Contents

Contents

Introduction

What's New in ChemDraw 8

For Users of ChemDraw 7

For Users of ChemDraw 5 or 6

About This User's Guide

Additional Information

Quick Reference Card

CambridgeSoft Web Pages

Installation and System Requirements

Site License Network Installation Instructions

ChemDraw Basics

The ChemDraw Graphical User Interface

The Main Tools Palette

Setting the Default Tool

Tearing Off Palettes

Optional Toolbars

Showing and Hiding Toolbars

Docking and Undocking Toolbars

The Analysis Window

The Chemical Properties Window

The Info Window

Customizing ChemDraw

Setting Preferences

Document and Object Settings

Default Stationery Pad

Saving Customized Settings as Stationery Pads

Applying Document Settings From Other Documents

Applying Object Settings from Other Documents

Using Documents

Setting the Default Document Location

Creating a Document

Creating a New Document

Creating a Document Using a Stationery Pad

Opening a Document

Setting the Default Open File Format

Saving Changes Automatically

Reversing and Repeating Actions

Undoing Actions

Redoing Actions

Repeating Actions

Discarding Recent Changes to a Document

Saving Documents

Setting the Default Save File Format

Saving a Document with a Different Name or Location

Saving a Document in a Different File Format

Closing a Document

Accessing Documents Quickly

The ChemDraw Items Folder

The Open Special Submenu

The Window Menu

Printing Background Color

Macintosh Print Preferences

Optimize Pictures for High-Resolution Non-PostScript Printing

Include PostScript

Include ChemDraw Laser Prep

Closing ChemDraw

Tutorials

Tutorial 1: Reaction Schemes

Tutorial 2: Drawing an Intermediate

Tutorial 3: Using Rings

Tutorial 4: Fischer Projections

Tutorial 5: Perspective Drawings

Tutorial 6: Newman Projections

Tutorial 7: Showing Stereochemistry

Drawing Chemical Structures

Drawing Settings

Configuring Settings for Documents

Configuring Settings for Objects

Double Either Bonds

Quadruple Bonds

Drawing Constrained Bonds

Drawing with Fixed Lengths

Drawing with Fixed Angles

Toggling Fixed Lengths and Fixed Angles

Dative Bonds and Wedged Bonds

Adding a Bond by Clicking

Adding Bonds by Dragging

Changing the Highlight Box Size

Drawing a Ring by Clicking

Drawing Cyclohexane Chair Rings

Drawing Resonance Delocalized Rings

Drawing Cyclopentadiene and Benzene Rings

Drawing Acyclic Chains

Changing Chain Direction

Changing Bond Types

Changing Double Bonds

Changing Orientation of Wedged and Dative Bonds

Changing Alignment of Double Bonds

Changing Bond Crossings

Changing the Bond Order

Automatic Warnings

Automatic Drawing-Structures from Chemical Names

Converting Names to Structures

Insert Structure

Converting Captions to Structures

Drawing Captions and Atom Labels

Creating a New Line and Closing Text Boxes

Formatting Text

Setting Font parameters

Setting the Baseline Style

Specifying Line Spacing

Automatic Alignment

Changing the Default Caption or Atom Label Text Format

Specifying Document Settings for New Text

Setting an Individual Text Format Before Typing

Changing the Spacing of Individual Text Objects

Fractional Character Widths (Macintosh)

Creating Captions

Changing the Caption Width

Editing a Caption

Adding Chemical Names

Labeling Atoms with the Text Tool

Specifying the Margin Width

Editing Atom Labels

Deleting an Atom Label

Labeling Atoms with HotKeys

Method 1: Labeling the last atom drawn

Method 2: Labeling an atom by pointing

Method 3: Labeling an Atom with a Selection Tool

Method 4: Labeling multiple atoms

Hard-Coded HotKeys

Creating HotKeys

Labeling Atoms With a Bond or Ring Tool

Repeating an Atom Label

Showing and Hiding Atom Numbers

Editing Atom Numbers

Positioning Atom Number Indicators

Using the Text Tool with the Lasso Tool

Using Bitmap Fonts When Available

Drawing Orbitals, Symbols, Arrows, Arcs, and Other Shapes

Selecting Tools From a Palette

The Orbital Tools Palette

Single Lobe Orbitals

Hybrid Orbitals

The Chemical Symbols Tools Palette

H-dot and H-dash

Radical Cation and Radical Anion

Attachment Points

Rotating a Symbol

The Arrow Tools Palette

Drawing an Arrow

Editing an Arrow

The Drawing Elements Tools Palette

Drawing Circles and Ovals

Resizing or Rotating Drawing Elements

Distorting Circle and Ovals

The Brackets Tools Palette

Drawing Single Brackets

Drawing Paired Brackets

Drawing Daggers

Framing Objects

The Arc Tools Palette

Drawing Bézier Curves by Dragging

Drawing Segments by Clicking

Editing a Curve

Changing the Shape of a Curve

Adding a Segment

Deleting a Segment

Applying a Style to a Shape

Filled and Closed Styles

Manipulating Drawings

Using a Selection Tool

Selecting Objects with the Lasso Tool

Selecting Objects with the Marquee Tool

Toggling Between Selection Tools

Toggling Between Other Tools

Selecting Objects by Clicking

Setting the Highlight Box Tolerance

Selecting Entire Structures

Making Multiple Selections

Removing Objects from the Selection

Selecting All Objects

Deselecting All Objects

Deleting Objects

Using the Clipboard

Duplicating Objects

Rotating Objects

Structure Perspective

Flatten Command

Reflecting Objects Through Planes

Flipping Objects

Creating Mirror Images

Resizing Objects

The Resize Handle

Scaling Objects

Distorting a Selection

Joining Objects

Grouping Objects

Ungrouping Objects

Creating Integral Groups

Advanced Drawing Techniques

Using Nicknames

Applying Nicknames

Defining Nicknames

Troubleshooting Nicknames

Viewing Nicknames

Deleting Nicknames

Contracting Labels

Expanding Labels

Multi-Attached Labels

Adding Bonds to an Atom Label

Using Multi-Center Bonds

Creating a Multi-Center Bond

Viewing Attachment Points

Using Variable Attachment Positions

Using Structure CleanUp

Working with Color

Coloring Objects

Displaying the Color Palette

Customizing the Color Palette

Macintosh Color Settings

Adding or Customizing Macintosh Colors

Removing Colors

Templates and Color

Saving Color Palette Settings

Drawing With Templates

The Templates Tool

Choosing a Template

Using Templates

Drawing a Template

Fusing a Template With an Existing Structure

Drawing with the Same Template

Creating Templates and Template Documents

Creating Templates

Orientation of Templates

Resizing Template Panes

Template Panels

Saving Template Documents

Working With Structures

Checking Chemistry

Check Structure

Check Structure when Copying to Clipboard or Exporting

Viewing Analysis Information

Showing Stereochemistry

Stereochemistry Indicators

Hiding Indicators

Removing Indicators

Positioning Indicators

Converting Structures to 3D

Viewing Chemical Properties

Viewing the Chemical Properties Window

Mass Fragmentation Tool

Spectrum-Structure Assignments

Assigning Structures to Spectra

Viewing Spectral Assignments

Removing Spectral Assignments

NMR Shift Information-ChemNMR

Drawing Query Structures

Atom Properties

Viewing Atom Property Values

Removing Atom Properties

Atom Property Options

Implicit Hydrogens

Ring Bond Count

Reaction Change

Reaction Stereo

Isotopic Abundance

Abnormal Valence

Bond Properties

Viewing Bond Property Values

Removing Bond Properties

Bond Property Options

Reaction Center

Query Tools Palette

Query Indicators

Viewing Query Indicators

Hiding Query Indicators

Removing Query Indicators

Positioning Query Indicators

Drawing Stereochemical Symbols

Drawing Free Sites

Generic Nicknames

Element Not-Lists

Representing Polymers and Other Repeating Units

Setting Bracket Properties

Structure-based Polymer Representations

Source-based Polymer Representations

Alternative Groups

Defining an Alternative Group

Defining Attachment Points

Multiple Attachment Points

Showing Attachment Rank Indicators

Attachment Point Numbering

Anonymous Alternative Groups

Atom-to-Atom Mapping

Always Display and Print Atom Mapping

Automatic Mapping

Clearing Reaction Mapping

Exporting Reaction Mapping

Export Compatibility

Working with Page Layout

Controlling the Drawing Area

Setting up Pages

Paged Document Setup

Poster Documents Setup

Creating Headers and Footers

Page Orientation

Reduce or Enlarge

Saving Page Setup Settings

35mm Slide Boundary Guides

Changing Perspectives

Magnifying with the View Menu

Using the Magnification Control

Arranging Objects

Using the Crosshair

Displaying the Crosshair

Moving the Crosshair

Aligning Objects using the Crosshair

Hiding the Crosshair

Centering on a Page

Aligning Objects

Distributing Objects

Front to Back Ordering

Creating Tables

Creating Tables with the Table Tool

Creating Tables with the Text Tool

Creating the First Row (column headings)

Creating a New Row

Adjusting Row or Column Spacing

Moving Around In Tables

Inserting a New Row

Sharing Information

Using the Clipboard

SMILES and SMIRKS Strings

Creating SMILES Strings

Pasting SMILES from Clipboard

Creating SLN Strings

Using Drag-and-Drop

Transferring Between ChemDraw Documents

Non-bond Objects and Color

Pasting to an Empty Document Window

Edit Graphic Object (Macintosh)

Transferring PostScript (Macintosh)

Importing and Exporting

Graphics export border preference

ChemDraw Template (*.ctp, *.ctr)

ChemDraw (*.cdx)

ChemDraw XML (*.xml)

ChemDraw 3.5 (*.chm)

ChemDraw 2.0 and ChemDraw 2.1 (*.chm) Import Only

ChemDraw Stationery/Style Sheet (*.cds)

Connection Table (*.ct)

Encapsulated PostScript

GIF Image (*.gif) Export Only

ISIS/SKC and ISIS/TGF

ISIS/Reactions (*.rxn)

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

MDL MolFile (*.mol)

Molecular Simulations MolFile (*.msm)

PNG file (*.png) Export Only

SPC (.*spc) Import Only

Template Style Sheet (*.cts)

TIFF file (*.tif) Export Only

Transferring ChemDraw Documents Across Platforms

Transferring from Macintosh to Windows

Transferring from Windows to Macintosh

Transferring Files to ChemDraw/Plus 3.1 for the Macintosh

Accessing the CambridgeSoft Web Site

Finding Chemical Suppliers on ChemStore.com

Finding Information on ChemFinder.com

Finding ACX Structures and Numbers

Browsing ChemStore.com

Browsing CambridgeSoft.com

Accessing the Online ChemDraw User's Guide

Accessing CambridgeSoft Technical Support

Registering Online

Using the ChemOffice SDK

Appendix A: The Chemistry of ChemDraw

Database Conventions

Chemical Conventions

Chemically Significant Text

Isotopes and Elements

Multi-center Attachments

Stereochemistry

Stereochemical Indicators

Stereochemical Flags

Polymer Representations

Query Properties

Analysis Messages

Appendix B: How ChemProp/Draw Works

Molar Refractivity

Appendix C: How ChemNMR Pro Works

ChemNMR Limitations

Appendix D: Shortcuts and Hotkeys

ChemDraw Hotkeys

Appendix E: Document Settings

ChemDraw Stationery Pads

Appendix F: Chemistry File Formats

Connection Table File Format

Appendix G: Technical Support

Troubleshooting

Index