting a New Row . . . . . . . . . . . . . . . . . .175

Chapter 11: Sharing Information . . . . . . . . 177

Using the Clipboard . . . . . . . . . . . . . . . . . . . . .177

SMILES and SMIRKS Strings . . . . . . . . . . . .177

Creating SMILES Strings . . . . . . . . . . . . . .177

Pasting SMILES from Clipboard . . . . . . . .178

Creating SLN Strings . . . . . . . . . . . . . . . . .178

Using Drag-and-Drop . . . . . . . . . . . . . . . . . . . .178

Transferring Between

ChemDraw Documents . . . . . . . . . . . . . . . . .179

Autoscaling . . . . . . . . . . . . . . . . . . . . . . . . . . . .179

Bonds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .179

Atom Labels . . . . . . . . . . . . . . . . . . . . . . . . . . .179

Captions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .180

Non-bond Objects and Color . . . . . . . . . . . . . .180

Pasting to an Empty Document Window . . . .180

Embedding Objects (Windows). . . . . . . . . . .181

Inserting Reference Numbers in

Microsoft Word . . . . . . . . . . . . . . . . . . . . . . . .181

Edit Graphic Object (Macintosh). . . . . . . . . .182

Transferring PostScript (Macintosh) . . . . . .182

Importing and Exporting . . . . . . . . . . . . . . . . .183

Graphics export border preference . . . . . . . . .184

File Formats. . . . . . . . . . . . . . . . . . . . . . . . . . . .184

Bitmap (.bmp) Export Only . . . . . . . . . . . . .184

ChemDraw Template (*.ctp, *.ctr) . . . . . . .184

ChemDraw (*.cdx) . . . . . . . . . . . . . . . . . . . .184

ChemDraw XML (*.xml) . . . . . . . . . . . . . . .185

ChemDraw 3.5 (*.chm) . . . . . . . . . . . . . . . .185

ChemDraw 8 Contents • v

Administrator

ChemDraw 2.0 and ChemDraw 2.1

(*.chm) Import Only . . . . . . . . . . . . . . . . . .185

ChemDraw Stationery/Style Sheet (*.cds) 185

Connection Table (*.ct) . . . . . . . . . . . . . . . .185

Encapsulated PostScript (Macintosh)

PostScript, *.eps (Windows) . . . . . . . . . . .185

GIF Image (*.gif) Export Only . . . . . . . . . .186

ISIS/SKC and ISIS/TGF . . . . . . . . . . . . . . .186

ISIS/Reactions (*.rxn) . . . . . . . . . . . . . . . . .186

JDX (*.jdx, *.dx) Import Only . . . . . . . . . . .187

MDL MolFile (*.mol) . . . . . . . . . . . . . . . . . . .187

Molecular Simulations MolFile (*.msm) . .187

PICT (Macintosh) . . . . . . . . . . . . . . . . . . . . .188

PICT scaled 4X (Macintosh) . . . . . . . . . . .188

PNG file (*.png) Export Only . . . . . . . . . . .188

SMD (*.smd) . . . . . . . . . . . . . . . . . . . . . . . . .188

SPC (.*spc) Import Only . . . . . . . . . . . . . . .188

Template Style Sheet (*.cts) . . . . . . . . . . .188

Windows Metafile (*.wmf) . . . . . . . . . . . . . .188

TIFF file (*.tif) Export Only . . . . . . . . . . . . .189

Inserting Graphics or Objects from Other

Applications (Windows only). . . . . . . . . . . . .190

Transferring ChemDraw Documents

Across Platforms . . . . . . . . . . . . . . . . . . . . . . .190

Transferring from Macintosh to Windows . . .191

Transferring from Windows to Macintosh . . .191

Transferring Files to ChemDraw/Plus 3.1

for the Macintosh . . . . . . . . . . . . . . . . . . . .191

Chapter 12: Accessing the CambridgeSoft

Web Site . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193

Finding Chemical Suppliers on

ChemStore.com . . . . . . . . . . . . . . . . . . . . . . . .193

Finding Information on ChemFinder.com. .193

Finding ACX Structures and Numbers . . . .194

ACX Structures . . . . . . . . . . . . . . . . . . . . . . . . .194

ACX Numbers. . . . . . . . . . . . . . . . . . . . . . . . . .194

Browsing ChemStore.com . . . . . . . . . . . . . . .194

Browsing CambridgeSoft.com . . . . . . . . . . .195

Accessing the Online ChemDraw

User’s Guide . . . . . . . . . . . . . . . . . . . . . . . . . . .195

Accessing CambridgeSoft

Technical Support . . . . . . . . . . . . . . . . . . . . . .196

Registering Online . . . . . . . . . . . . . . . . . . . . . .196

Using the ChemOffice SDK . . . . . . . . . . . . . .197

Section II: Desktop Addins . . . . . . . . . . . . . . . 199

ChemDraw/Excel . . . . . . . . . . . . . . . . . . . . . . . .199

CAMEO/Excel . . . . . . . . . . . . . . . . . . . . . . . . . . .199

.ChemDraw/Excel . . . . . . . . . . . . . . . . . . . . . . . . . 201

Starting ChemDraw/Excel . . . . . . . . . . . . . . . 201

Setting Excel Security . . . . . . . . . . . . . . . . . . . 201

Importing Tables. . . . . . . . . . . . . . . . . . . . . . . . 201

Converting and Updating a Worksheet . . . 202

Importing Hit Lists . . . . . . . . . . . . . . . . . . . . . . 202

Importing a Hitlist . . . . . . . . . . . . . . . . . . . . . . 202

Error Messages. . . . . . . . . . . . . . . . . . . . . . . . . 203

Exporting Tables. . . . . . . . . . . . . . . . . . . . . . . . 203

Adding Molecules. . . . . . . . . . . . . . . . . . . . . . . 204

Adding Molecules with ChemDraw. . . . . . . . 204

Adding Structure Files. . . . . . . . . . . . . . . . . . . 204

Adding SMILES Strings . . . . . . . . . . . . . . . . . 204

Adding Molecules by Name . . . . . . . . . . . . . . 205

Saving Molecules . . . . . . . . . . . . . . . . . . . . . . . 205

Searching . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 205

Filter Tables . . . . . . . . . . . . . . . . . . . . . . . . . . . 205

Similarity Searches . . . . . . . . . . . . . . . . . . . . . 206

Working with Structures. . . . . . . . . . . . . . . . . 207

Naming Molecules . . . . . . . . . . . . . . . . . . . . . . 207

Using the Clipboard . . . . . . . . . . . . . . . . . . . . . 207

Viewing Structures. . . . . . . . . . . . . . . . . . . . . . 207

Showing and Hiding Structures . . . . . . . . 207

Aligning Structures . . . . . . . . . . . . . . . . . . . 208

Resizing Structures . . . . . . . . . . . . . . . . . . 208

Resizing Multiple Structures . . . . . . . . . . . 208

Using ChemDraw/Excel Functions . . . . . . . 208

Using ChemProp Pro Functions . . . . . . . . . . . 210

ChemProp Properties . . . . . . . . . . . . . . . . . 210

Inserting Functions. . . . . . . . . . . . . . . . . . . . . . 211

CAMEO . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 213

In this Chapter . . . . . . . . . . . . . . . . . . . . . . . . . 213

Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 213

Minimum System Requirements . . . . . . . . . . 214

Operating System Options . . . . . . . . . . . . 214

Software Requirements . . . . . . . . . . . . . . . 214

Configuring and Starting CAMEO/Excel . . 214

From ChemDraw . . . . . . . . . . . . . . . . . . . . . 214

From Excel . . . . . . . . . . . . . . . . . . . . . . . . . . 214

Submitting a Reaction. . . . . . . . . . . . . . . . . . . 215

Reaction Module . . . . . . . . . . . . . . . . . . . . . . . 215

Reaction Parameters. . . . . . . . . . . . . . . . . . . . . 215

Reaction Condition . . . . . . . . . . . . . . . . . . . 215

Temperature Range . . . . . . . . . . . . . . . . . . 216

Stoichiometry . . . . . . . . . . . . . . . . . . . . . . . . 216

Reagent . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 216

vi • Contents CambridgeSoft

Solvent Information . . . . . . . . . . . . . . . . . . . . . 216

Solvent Dilution . . . . . . . . . . . . . . . . . . . . . . 216

Protic Solvent . . . . . . . . . . . . . . . . . . . . . . . 216

Additional Solvent . . . . . . . . . . . . . . . . . . . . 217

Output Options . . . . . . . . . . . . . . . . . . . . . . 217

Special Condition . . . . . . . . . . . . . . . . . . . . 217

Reporting Options . . . . . . . . . . . . . . . . . . . . . . 217

Example - Submit a Reaction . . . . . . . . . . . . . 217

Creating a Script. . . . . . . . . . . . . . . . . . . . . . . . 218

Reaction Parameters Tab . . . . . . . . . . . . . . . . . 218

Display Option Parameters Tab . . . . . . . . . . . 219

Cdx Input From File . . . . . . . . . . . . . . . . . . 219

Result Display Layout . . . . . . . . . . . . . . . . 219

Reporting Options for Excel . . . . . . . . . . . 219

Save and Append . . . . . . . . . . . . . . . . . . . . . . . 220

Editing a Script . . . . . . . . . . . . . . . . . . . . . . . . . 220

Save Reaction. . . . . . . . . . . . . . . . . . . . . . . . . . 221

Next . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 221

Exit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 221

Running a Script. . . . . . . . . . . . . . . . . . . . . . . . 221

Appendices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A1

Appendix A: The Chemistry of ChemDraw

A3

Database Conventions . . . . . . . . . . . . . . . . . . .A3

Chemical Conventions . . . . . . . . . . . . . . . . . . .A4

Atom Labels . . . . . . . . . . . . . . . . . . . . . . . . . . . .A4

Chemically Significant Text . . . . . . . . . . . . . . .A5

Charges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .A6

Isotopes and Elements . . . . . . . . . . . . . . . . . . . .A7

Radicals. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .A7

H-Dot/H-Dash . . . . . . . . . . . . . . . . . . . . . . . . . .A7

Complexes . . . . . . . . . . . . . . . . . . . . . . . . . . . . .A7

Multi-center Attachments . . . . . . . . . . . . . . . . .A8

Stereochemistry . . . . . . . . . . . . . . . . . . . . . . . . .A8

Stereochemical Indicators . . . . . . . . . . . . . .A9

Stereochemical Flags . . . . . . . . . . . . . . . . . . . . .A9

Polymer Representations. . . . . . . . . . . . . . . . .A10

References . . . . . . . . . . . . . . . . . . . . . . . . .A10

Query Properties. . . . . . . . . . . . . . . . . . . . . . . .A10

Analysis Messages . . . . . . . . . . . . . . . . . . . . . A10

Appendix B:

How ChemProp/Draw Works . . . . . . . . . . . A13

LogP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A13

Henry’s Law . . . . . . . . . . . . . . . . . . . . . . . . . . . A13

Molar Refractivity . . . . . . . . . . . . . . . . . . . . . . A14

ClogP and CMR . . . . . . . . . . . . . . . . . . . . . . . . A14

Appendix C:

How ChemNMR Pro Works . . . . . . . . . . . . A15

ChemNMR Limitations . . . . . . . . . . . . . . . . . . A15

Appendix D: Automation . . . . . . . . . . . . . . . . A17

Macintosh . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A17

Windows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A17

Appendix E: Document Settings . . . . . . . . . A19

ChemDraw Style Sheets or

Stationery Pads . . . . . . . . . . . . . . . . . . . . . . . A20

Appendix F: Chemistry File Formats . . . A31

Connection Table File Format . . . . . . . . . . . A31

Appendix G: Technical Support . . . . . . . . . A35

Serial Numbers . . . . . . . . . . . . . . . . . . . . . . . . A35

Macintosh . . . . . . . . . . . . . . . . . . . . . . . . . . . . A35

Windows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A35

Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . A36

Launching . . . . . . . . . . . . . . . . . . . . . . . . . . . . A36

Performance. . . . . . . . . . . . . . . . . . . . . . . . . . . A36

System Crashes . . . . . . . . . . . . . . . . . . . . . . . . A36

Appendix H: CAMEO Predefined Reagents

and Solvents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

Extra Reagent Drop Down Menu. . . . . . . . . A39

Solvents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A42

Base, Carbene Reagents. . . . . . . . . . . . . . . . A43

Radical Reaction Reagents . . . . . . . . . . . . . A43

Acidic, Aromatic-Electrophilic Reaction

Reagents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A44

Hetero, Pericycle Reaction Reagents . . . . A45

Oxidation Reduction Reaction Reagents . A46

Organometallic Reaction Reagents . . . . . . A47

Index

ChemDraw 8 Contents • vii

Administrator

viii • Contents CambridgeSoft

Section I: ChemDraw

Overview

This section describes the ChemDraw ® application.

Section 2 describes ChemDraw addins.

ChemDraw is a tool to enable professional

scientists, science students, and scientific authors to

communicate chemical structures. It is designed to

work according to conventions we found most

intuitive for such users. Our goal has been to make

ChemDraw as easy to use as possible while

providing superior drawing quality.

What’s New in

ChemDraw 8

ChemDraw 8 is enhanced by the following features:

• Completely rewritten Struct=Name–

Generate systematic names for chemical

structures, including comprehensive support for

the Cahn-Ingold-Prelog (CIP) rules for absolute

stereochemistry (R, S, E, Z, etc.). See “Adding

Chemical Names” on page 72.

• Floating periodic table and character map–

Keep information about all elements at your

fingertips. It's now even easier to create labeled

atoms and to add special characters from any

font with ease. See “Periodic Table”and

“Character Map” on page 11.

• Improved Carbon-13 NMR predictions–

Shift values are, on average, more than twice as

accurate as before. See “NMR Shift

Information—ChemNMR” on page 135.

• Improved Proton NMR predictions–Splitting

patterns make predicted spectra look more like

real-life. See “NMR Shift Information—

ChemNMR” on page 135.

• TLC Plate tool– Easily depict Thin Layer

Chromatography plates within a ChemDraw

document. See “The TLC Tool” on page 93.

• Structure perspective– Rotate molecules and

add perspective. See “Structure Perspective” on

page 102.

• 3D query features– Create pharmacophore

queries with 3D constraints for searching in 3Denabled

databases. See “3D Properties” on page

145.

• Mass fragmentation tool– Quickly examine

potential Mass Spectra fragment patterns by

drawing lines across breaking bonds. See

“Mass Fragmentation Tool” on page 133.

• Enhanced chemical intelligence– including

multistep reaction interpretation and layout, and

isotopic abundance atom property. See “Atomto-Atom

Mapping” on page 157 and “Isotopic

Abundance” on page 141.

• Typo recognition in Name=Struct–

Name=Struct batch utility contains extensive

typo recognition and correction. See

“Converting Names to Structures” on page 62.

• New attachment point depictions–for solid

phase synthesis and parent structures. See

“Attachment Points” on page 86.

ChemDraw 8 Section I: ChemDraw • 1

What’s New in ChemDraw 8

ChemDraw

Administrator

For Users of ChemDraw 7

The Main Tools Palette has changed to

accommodate new tools. In Pro and Ultra versions,

Arcs are no longer a separate tool. They are included

in the Drawing Elements tool. Attachment points

(there are now four options) are on the Chemical

Symbols tool.

For Users of ChemDraw 5 or 6

If you are upgrading from ChemDraw 5 or 6, note

that some features have been relocated. The

following table shows the new location.

Feature ChemDraw 5

or 6

Analyze

Structure

Caption Text

Settings

Pro

Chemical

Properties

Ultra

CLogP

Structure menu

or toolbar

ChemDraw 8

View menu,

Show Analysis

window

File menu Object menu,

Settings,

Captions tab

Structure menu

or toolbar

CLogP menu

(6.0.2 or later)

View menu,

Show Chemical

Properties

window

View menu,

Show Chemical

Properties

window

Color Palette File menu Color menu or

Document

Settings dialog

box

Feature ChemDraw 5

or 6

Document

Setup

Drawing

Settings

Label Text

Settings

File menu File Menu,

Document

Settings, Layout

and Footer tabs

File menu File menu,

Document

Settings,

Drawing tab

File Menu File menu,

Document

Settings, Atom

Labels tab

m/e values Status bar View menu,

Show Analysis

window

Positioning

and size

information

Fixed lengths

and angles

Status bar View menu,

Show Info

window, or in

drawing area

Tools menu Object menu

Format Text menu File menu,

Document

Settings,

Captions and

Atom Labels tab

Add or delete

Template rows

or columns

ChemDraw 8

Tools menu Edit menu

2 • Section I: ChemDraw CambridgeSoft

What’s New in ChemDraw 8

Feature ChemDraw 5

or 6

NMR

estimates

Tools menu

items

Estimate or

Scripts menu

About This User’s Guide

This User’s Manual contains information for the

ChemDraw application for Windows and

Macintosh. It assumes that you are familiar with the

basics of your Windows operating system. If you are

not, please refer to your system manual before using

the applications. Some of the material describes

tasks that must be performed in conjuction with

other integrated CambridgeSoft products. The

material on the Addins describes tasks that must be

performed in conjuction with Microsoft Excel or

Word. If you are not familiar with these products,

please consult the relevant User’s Manual for more

detailed information.

The chapters in this guide are organized by task.

They are intended to help you familiarize yourself

with the ChemDraw applications and start using

them as quickly and efficiently as possible. New

users should read the Basics chapter to get an

overview of the product and how it works. Chapter

2 Tutorials, demonstrates most of the features of the

application. Perform the tutorials in the order they

are presented. Experienced users can skip to

Chapter 3 and the subsequent chapters, which

provide more detailed information.

Conventions

ChemDraw 8

Structure menu

Tools menu View menu

The following notations are used throughout this

user’s guide:

Ultra

The Ultra symbol indicates that a feature is

available in the Ultra version only.

Pro

The Pro symbol indicates that a feature is

available in both the Pro and Ultra versions.

Features that are available in the Standard version

are not indicated by a symbol.

NOTE: Notes such as this are used to highlight

information supplemental to the main text.

Shortcut key sequences are indicated with a + sign,

for example: “Use the command: Ctrl+L to toggle

fixed bond lengths.”

A bold font is used to indicate that you are to take a

particular action, for example: “From the Help

Menu, choose Help Contents.”

Additional Information

Additional sources of ChemDraw information are:

• The Quick Reference Card.

• The Help system

• CambridgeSoft Web Pages.

http://www.cambridgesoft.com/support

Quick Reference Card

The ChemDraw Quick Reference Card is located in

the back of the manual. The card provides

summaries of ChemDraw commands and features.

Because many of the instructions require knowledge

of the interface elements, use the Quick Reference

card as you perform the tutorials in “Chapter 2:

Tutorials”.

Help System

ChemDraw provides the following types of Help:

• Help—An HTML reference guide.

ChemDraw 8 Section I: ChemDraw • 3

About This User’s Guide

ChemDraw

Administrator

• Context-sensitive Help (Windows)— Help

topics related to user interface objects. To

access Context sensitive Help type Shift+F1.

• ToolTips—Short descriptions of user interface

objects displayed by pointing.

• Status Bar—The lower left corner of the GUI

displays useful information as you work.

CambridgeSoft Web Pages

The following table contains the addresses of

ChemDraw-related web pages.

For

information

about …

Technical

Support

ChemDraw

Plugin

Software

Developer’s kit

ActiveX

control

Purchasing

CambridgeSoft

products and

chemicals

Access …

http://www.cambridgesoft.com/

support/

http://www.cambridgesoft.com/

support/documentation/chemdra

wplugin/

http://sdk.cambridgesoft.com/

http://chemstore.cambridgesoft.

com/

Installation and System

Requirements

Before installation, see the “ReadMeFirst” and any

other ReadMe documents on the installation CD-

ROM.

NOTE: You should set your monitor’s screen

resolution to at least 800x600. Lower resolutions

are not supported.

Microsoft ® Windows ®

Requirements

• Windows 98, Me, NT4 (SP-6 or higher), 2000,

or XP

• Microsoft ® Office add-ins require Office 2000

or XP.

Plugins/ActiveX ® controls support Netscape ® 6.2

or greater, Mozilla 1.x, and Microsoft ® Internet

Explorer 5.x and 6.x.

Macintosh ® Requirements

Mac ® OS 9.x (running CarbonLib 1.5 or later);

MacOS X 10.1.x, MacOS X 10.2.3 or later. Plugin

supports Mozilla 1.0.x to 1.2.x and Netscape 7.x,

Mac OS X builds only.

NOTE: The Mac OS X builds of Netscape/Mozilla

will run properly under Mac OS 9.x as well.

Site License Network

Installation Instructions

If you have purchased a site license, please see the

following web site for network installation

instructions:

http://www.cambridgesoft.com/support/sl/

4 • Section I: ChemDraw CambridgeSoft

Installation and System Requirements

Chapter 1: ChemDraw Basics

Overview

The information required to begin using ChemDraw

includes how to do the following:

• Identify the parts of the ChemDraw interface.

• Customize parts of the user environment.

• Create, open, and save documents.

• Set printing preferences.

Title bar

Menu bar

Text style

toolbar

General

toolbar

Main tool

palette

Status bar

Magnification control

The ChemDraw

Graphical User Interface

Although the Macintosh and Windows versions of

the ChemDraw graphical user interface (GUI) differ

slightly, the essential GUI consists of the same

elements. The Windows version of ChemDraw is

shown below.

Object toolbar

Minimize button

Maximize button

Close button

Scroll bars

Resize

ChemDraw 8 Chapter 1: ChemDraw Basics • 5

The ChemDraw Graphical User Interface

ChemDraw

Administrator

The Mac GUI is shown below.

Menu bar

General

toolbar

Main tool

palette

The Main Tools Palette

Use the main tools palette to create and manipulate

drawings. The appearance of the toolbar is slightly

different for the different versions of ChemDraw.

The toolbar for ChemDraw Ultra is shown below.

The table below describes the functions of the tools

for all versions. Some of the tools have multiple

options that can be selected from a tool palette.

Tool Use to…

Selection Lasso—select objects by dragging

around them.

Marquee—select objects by dragging

diagonally across them.

Selected objects can be further

manipulated using menu commands.

Magnification control

Tool Use to…

Structure

Perspective

Ultra

Mass Fragmentation

tool

Object toolbar

Title bar

Scroll bar

Resize

Rotate a selected object in three

dimensions.

splits molecules across specific bonds.

Bond Draw bonds and set bond properties.

Eraser Delete objects. Click on an object to

delete; drag to delete multiple objects.

Multiple

Bonds

Draw multiple bonds and set bond

properties. Bonds of different types

can be selected from the Multiple

Bonds tool palette.

6 • Chapter 1: ChemDraw Basics CambridgeSoft

The Main Tools Palette

Tool Use to…

Text Create atom labels and captions.

Pen Draw freehand shapes such as custom

arrows and orbitals.

Arrow Draw arrows. Arrows of different

types can be selected from the Arrows

tool palette.

Orbital Draw orbitals. Orbitals of different

types can be selected from the Orbitals

tool palette.

Drawing

Elements

Draw annotations that lack chemical

significance, such as boxes and lines.

Drawing Elements of different types

can be selected from the Drawing

Elements tool palette.

Includes the Arc tools.

Brackets Draw brackets, parentheses, and

braces. Brackets of different types can

be selected from the Brackets tool

palette.

Chemical

Symbols

Draw chemically significant symbols

such as charges, radicals, and lone

pairs. Symbols of different types can

be selected from the Symbols tool

palette.

Arc Draw arcs. Arcs of different degrees

can be selected from the Arcs tool

palette.

NOTE: The Arcs tool is a separate

tool only on ChemDraw Standard.

Acyclic

Chain

Pro

Draw chains of any length.

Tool Use to…

Query

Tools

Draw stereochemical flags, indicate

free sites, alternative groups and

correspondences between atoms in

query structures. Various options can

be selected from the Query tool

palette.

Templates Draw structures with templates stored

in template documents. Templates can

be selected from the Templates tool

palette.

Rings Draw common structural components.

Table Draw tables with multiple rows and

columns.

TLC Plate Draw TLC plates with multiple lanes

and adjustable solvent front and spots.

ChemDraw 8 Chapter 1: ChemDraw Basics • 7

The Main Tools Palette

ChemDraw

Administrator

Lasso

Structure Perspective

Solid Bond

Multiple Bonds

Dashed Bond

Hashed Bond

Hashed Wedged Bond

Bold Bond

Bold Wedged Bond

Hollow Wedged Bond

Wavy bond

Table

Acyclic Chain

Cyclopropane Ring

Cyclopentane Ring

Cycloheptane Ring

Cyclohexane chair 1

Cyclopentadiene Ring

Setting the Default Tool

Use the Preferences dialog box to set which tool is

automatically selected when you open documents.

To set the default tool:

1. From the File menu, choose Preferences.

The Preferences dialog box appears.

2. Click the Open/Save tab.

Marquee

Mass Fragment

Eraser

Text

Pen

Arrows

Orbitals

Drawing Elements

Brackets

Chemical Symbols

Query tools

TLC plate

Templates

Cyclobutane Ring

Cyclohexane Ring

Cyclooctane Ring

Cyclohexane chair 2

Benzene Ring

3. In the Opening Files section, click the Default

Tool to be automatically selected when you

open a document.

Tearing Off Palettes

Some tools have tool palettes extending from them,

indicated by an arrow at the bottom right of the tool

button.

You can “tear off” these palettes and place them

anywhere in the ChemDraw screen. You cannot

dock torn off palettes.

To tear off a palette:

DefaultTool 150 dpi

• Click the arrow on the lower right of the tool.

• Holding the mouse button down, point to the

title bar and release the mouse button.

You can drag the palette by its title bar to

reposition it.

You can also show or hide a palette by selecting it

from the Other Toolbars submenu on the View

menu.

Optional Toolbars

ChemDraw provides a number of optional toolbars

and information windows to facilitate production of

ChemDraw documents. These toolbars are accessed

from the View menu. They are divided into three

basic groups:

8 • Chapter 1: ChemDraw Basics CambridgeSoft

Optional Toolbars

• Standard Toolbars and Show Windows

• Tool Palettes

• Templates

templates

Showing and Hiding Toolbars

To show or hide a toolbar:

standard

toolbars

information

windows

• From the View menu, select a toolbar.

A check mark appears next to the item when the

toolbar is displayed.

Docking and Undocking

Toolbars

tool

palettes

The standard toolbars, can be docked or undocked.

Docked toolbars can attach to any edge of the

ChemDraw window. Undocked toolbars can float

anywhere in the ChemDraw screen.

To dock a toolbar:

• Drag the toolbar to the edge of the ChemDraw

screen where you want it to dock.

• Double-click the toolbar background. This will

dock the toolbar in the default position. (All

toolbars default to the top of the ChemDraw

window, except for the Tools toolbar which

defaults to the left side.)

To undock a toolbar:

• Drag the toolbar into the position you want.

The Status Bar or Message

Area (Windows)

The status bar or message area displays information

about the menu or toolbar you are using.

The Analysis Window

The Analysis window displays the chemical

analysis of the selected structure. If nothing is

selected, the values shown are for the entire

document.

See “Viewing Analysis Information” on page 128

for information on the Analysis window.

ChemDraw 8 Chapter 1: ChemDraw Basics • 9

Optional Toolbars

ChemDraw

Administrator

The Paste button inserts all selected items into the

document. The button shrinks the window to

just the title bar.

The Chemical Properties

Window

The Chemical Properties window displays

properties of the selected structure. When no

structure is selected, properties will be displayed

only if there is one (and only one) structure in the

document.

The Paste button inserts all selected items into the

document. The button shrinks the window to

just the title bar, while leaving it active.

Ultra

CLogP and CMR values are displayed.

The Info Window

The Information window shows size/positioning

information about what's going on in ChemDraw.

The fields show the following:

Field Shows…

Pointer:

X/Y

Pointer:

dX/dY

Selection:

X/Y

W/H

Periodic Table

current mouse coordinates

change in X and Y coordinates

of a moved selection

position of a selection

width/height of a selection

Angle: angle of a bond; rotation of a

selection

Dist: length of a bond; distance a

selection has been moved

% % of original size when resizing

a selection

The Periodic Table window displays a floating

periodic table. It can be used both for reference and

to insert elements into structures.

10 • Chapter 1: ChemDraw Basics CambridgeSoft

Optional Toolbars

Click an element symbol to highlight the element

and activate the Text tool. Drag across the table to

highlight each element in turn. Click the button

to show or hide the detailed information.

After selecting an element, click in the document to

add an atom label consisting of that element and the

appropriate number of hydrogens. Labeling

behavior is as follows:

click on… to…

an existing

unlabeled

atom

an existing

labeled

atom

an empty

space

label the atom

Double-clicking on an existing atom will open it for

editing without changing the label.

NOTE: Some element names conflict with

ChemDraw Hotkeys, and may not be interpreted

correctly by Chemical Warnings or Check Structure.

For more information and troubleshooting see

“Defining Nicknames” on page 110.

Character Map

cycle the hydrogen count (if it

matches the selected element)

or change the label

create a new atom

The floating Character Map window displays the

256 ASCII characters in any font. The default font is

Symbol. Use it to add symbols or styled fonts to

labels.‘

The character map is active only when a text box is

open for editing. It will appear grayed-out at all

other times. With a text box open, mouse over the

character map to view a larger version of the

characters in the top right corner of the window.

Click any character in the table to enter that

character in the text box. The selected font (shown

in the character map window) is applied to that

character only. It does not change the active font in

the text box.

NOTE: You can cancel a selection by dragging to

some other character before releasing.

The 8 most recently used characters are displayed at

the top of the window. These characters “remember”

their font and are not affected by changes to the

window. A single character may appear more than

once in this section if the versions use different

fonts.

Click the button to toggle between the 8 most

recently used characters and the entire character

map.

ChemDraw 8 Chapter 1: ChemDraw Basics • 11

Optional Toolbars

ChemDraw

Administrator

Customizing ChemDraw

You can customize ChemDraw by configuring

Preferences and Document Settings.

Preferences allow you to change the default

behavior of certain options that apply to every open

document. Document Settings allow you to change

the default behavior of options that will affect only

the active document.

Setting Preferences

Preferences affect the way the ChemDraw

application works, regardless of the document with

which you are working.

To open the Preferences dialog box:

• From the File menu, choose Preferences.

The Preferences dialog box appears:

Preferences-Gen 150dpi

To restore the CambridgeSoft default settings:

• Click the Use Defaults button.

Document and Object Settings

Document and object settings are user-definable

settings that are applied to the current document.

Settings include:

• Drawing settings—set drawing options such as

the fixed length used to draw bonds

• Caption and label text settings—set text options

such as the font used for atom labels and

captions

• Color settings—set available colors for objects

and the document background

• Print/Page Setup—set options such as the page

size used and text displayed in footers

You can apply document settings in the following

ways:

• Customize settings for the entire document

using the Document Settings dialog box

• Apply settings to the entire current document

from an existing document

• Apply settings to selected objects in the current

document from an existing document

Default Style Sheet or Stationery Pad

When you open ChemDraw, the last Style Sheet or

Stationery Pad used opens as the default. If you

choose another Style Sheet or Stationery Pad, that

file becomes the default.

To view the default Style Sheet or Stationery Pad:

• Click the File menu.

The “New” menu item displays the name of the

Style Sheet or Stationery Pad.

12 • Chapter 1: ChemDraw Basics CambridgeSoft

Customizing ChemDraw

Saving Customized Settings as Style

Sheets or Stationery Pads

Every new document created with ChemDraw uses

a Style Sheet or Stationery Pad to obtain its

document settings. Style Sheets or Stationery Pads

can also contain predefined objects. When you

create a new document, you actually create an

untitled copy of the Style Sheet or Stationery Pad.

Any changes you make to the copy of the Style

Sheet or Stationery Pad do not affect the Style Sheet

or Stationery Pad itself.

You can create a Style Sheet or Stationery Pad with

your own customized setting by saving it as a .cds

file. If you store the .cds file in the ChemDraw Items

folder, it appears in the Open Special menu so you

can access it from the File menu.

To save a document’s setting as a Style Sheet or

Stationery Pad:

1. Choose Save As from the File menu.

The Save As dialog box appears.

SaveAs 200 dpi

2. Name the file and change the type (in OS X:

format) to CD Style Sheet (cds) or ChemDraw

Stationery.

3. To save the file in the ChemDraw items folder,

click the Go To ChemDraw Items button.

4. Click Save.

Applying Document Settings From

ChemDraw 8.0 User's Manual - CambridgeSoft

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Delete template?

Save as template ?

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